Academic Appointments


Current Research and Scholarly Interests


We examine how cells communicate and function during fetal development. The work in my laboratory focuses on the establishment of specific cell fates using genomics to decipher interactions between chromatin and developmental signaling cascades, between genomes and rapidly evolving cell types, and between genomic copy number variation and gene expression. In recent years we have focused on the vastly understudied biology of the trophoblast lineage, particularly how this lineage evolved.

2020-21 Courses


Stanford Advisees


Graduate and Fellowship Programs


All Publications


  • The genomes of the livebearing fish species Poeciliopsis retropinna and Poeciliopsis turrubarensis reflect their different reproductive strategies. Molecular biology and evolution van Kruistum, H., Guernsey, M. W., Baker, J. C., Kloet, S. L., Groenen, M. A., Pollux, B. J., Megens, H. 2020

    Abstract

    The evolution of a placenta is predicted to be accompanied by rapid evolution of genes involved in processes that regulate mother-offspring interactions during pregnancy, such as placenta formation, embryonic development and nutrient transfer to offspring. However, these predictions have only been tested in mammalian species, where only a single instance of placenta evolution has occurred. In this light, the genus Poeciliopsis is a particularly interesting model for placenta evolution, because in this genus a placenta has evolved independently from the mammalian placenta. Here, we present and compare genome assemblies of two species of the livebearing fish genus Poeciliopsis (family Poeciliidae) that differ in their reproductive strategy: Poeciliopsis retropinna which has a well-developed complex placenta and Poeciliopsis turrubarensis which lacks a placenta. We applied different assembly strategies for each species: PacBio sequencing for P. retropinna (622Mbp assembly, contig N50 of 21.6 Mbp) and 10X Genomics Chromium technology for P. turrubarensis (597Mbp assembly, contig N50 of 4.2Mbp). Using the high contiguity of these genome assemblies and near-completeness of gene annotations to our advantage, we searched for gene duplications and performed a genome-wide scan for genes evolving under positive selection. We find rapid evolution in major parts of several molecular pathways involved in parent-offspring interaction in P. retropinna, both in the form of gene duplications as well as positive selection. We conclude that the evolution of the placenta in the genus Poeciliopsis is accompanied by rapid evolution of genes involved in similar genomic pathways as found in mammals.

    View details for DOI 10.1093/molbev/msaa011

    View details for PubMedID 31960923

  • Metabolism of cholesterol and progesterone is differentially regulated in primary trophoblastic subtypes and might be disturbed in recurrent miscarriages. Journal of lipid research Vondra, S., Kunihs, V., Eberhart, T., Eigner, K., Bauer, R., Haslinger, P., Haider, S., Windsperger, K., Klambauer, G., Schutz, B., Mikula, M., Zhu, X., Urban, A. E., Hannibal, R. L., Baker, J., Knofler, M., Stangl, H., Pollheimer, J., Rohrl, C. 2019

    Abstract

    During pregnancy, extravillous trophoblasts (EVTs) invade the maternal decidua and remodel the local vasculature to establish blood supply for the growing fetus. Compromised EVT-function has been linked to aberrant pregnancy associated with maternal and fetal morbidity and mortality. However, metabolic features of this invasive trophoblast subtype are largely unknown. Using primary human trophoblasts, isolated from first trimester placenta tissues, we show that cellular cholesterol homeostasis is differentially regulated in EVTs compared to villous cytotrophoblasts. Utilizing RNA-seq, gene set-enrichment analysis and functional validation we provide evidence that EVTs display increased levels of free and esterified cholesterol. In line, EVTs are characterized by increased expression of the HDL-receptor SR-BI and reduced expression of the liver X-receptor (LXR) and its target genes. We further reveal that EVTs express elevated levels of HSD3B1 (a rate-limiting enzyme in progesterone synthesis) and are capable of secreting progesterone. Increasing cholesterol export by LXR-activation reduced progesterone secretion in an ABCA1-dependent manner. Importantly, HSD3B1 expression was decreased in EVTs of idiopathic recurrent spontaneous abortions (RSA), pointing towards compromised progesterone metabolism in EVTs of early miscarriages. Here, we provide insights into the regulation of cholesterol and progesterone metabolism in trophoblastic subtypes and its putative relevance in human miscarriage.

    View details for DOI 10.1194/jlr.P093427

    View details for PubMedID 31530576

  • Gene expression across mammalian organ development. Nature Cardoso-Moreira, M., Halbert, J., Valloton, D., Velten, B., Chen, C., Shao, Y., Liechti, A., Ascencao, K., Rummel, C., Ovchinnikova, S., Mazin, P. V., Xenarios, I., Harshman, K., Mort, M., Cooper, D. N., Sandi, C., Soares, M. J., Ferreira, P. G., Afonso, S., Carneiro, M., Turner, J. M., VandeBerg, J. L., Fallahshahroudi, A., Jensen, P., Behr, R., Lisgo, S., Lindsay, S., Khaitovich, P., Huber, W., Baker, J., Anders, S., Zhang, Y. E., Kaessmann, H. 2019

    Abstract

    The evolution of gene expression in mammalian organ development remains largely uncharacterized. Here we report the transcriptomes of seven organs (cerebrum, cerebellum, heart, kidney, liver, ovary and testis) across developmental time points from early organogenesis to adulthood for human, rhesusmacaque, mouse, rat, rabbit, opossum and chicken. Comparisons of gene expression patterns identified correspondences of developmental stagesacross species, and differences in the timing of key events during the development of the gonads. We found that the breadth of gene expression and the extent of purifying selection gradually decrease during development, whereas the amount of positive selection and expression of new genes increase. We identified differences in the temporal trajectories of expression of individual genes across species, with brain tissues showing the smallest percentage of trajectory changes, and the liver and testis showing the largest. Our work provides a resource of developmental transcriptomes of seven organs across seven species, and comparative analyses that characterize the development and evolution of mammalian organs.

    View details for DOI 10.1038/s41586-019-1338-5

    View details for PubMedID 31243369

  • The Genomic Landscape of the Peruvian Andes Nieves-Colon, M. A., Rawls, E., Obregon-Tito, A., Tito, R., Lewis, C., Sandoval Mendoza, K., Bustamante, C. D., Wojcik, G. L., Gignoux, C., Baker, J., Fejerman, L., Vidaurre, T., Lizarraga, B., Rubin De Celis, V., Stone, A. C., Moreno-Estrada, A. WILEY. 2019: 176
  • Molecular and Cellular Characterization of Placenta Previa and Accreta. Zhang, E. T., Rivera, K., Hannibal, R. L., McGowan, K., Zhu, X., Meinhardt, G., Knoefler, M., Pollheimer, J., Folkins, A., Lyell, D. J., Baker, J. C. SAGE PUBLICATIONS INC. 2019: 262A–263A
  • Siva plays a critical role in mouse embryonic development. Cell death and differentiation Jacobs, S. B., Van Nostrand, J. L., Bowen, M. E., Baker, J. C., Attardi, L. D. 2019

    Abstract

    The Siva protein, named after the Hindu God of Destruction, plays important roles in apoptosis in various contexts, including downstream of death receptor activation or p53 tumor suppressor engagement. The function of Siva in organismal development and homeostasis, however, has remained uncharacterized. Here, we generate Siva knockout mice to characterize the physiological function of Siva in vivo. Interestingly, we find that Siva deficiency causes early embryonic lethality accompanied by multiple phenotypes, including developmental delay, abnormal neural tube closure, and defective placenta and yolk sac formation. Examination of Siva expression during embryogenesis shows that Siva is expressed in both embryonic and extra-embryonic tissues, including within the mesoderm, which may explain the vascular defects observed in the placenta and yolk sac. The embryonic phenotypes caused by Siva loss are not rescued by p53 deficiency, nor do they resemble those of p53 null embryos, suggesting that the embryonic function of Siva is not related to the p53 pathway. Moreover, loss of the Ripk3 necroptosis protein does not rescue the observed lethality or developmental defects, suggesting that Siva may play a non-apoptotic role in development. Collectively, these studies reveal a key role for Siva in proper embryonic development.

    View details for DOI 10.1038/s41418-019-0358-x

    View details for PubMedID 31164717

  • Genome amplification and cellular senescence are hallmarks of human placenta development. PLoS genetics Velicky, P., Meinhardt, G., Plessl, K., Vondra, S., Weiss, T., Haslinger, P., Lendl, T., Aumayr, K., Mairhofer, M., Zhu, X., Schutz, B., Hannibal, R. L., Lindau, R., Weil, B., Ernerudh, J., Neesen, J., Egger, G., Mikula, M., Rohrl, C., Urban, A. E., Baker, J., Knofler, M., Pollheimer, J. 2018; 14 (10): e1007698

    Abstract

    Genome amplification and cellular senescence are commonly associated with pathological processes. While physiological roles for polyploidization and senescence have been described in mouse development, controversy exists over their significance in humans. Here, we describe tetraploidization and senescence as phenomena of normal human placenta development. During pregnancy, placental extravillous trophoblasts (EVTs) invade the pregnant endometrium, termed decidua, to establish an adapted microenvironment required for the developing embryo. This process is critically dependent on continuous cell proliferation and differentiation, which is thought to follow the classical model of cell cycle arrest prior to terminal differentiation. Strikingly, flow cytometry and DNAseq revealed that EVT formation is accompanied with a genome-wide polyploidization, independent of mitotic cycles. DNA replication in these cells was analysed by a fluorescent cell-cycle indicator reporter system, cell cycle marker expression and EdU incorporation. Upon invasion into the decidua, EVTs widely lose their replicative potential and enter a senescent state characterized by high senescence-associated (SA) beta-galactosidase activity, induction of a SA secretory phenotype as well as typical metabolic alterations. Furthermore, we show that the shift from endocycle-dependent genome amplification to growth arrest is disturbed in androgenic complete hydatidiform moles (CHM), a hyperplastic pregnancy disorder associated with increased risk of developing choriocarinoma. Senescence is decreased in CHM-EVTs, accompanied by exacerbated endoreduplication and hyperploidy. We propose induction of cellular senescence as a ploidy limiting mechanism during normal human placentation and unravel a link between excessive polyploidization and reduced senescence in CHM.

    View details for PubMedID 30312291

  • CONVERGENCE AND DIVERGENCE: THE STORY OF PLACENTA EVOLUTION AS TOLD BY POECILIOPSIS FISHES Guernsey, M., Hagmayer, A., Reznick, D., Pollux, B., Baker, J. W B SAUNDERS CO LTD. 2018: E7–E8
  • Investigating human placentation and pregnancy using first trimester chorionic villi. Placenta Hannibal, R. L., Cardoso-Moreira, M., Chetty, S. P., Lau, J., Qi, Z., Gonzalez-Maldonado, E., Cherry, A. M., Yu, J., Norton, M. E., Baker, J. C. 2018; 65: 65–75

    Abstract

    Chorionic villus sampling (CVS), routinely used for prenatal diagnosis of cytogenetic disorders, also possesses great potential for the study of placentation. To better understand villus biology, human placentation, and how these relate to pregnancy outcomes, we examined the morphology and transcriptomes of villi obtained via CVS from 10 to 14 weeks of pregnancy and correlated these with pregnancy attributes and clinical outcomes. First, we established a morphological scoring system based on three main villus features: branching, budding and vascularization. We then tested whether morphology scores were predictive of pregnancy attributes and clinical outcomes. Finally, we used RNA sequencing to assess the transcriptional basis of villus morphology and tested the hypothesis that gene expression may predict pregnancy outcomes. We demonstrate that villus morphology varies tremendously between patients, irrespective of gestational age, and that transcriptional differences are highly predictive of villus morphology. We show that pre-eclampsia markers are associated with villi with low morphology scores. Additionally, we identify SVEP1 as a possible biomarker for defining gestational age. Overall, chorionic villi in the first trimester remain one of the few means to correlate placental function with pregnancy outcome and these samples are a valuable and increasingly rare resource.

    View details for PubMedID 29908643

  • IFPA meeting 2016 workshop report I: Genomic communication, bioinformatics, trophoblast biology and transport systems. Placenta Albrecht, C., Baker, J. C., Blundell, C., Chavez, S. L., Carbone, L., Chamley, L., Hannibal, R. L., Illsley, N., Kurre, P., Laurent, L. C., McKenzie, C., Morales-Prieto, D., Pantham, P., Paquette, A., Powell, K., Price, N., Rao, B. M., Sadovsky, Y., Salomon, C., Tuteja, G., Wilson, S., O'Tierney-Ginn, P. F. 2017

    Abstract

    Workshops are an important part of the IFPA annual meeting as they allow for discussion of specialized topics. At IFPA meeting 2016 there were twelve themed workshops, four of which are summarized in this report. These workshops covered innovative technologies applied to new and traditional areas of placental research: 1) genomic communication; 2) bioinformatics; 3) trophoblast biology and pathology; 4) placental transport systems.

    View details for DOI 10.1016/j.placenta.2017.01.103

    View details for PubMedID 28108031

  • Molecular conservation of marsupial and eutherian placentation and lactation. eLife Guernsey, M. W., Chuong, E. B., Cornelis, G., Renfree, M. B., Baker, J. C. 2017; 6

    Abstract

    Eutherians are often mistakenly termed 'placental mammals', but marsupials also have a placenta to mediate early embryonic development. Lactation is necessary for both infant and fetal development in eutherians and marsupials, although marsupials have a far more complex milk repertoire that facilitates morphogenesis of developmentally immature young. In this study, we demonstrate that the anatomically simple tammar placenta expresses a dynamic molecular program that is reminiscent of eutherian placentation, including both fetal and maternal signals. Further, we provide evidence that genes facilitating fetal development and nutrient transport display convergent co-option by placental and mammary gland cell types to optimize offspring success.

    View details for PubMedID 28895534

    View details for PubMedCentralID PMC5595433

  • Desynchronizing Embryonic Cell Division Waves Reveals the Robustness of Xenopus laevis Development. Cell reports Anderson, G. A., Gelens, L., Baker, J. C., Ferrell, J. E. 2017; 21 (1): 37–46

    Abstract

    The early Xenopus laevis embryo is replete with dynamic spatial waves. One such wave, the cell division wave, emerges from the collective cell division timing of first tens and later hundreds of cells throughout the embryo. Here, we show that cell division waves do not propagate between neighboring cells and do not rely on cell-to-cell coupling to maintain their division timing. Instead, intrinsic variation in division period autonomously and gradually builds these striking patterns of cell division. Disrupting this pattern of division by placing embryos in a temperature gradient resulted in highly asynchronous entry to the midblastula transition and misexpression of the mesodermal marker Xbra. Remarkably, this gene expression defect is corrected during involution, resulting in delayed yet normal Xbra expression and viable embryos. This implies the existence of a previously unknown mechanism for normalizing mesodermal gene expression during involution.

    View details for PubMedID 28978482

    View details for PubMedCentralID PMC5679461

  • Transcriptional dynamics of tail regeneration in Xenopus tropicalis GENESIS Chang, J., Baker, J., Wills, A. 2017; 55 (1-2)

    Abstract

    In contrast to humans, many amphibians are able to rapidly and completely regenerate complex tissues, including entire appendages. Following tail amputation, Xenopus tropicalis tadpoles quickly regenerate muscle, spinal cord, cartilage, vasculature and skin, all properly patterned in three dimensions. To better understand the molecular basis of this regenerative competence, we performed a transcriptional analysis of the first 72 h of tail regeneration using RNA-Seq. Our analysis refines the windows during which many key biological signaling processes act in regeneration, including embryonic patterning signals, immune responses, bioelectrical signaling and apoptosis. Our work provides a deep database for researchers interested in appendage regeneration, and points to new avenues for further study.

    View details for DOI 10.1002/dvg.23015

    View details for Web of Science ID 000393958400021

    View details for PubMedID 28095651

  • GLOBAL RE-WIRING OF MOLECULAR NETWORKS IN PLACENTA ACCRETA Hannibal, R., Song, J., McGowan, K., Folkins, A., Heerema-McKenney, A., Lyell, D., Baker, J. W B SAUNDERS CO LTD. 2016: 92
  • XenMine: A genomic interaction tool for the Xenopus community. Developmental biology Reid, C. D., Karra, K., Chang, J., Piskol, R., Li, Q., Li, J. B., Cherry, J. M., Baker, J. C. 2016

    Abstract

    The Xenopus community has embraced recent advances in sequencing technology, resulting in the accumulation of numerous RNA-Seq and ChIP-Seq datasets. However, easily accessing and comparing datasets generated by multiple laboratories is challenging. Thus, we have created a central space to view, search and analyze data, providing essential information on gene expression changes and regulatory elements present in the genome. XenMine (www.xenmine.org) is a user-friendly website containing published genomic datasets from both Xenopus tropicalis and Xenopus laevis. We have established an analysis pipeline where all published datasets are uniformly processed with the latest genome releases. Information from these datasets can be extracted and compared using an array of pre-built or custom templates. With these search tools, users can easily extract sequences for all putative regulatory domains surrounding a gene of interest, identify the expression values of a gene of interest over developmental time, and analyze lists of genes for gene ontology terms and publications. Additionally, XenMine hosts an in-house genome browser that allows users to visualize all available ChIP-Seq data, extract specifically marked sequences, and aid in identifying important regulatory elements within the genome. Altogether, XenMine is an excellent tool for visualizing, accessing and querying analyzed datasets rapidly and efficiently.

    View details for DOI 10.1016/j.ydbio.2016.02.034

    View details for PubMedID 27157655

  • Human Embryonic Stem Cell Lines with Lesions in FOXP3 and NF1 PLOS ONE Zhu, H., Behr, B., Reddy, V. V., Hughes, M., Pan, Y., Baker, J. 2016; 11 (3)

    Abstract

    Human embryonic stem cells (hESCs) are derived from the inner cell mass (ICM) of blastocyst staged embryos. Spare blastocyst staged embryos were obtained by in vitro fertilization (IVF) and donated for research purposes. hESCs carrying specific mutations can be used as a powerful cell system in modeling human genetic disorders. We obtained preimplantation genetic diagnosed (PGD) blastocyst staged embryos with genetic mutations that cause human disorders and derived hESCs from these embryos. We applied laser assisted micromanipulation to isolate the inner cell mass from the blastocysts and plated the ICM onto the mouse embryonic fibroblast cells. Two hESC lines with lesions in FOXP3 and NF1 were established. Both lines maintain a typical undifferentiated hESCs phenotype and present a normal karyotype. The two lines express a panel of pluripotency markers and have the potential to differentiate to the three germ layers in vitro and in vivo. The hESC lines with lesions in FOXP3 and NF1 are available for the scientific community and may serve as an important resource for research into these disease states.

    View details for DOI 10.1371/journal.pone.0151836

    View details for Web of Science ID 000372582800106

    View details for PubMedCentralID PMC4798423

  • Selective Amplification of the Genome Surrounding Key Placental Genes in Trophoblast Giant Cells. Current biology Hannibal, R. L., Baker, J. C. 2016; 26 (2): 230-236

    Abstract

    While most cells maintain a diploid state, polyploid cells exist in many organisms and are particularly prevalent within the mammalian placenta [1], where they can generate more than 900 copies of the genome [2]. Polyploidy is thought to be an efficient method of increasing the content of the genome by avoiding the costly and slow process of cytokinesis [1, 3, 4]. Polyploidy can also affect gene regulation by amplifying a subset of genomic regions required for specific cellular function [1, 3, 4]. This mechanism is found in the fruit fly Drosophila melanogaster, where polyploid ovarian follicle cells amplify genomic regions containing chorion genes, which facilitate secretion of eggshell proteins [5]. Here, we report that genomic amplification also occurs in mammals at selective regions of the genome in parietal trophoblast giant cells (p-TGCs) of the mouse placenta. Using whole-genome sequencing (WGS) and digital droplet PCR (ddPCR) of mouse p-TGCs, we identified five amplified regions, each containing a gene family known to be involved in mammalian placentation: the prolactins (two clusters), serpins, cathepsins, and the natural killer (NK)/C-type lectin (CLEC) complex [6-12]. We report here the first description of amplification at selective genomic regions in mammals and present evidence that this is an important mode of genome regulation in placental TGCs.

    View details for DOI 10.1016/j.cub.2015.11.060

    View details for PubMedID 26774788

  • Human Embryonic Stem Cell Lines with Lesions in FOXP3 and NF1. PloS one Zhu, H., Behr, B., Reddy, V. V., Hughes, M., Pan, Y., Baker, J. 2016; 11 (3)

    Abstract

    Human embryonic stem cells (hESCs) are derived from the inner cell mass (ICM) of blastocyst staged embryos. Spare blastocyst staged embryos were obtained by in vitro fertilization (IVF) and donated for research purposes. hESCs carrying specific mutations can be used as a powerful cell system in modeling human genetic disorders. We obtained preimplantation genetic diagnosed (PGD) blastocyst staged embryos with genetic mutations that cause human disorders and derived hESCs from these embryos. We applied laser assisted micromanipulation to isolate the inner cell mass from the blastocysts and plated the ICM onto the mouse embryonic fibroblast cells. Two hESC lines with lesions in FOXP3 and NF1 were established. Both lines maintain a typical undifferentiated hESCs phenotype and present a normal karyotype. The two lines express a panel of pluripotency markers and have the potential to differentiate to the three germ layers in vitro and in vivo. The hESC lines with lesions in FOXP3 and NF1 are available for the scientific community and may serve as an important resource for research into these disease states.

    View details for DOI 10.1371/journal.pone.0151836

    View details for PubMedID 26990425

    View details for PubMedCentralID PMC4798423

  • Constraint and divergence of global gene expression in the mammalian embryo ELIFE Spies, N., Smith, C. L., Rodriguez, J. M., Baker, J. C., Batzoglou, S., Sidow, A. 2015; 4

    Abstract

    The effects of genetic variation on gene regulation in the developing mammalian embryo remain largely unexplored. To globally quantify these effects, we crossed two divergent mouse strains and asked how genotype of the mother or of the embryo drives gene expression phenotype genomewide. Embryonic expression of 331 genes depends on the genotype of the mother. Embryonic genotype controls allele-specific expression of 1594 genes and a highly overlapping set of cis-expression quantitative trait loci (eQTL). A marked paucity of trans-eQTL suggests that the widespread expression differences do not propagate through the embryonic gene regulatory network. The cis-eQTL genes exhibit lower-than-average evolutionary conservation and are depleted for developmental regulators, consistent with purifying selection acting on expression phenotype of pattern formation genes. The widespread effect of maternal and embryonic genotype in conjunction with the purifying selection we uncovered suggests that embryogenesis is an important and understudied reservoir of phenotypic variation.

    View details for DOI 10.7554/eLife.05538

    View details for Web of Science ID 000373792400001

    View details for PubMedID 25871848

    View details for PubMedCentralID PMC4417935

  • HEB associates with PRC2 and SMAD2/3 to regulate developmental fates NATURE COMMUNICATIONS Yoon, S., Foley, J. W., Baker, J. C. 2015; 6

    Abstract

    In embryonic stem cells, extracellular signals are required to derepress developmental promoters to drive lineage specification, but the proteins involved in connecting extrinsic cues to relaxation of chromatin remain unknown. We demonstrate that the helix-loop-helix (HLH) protein, HEB, directly associates with the Polycomb repressive complex 2 (PRC2) at a subset of developmental promoters, including at genes involved in mesoderm and endoderm specification and at the Hox and Fox gene families. While we show that depletion of HEB does not affect mouse ESCs, it does cause premature differentiation after exposure to Activin. Further, we find that HEB deposition at developmental promoters is dependent upon PRC2 and independent of Nodal, whereas HEB association with SMAD2/3 elements is dependent of Nodal, but independent of PRC2. We suggest that HEB is a fundamental link between Nodal signalling, the derepression of a specific class of poised promoters during differentiation, and lineage specification in mouse ESCs.

    View details for DOI 10.1038/ncomms7546

    View details for Web of Science ID 000352720200002

    View details for PubMedID 25775035

  • E2a Is Necessary for Smad2/3-Dependent Transcription and the Direct Repression of lefty during Gastrulation. Developmental cell Wills, A. E., Baker, J. C. 2015; 32 (3): 345-357

    Abstract

    Transcription factor complexes have varied effects on cell fate and behavior, but how this diversification of function occurs is largely unknown. The Nodal signaling pathway has many biological functions that all converge on the transcription factors Smad2/3. Smad2/3 has many cofactors, and alternative usage of these may provide a mechanism for modulating Smad2/3 function. Here, we investigate how perturbation of the cofactor E2a affects global patterns of Smad2/3 binding and gene expression during gastrulation. We find that E2a regulates early development in two ways. E2a changes the position of Smad2/3 binding at the Nodal inhibitor lefty, resulting in direct repression of lefty that is critical for mesendoderm specification. Separately, E2a is necessary to drive transcription of Smad2/3 target genes, including critical regulators of dorsal cell fate and morphogenesis. Overall, we find that E2a functions as both a transcriptional repressor and activator to precisely regulate Nodal signaling.

    View details for DOI 10.1016/j.devcel.2014.11.034

    View details for PubMedID 25669884

  • HEB associates with PRC2 and SMAD2/3 to regulate developmental fates. Nature communications Yoon, S., Foley, J. W., Baker, J. C. 2015; 6: 6546-?

    Abstract

    In embryonic stem cells, extracellular signals are required to derepress developmental promoters to drive lineage specification, but the proteins involved in connecting extrinsic cues to relaxation of chromatin remain unknown. We demonstrate that the helix-loop-helix (HLH) protein, HEB, directly associates with the Polycomb repressive complex 2 (PRC2) at a subset of developmental promoters, including at genes involved in mesoderm and endoderm specification and at the Hox and Fox gene families. While we show that depletion of HEB does not affect mouse ESCs, it does cause premature differentiation after exposure to Activin. Further, we find that HEB deposition at developmental promoters is dependent upon PRC2 and independent of Nodal, whereas HEB association with SMAD2/3 elements is dependent of Nodal, but independent of PRC2. We suggest that HEB is a fundamental link between Nodal signalling, the derepression of a specific class of poised promoters during differentiation, and lineage specification in mouse ESCs.

    View details for DOI 10.1038/ncomms7546

    View details for PubMedID 25775035

  • Is there a correlation between chorionic villi morphology, gene expression and pregnancy outcomes? Chetty, S., Hannibal, R., Moreira, M., Baker, J., Norton, M. MOSBY-ELSEVIER. 2015: S125
  • Identifying direct targets of transcription factor Rfx2 that coordinate ciliogenesis and cell movement. Genomics data Kwon, T., Chung, M., Gupta, R., Baker, J. C., Wallingford, J. B., Marcotte, E. M. 2014; 2: 192-194

    Abstract

    Recently, using the frog Xenopus laevis as a model system, we showed that transcription factor Rfx2 coordinates many genes involved in ciliogenesis and cell movement in multiciliated cells (Chung et al., 2014). To our knowledge, it was the first paper to utilize the genomic resources, including genome sequences and interim gene annotations, from the ongoing Xenopus laevis genome project. For researchers who are interested in the application of genomics and systems biology approaches in Xenopus studies, here we provide additional details about our dataset (NCBI GEO accession number GSE50593) and describe how we analyzed RNA-seq and ChIP-seq data to identify direct targets of Rfx2.

    View details for PubMedID 25419512

  • Developmental enhancers are marked independently of zygotic Nodal signals in Xenopus DEVELOPMENTAL BIOLOGY Gupta, R., Wills, A., Ucar, D., Baker, J. 2014; 395 (1): 38-49

    Abstract

    To determine the hierarchy of transcriptional regulation within the in vivo vertebrate embryo, we examined whether developmental enhancers were influenced by Nodal signaling during early embryogenesis in Xenopus tropicalis. We find that developmental enhancers, defined by the active enhancer chromatin marks H3K4me1 and H3K27ac, are established as early as blastula stage and that Smad2/3 only strongly associates with these regions at gastrula stages. Significantly, when we perturb Nodal signaling using the drug SB431542, most enhancers remain marked, including at genes known to be sensitive to Nodal signaling. Overall, as enhancers are in an active conformation prior to Nodal signaling and are established independently of Nodal signaling, we suggest that many developmental enhancers are marked maternally, prior to exposure to extrinsic signals.

    View details for DOI 10.1016/j.ydbio.2014.08.034

    View details for Web of Science ID 000343195000005

    View details for PubMedCentralID PMC4517478

  • Developmental enhancers are marked independently of zygotic Nodal signals in Xenopus. Developmental biology Gupta, R., Wills, A., Ucar, D., Baker, J. 2014; 395 (1): 38-49

    Abstract

    To determine the hierarchy of transcriptional regulation within the in vivo vertebrate embryo, we examined whether developmental enhancers were influenced by Nodal signaling during early embryogenesis in Xenopus tropicalis. We find that developmental enhancers, defined by the active enhancer chromatin marks H3K4me1 and H3K27ac, are established as early as blastula stage and that Smad2/3 only strongly associates with these regions at gastrula stages. Significantly, when we perturb Nodal signaling using the drug SB431542, most enhancers remain marked, including at genes known to be sensitive to Nodal signaling. Overall, as enhancers are in an active conformation prior to Nodal signaling and are established independently of Nodal signaling, we suggest that many developmental enhancers are marked maternally, prior to exposure to extrinsic signals.

    View details for DOI 10.1016/j.ydbio.2014.08.034

    View details for PubMedID 25205067

    View details for PubMedCentralID PMC4517478

  • GLOBAL REWIRING OF MOLECULAR NETWORKS IN PLACENTA PREVIA AND ACCRETE Hannibal, R., Song, J., Folkins, A., Lyell, D., Heerema-McKenney, A., Baker, J. W B SAUNDERS CO LTD. 2014: A47
  • H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency. Cell Benayoun, B. A., Pollina, E. A., Ucar, D., Mahmoudi, S., Karra, K., Wong, E. D., Devarajan, K., Daugherty, A. C., Kundaje, A. B., Mancini, E., Hitz, B. C., Gupta, R., Rando, T. A., Baker, J. C., Snyder, M. P., Cherry, J. M., Brunet, A. 2014; 158 (3): 673-688

    Abstract

    Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to mark the transcription start sites of active genes. Here, we show that H3K4me3 domains that spread more broadly over genes in a given cell type preferentially mark genes that are essential for the identity and function of that cell type. Using the broadest H3K4me3 domains as a discovery tool in neural progenitor cells, we identify novel regulators of these cells. Machine learning models reveal that the broadest H3K4me3 domains represent a distinct entity, characterized by increased marks of elongation. The broadest H3K4me3 domains also have more paused polymerase at their promoters, suggesting a unique transcriptional output. Indeed, genes marked by the broadest H3K4me3 domains exhibit enhanced transcriptional consistency and [corrected] increased transcriptional levels, and perturbation of H3K4me3 breadth leads to changes in transcriptional consistency. Thus, H3K4me3 breadth contains information that could ensure transcriptional precision at key cell identity/function genes.

    View details for DOI 10.1016/j.cell.2014.06.027

    View details for PubMedID 25083876

  • Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta. Developmental biology Finn, E. H., Smith, C. L., Rodriguez, J., Sidow, A., Baker, J. C. 2014; 390 (1): 80-92

    Abstract

    To investigate the epigenetic landscape at the interface between mother and fetus, we provide a comprehensive analysis of parent-of-origin bias in the mouse placenta. Using F1 interspecies hybrids between mus musculus (C57BL/6J) and mus musculus castaneus, we sequenced RNA from 23 individual midgestation placentas, five late stage placentas, and two yolk sac samples and then used SNPs to determine whether transcripts were preferentially generated from the maternal or paternal allele. In the placenta, we find 103 genes that show significant and reproducible parent-of-origin bias, of which 78 are novel candidates. Most (96%) show a strong maternal bias which we demonstrate, via multiple mathematical models, pyrosequencing, and FISH, is not due to maternal decidual contamination. Analysis of the X chromosome also reveals paternal expression of Xist and several genes that escape inactivation, most significantly Alas2, Fhl1, and Slc38a5. Finally, sequencing individual placentas allowed us to reveal notable expression similarity between littermates. In all, we observe a striking preference for maternal transcription in the midgestation mouse placenta and a dynamic imprinting landscape in extraembryonic tissues, reflecting the complex nature of epigenetic pathways in the placenta.

    View details for DOI 10.1016/j.ydbio.2014.02.020

    View details for PubMedID 24594094

  • Copy number variation is a fundamental aspect of the placental genome. PLoS genetics Hannibal, R. L., Chuong, E. B., Rivera-Mulia, J. C., Gilbert, D. M., Valouev, A., Baker, J. C. 2014; 10 (5)

    Abstract

    Discovery of lineage-specific somatic copy number variation (CNV) in mammals has led to debate over whether CNVs are mutations that propagate disease or whether they are a normal, and even essential, aspect of cell biology. We show that 1,000 N polyploid trophoblast giant cells (TGCs) of the mouse placenta contain 47 regions, totaling 138 Megabases, where genomic copies are underrepresented (UR). UR domains originate from a subset of late-replicating heterochromatic regions containing gene deserts and genes involved in cell adhesion and neurogenesis. While lineage-specific CNVs have been identified in mammalian cells, classically in the immune system where V(D)J recombination occurs, we demonstrate that CNVs form during gestation in the placenta by an underreplication mechanism, not by recombination nor deletion. Our results reveal that large scale CNVs are a normal feature of the mammalian placental genome, which are regulated systematically during embryogenesis and are propagated by a mechanism of underreplication.

    View details for DOI 10.1371/journal.pgen.1004290

    View details for PubMedID 24785991

    View details for PubMedCentralID PMC4006706

  • Copy number variation is a fundamental aspect of the placental genome. PLoS genetics Hannibal, R. L., Chuong, E. B., Rivera-Mulia, J. C., Gilbert, D. M., Valouev, A., Baker, J. C. 2014; 10 (5)

    View details for DOI 10.1371/journal.pgen.1004290

    View details for PubMedID 24785991

  • Chromatin immunoprecipitation and deep sequencing in Xenopus tropicalis and Xenopus laevis. Methods (San Diego, Calif.) Wills, A. E., Gupta, R., Chuong, E., Baker, J. C. 2014; 66 (3): 410-421

    Abstract

    Chromatin immunoprecipitation and deep sequencing (ChIP-SEQ) represents a powerful tool for identifying the genomic targets of transcription factors, chromatin remodeling factors, and histone modifications. The frogs Xenopus laevis and Xenopus tropicalis have historically been outstanding model systems for embryology and cell biology, with emerging utility as highly accessible embryos for genome-wide studies. Here we focus on the particular strengths and limitations of Xenopus cell biology and genomics as they apply to ChIP-SEQ, and outline a methodology for ChIP-SEQ in both species, providing detailed strategies for sample preparation, antibody selection, quality control, sequencing library preparation, and basic analysis.

    View details for DOI 10.1016/j.ymeth.2013.09.010

    View details for PubMedID 24064036

  • The evolution of lncRNA repertoires and expression patterns in tetrapods NATURE Necsulea, A., Soumillon, M., Warnefors, M., Liechti, A., Daish, T., Zeller, U., Baker, J. C., Gruetzner, F., Kaessmann, H. 2014; 505 (7485): 635-?

    Abstract

    Only a very small fraction of long noncoding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but the absence of lncRNA annotations in non-model organisms has precluded comparative analyses. Here we present a large-scale evolutionary study of lncRNA repertoires and expression patterns, in 11 tetrapod species. We identify approximately 11,000 primate-specific lncRNAs and 2,500 highly conserved lncRNAs, including approximately 400 genes that are likely to have originated more than 300 million years ago. We find that lncRNAs, in particular ancient ones, are in general actively regulated and may function predominantly in embryonic development. Most lncRNAs evolve rapidly in terms of sequence and expression levels, but tissue specificities are often conserved. We compared expression patterns of homologous lncRNA and protein-coding families across tetrapods to reconstruct an evolutionarily conserved co-expression network. This network suggests potential functions for lncRNAs in fundamental processes such as spermatogenesis and synaptic transmission, but also in more specific mechanisms such as placenta development through microRNA production.

    View details for DOI 10.1038/nature12943

    View details for Web of Science ID 000330321000031

    View details for PubMedID 24463510

  • Coordinated genomic control of ciliogenesis and cell movement by RFX2 ELIFE Chung, M., Kwon, T., Tu, F., Brooks, E. R., Gupta, R., Meyer, M., Baker, J. C., Marcotte, E. M., Wallingford, J. B. 2014; 3

    Abstract

    The mechanisms linking systems-level programs of gene expression to discrete cell biological processes in vivo remain poorly understood. In this study, we have defined such a program for multi-ciliated epithelial cells (MCCs), a cell type critical for proper development and homeostasis of the airway, brain and reproductive tracts. Starting from genomic analysis of the cilia-associated transcription factor Rfx2, we used bioinformatics and in vivo cell biological approaches to gain insights into the molecular basis of cilia assembly and function. Moreover, we discovered a previously un-recognized role for an Rfx factor in cell movement, finding that Rfx2 cell-autonomously controls apical surface expansion in nascent MCCs. Thus, Rfx2 coordinates multiple, distinct gene expression programs in MCCs, regulating genes that control cell movement, ciliogenesis, and cilia function. As such, the work serves as a paradigm for understanding genomic control of cell biological processes that span from early cell morphogenetic events to terminally differentiated cellular functions. DOI: http://dx.doi.org/10.7554/eLife.01439.001.

    View details for DOI 10.7554/eLife.01439

    View details for Web of Science ID 000330172400003

    View details for PubMedID 24424412

    View details for PubMedCentralID PMC3889689

  • Evolutionary perspectives into placental biology and disease. Applied & translational genomics Chuong, E. B., Hannibal, R. L., Green, S. L., Baker, J. C. 2013; 2: 64-69

    Abstract

    In all mammals including humans, development takes place within the protective environment of the maternal womb. Throughout gestation, nutrients and waste products are continuously exchanged between mother and fetus through the placenta. Despite the clear importance of the placenta to successful pregnancy and the health of both mother and offspring, relatively little is understood about the biology of the placenta and its role in pregnancy-related diseases. Given that pre- and peri-natal diseases involving the placenta affect millions of women and their newborns worldwide, there is an urgent need to understand placenta biology and development. Here, we suggest that the placenta is an organ under unique selective pressures that have driven its rapid diversification throughout mammalian evolution. The high divergence of the placenta complicates the use of non-human animal models and necessitates an evolutionary perspective when studying its biology and role in disease. We suggest that diversifying evolution of the placenta is primarily driven by intraspecies evolutionary conflict between mother and fetus, and that many pregnancy diseases are a consequence of this evolutionary force. Understanding how maternal-fetal conflict shapes both basic placental and reproductive biology - in all species - will provide key insights into diseases of pregnancy.

    View details for PubMedID 27896057

  • REPLICATION TIMING PREDICTS UNDERREPLICATED DOMAINS IN POLYPLOID TROPHOBLAST GIANT CELLS Hannibal, R., Chuong, E., Mulia, J., Gilbert, D., Valouev, A., Baker, J. W B SAUNDERS CO LTD. 2013: A8
  • Synthesis of a photocaged tamoxifen for light-dependent activation of Cre-ER recombinase-driven gene modification. Chemical communications Inlay, M. A., Choe, V., Bharathi, S., Fernhoff, N. B., Baker, J. R., Weissman, I. L., Choi, S. K. 2013; 49 (43): 4971-4973

    Abstract

    We report the design of a water-soluble, quaternized tamoxifen photoprobe and demonstrate its application in light-controlled induction of green fluorescent protein expression via a Cre-ER recombinase system.

    View details for DOI 10.1039/c3cc42179a

    View details for PubMedID 23612712

  • Transdisciplinary translational science and the case of preterm birth JOURNAL OF PERINATOLOGY Stevenson, D. K., Shaw, G. M., Wise, P. H., Norton, M. E., Druzin, M. L., Valantine, H. A., McFarland, D. A. 2013; 33 (4): 251-258

    Abstract

    Medical researchers have called for new forms of translational science that can solve complex medical problems. Mainstream science has made complementary calls for heterogeneous teams of collaborators who conduct transdisciplinary research so as to solve complex social problems. Is transdisciplinary translational science what the medical community needs? What challenges must the medical community overcome to successfully implement this new form of translational science? This article makes several contributions. First, it clarifies the concept of transdisciplinary research and distinguishes it from other forms of collaboration. Second, it presents an example of a complex medical problem and a concrete effort to solve it through transdisciplinary collaboration: for example, the problem of preterm birth and the March of Dimes effort to form a transdisciplinary research center that synthesizes knowledge on it. The presentation of this example grounds discussion on new medical research models and reveals potential means by which they can be judged and evaluated. Third, this article identifies the challenges to forming transdisciplines and the practices that overcome them. Departments, universities and disciplines tend to form intellectual silos and adopt reductionist approaches. Forming a more integrated (or 'constructionist'), problem-based science reflective of transdisciplinary research requires the adoption of novel practices to overcome these obstacles.

    View details for DOI 10.1038/jp.2012.133

    View details for PubMedID 23079774

  • Endogenous retroviruses function as species-specific enhancer elements in the placenta NATURE GENETICS Chuong, E. B., Rumi, M. A., Soares, M. J., Baker, J. C. 2013; 45 (3): 325-329

    Abstract

    The mammalian placenta is remarkably distinct between species, suggesting a history of rapid evolutionary diversification. To gain insight into the molecular drivers of placental evolution, we compared biochemically predicted enhancers in mouse and rat trophoblast stem cells (TSCs) and found that species-specific enhancers are highly enriched for endogenous retroviruses (ERVs) on a genome-wide level. One of these ERV families, RLTR13D5, contributes hundreds of mouse-specific histone H3 lysine 4 monomethylation (H3K4me1)- and histone H3 lysine 27 acetylation (H3K27ac)-defined enhancers that functionally bind Cdx2, Eomes and Elf5-core factors that define the TSC regulatory network. Furthermore, we show that RLTR13D5 is capable of driving gene expression in rat placental cells. Analysis in other tissues shows that species-specific ERV enhancer activity is generally restricted to hypomethylated tissues, suggesting that tissues permissive for ERV activity gain access to an otherwise silenced source of regulatory variation. Overall, our results implicate ERV enhancer co-option as a mechanism underlying the extensive evolutionary diversification of placental development.

    View details for DOI 10.1038/ng.2553

    View details for Web of Science ID 000315664800020

    View details for PubMedID 23396136

  • RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development GENOME RESEARCH Tan, M. H., Au, K. F., Yablonovitch, A. L., Wills, A. E., Chuang, J., Baker, J. C., Wong, W. H., Li, J. B. 2013; 23 (1): 201-216

    Abstract

    The Xenopus embryo has provided key insights into fate specification, the cell cycle, and other fundamental developmental and cellular processes, yet a comprehensive understanding of its transcriptome is lacking. Here, we used paired end RNA sequencing (RNA-seq) to explore the transcriptome of Xenopus tropicalis in 23 distinct developmental stages. We determined expression levels of all genes annotated in RefSeq and Ensembl and showed for the first time on a genome-wide scale that, despite a general state of transcriptional silence in the earliest stages of development, approximately 150 genes are transcribed prior to the midblastula transition. In addition, our splicing analysis uncovered more than 10,000 novel splice junctions at each stage and revealed that many known genes have additional unannotated isoforms. Furthermore, we used Cufflinks to reconstruct transcripts from our RNA-seq data and found that ∼13.5% of the final contigs are derived from novel transcribed regions, both within introns and in intergenic regions. We then developed a filtering pipeline to separate protein-coding transcripts from noncoding RNAs and identified a confident set of 6686 noncoding transcripts in 3859 genomic loci. Since the current reference genome, XenTro3, consists of hundreds of scaffolds instead of full chromosomes, we also performed de novo reconstruction of the transcriptome using Trinity and uncovered hundreds of transcripts that are missing from the genome. Collectively, our data will not only aid in completing the assembly of the Xenopus tropicalis genome but will also serve as a valuable resource for gene discovery and for unraveling the fundamental mechanisms of vertebrate embryogenesis.

    View details for DOI 10.1101/gr.141424.112

    View details for Web of Science ID 000312963400019

    View details for PubMedID 22960373

    View details for PubMedCentralID PMC3530680

  • Evolutionary perspectives into placental biology and disease Applied & Translational Genomics Chuong, E. B., Hannibal, R. L., Green, S. L., Baker, J. C. 2013; 2: 64-69

    Abstract

    In all mammals including humans, development takes place within the protective environment of the maternal womb. Throughout gestation, nutrients and waste products are continuously exchanged between mother and fetus through the placenta. Despite the clear importance of the placenta to successful pregnancy and the health of both mother and offspring, relatively little is understood about the biology of the placenta and its role in pregnancy-related diseases. Given that pre- and peri-natal diseases involving the placenta affect millions of women and their newborns worldwide, there is an urgent need to understand placenta biology and development. Here, we suggest that the placenta is an organ under unique selective pressures that have driven its rapid diversification throughout mammalian evolution. The high divergence of the placenta complicates the use of non-human animal models and necessitates an evolutionary perspective when studying its biology and role in disease. We suggest that diversifying evolution of the placenta is primarily driven by intraspecies evolutionary conflict between mother and fetus, and that many pregnancy diseases are a consequence of this evolutionary force. Understanding how maternal-fetal conflict shapes both basic placental and reproductive biology - in all species - will provide key insights into diseases of pregnancy.

    View details for DOI 10.1016/j.atg.2013.07.001

    View details for PubMedCentralID PMC5121266

  • The RB family is required for the self-renewal and survival of human embryonic stem cells NATURE COMMUNICATIONS Conklin, J. F., Baker, J., Sage, J. 2012; 3

    Abstract

    The mechanisms ensuring the long-term self-renewal of human embryonic stem cells are still only partly understood, limiting their use in cellular therapies. Here we found that increased activity of the RB cell cycle inhibitor in human embryonic stem cells induces cell cycle arrest, differentiation and cell death. Conversely, inactivation of the entire RB family (RB, p107 and p130) in human embryonic stem cells triggers G2/M arrest and cell death through functional activation of the p53 pathway and the cell cycle inhibitor p21. Differences in E2F target gene activation upon loss of RB family function between human embryonic stem cells, mouse embryonic stem cells and human fibroblasts underscore key differences in the cell cycle regulatory networks of human embryonic stem cells. Finally, loss of RB family function promotes genomic instability in both human and mouse embryonic stem cells, uncoupling cell cycle defects from chromosomal instability. These experiments indicate that a homeostatic level of RB activity is essential for the self-renewal and the survival of human embryonic stem cells.

    View details for DOI 10.1038/ncomms2254

    View details for Web of Science ID 000316356700012

    View details for PubMedID 23212373

  • Distinguishing Human Cell Types Based on Housekeeping Gene Signatures STEM CELLS Oyolu, C., Zakharia, F., Baker, J. 2012; 30 (3): 580-584

    Abstract

    'In this report, we use single cell gene expression to identify transcriptional patterns emerging during the differentiation of human embryonic stem cells (hESCs) into the endodermal lineage. Endoderm-specific transcripts are highly variable between individual CXCR4(+) endodermal cells, suggesting that either the cells generated from in vitro differentiation are distinct or that these embryonic cells tolerate a high degree of transcript variability. Housekeeping transcripts, on the other hand, are far more consistently expressed within the same cellular population. However, when we compare the levels of housekeeping transcripts between hESCs and derived endoderm, patterns emerge that can be used to clearly separate the two embryonic cell types. We further compared four additional human cell types, including 293T, induced pluripotent stem cell (iPSC), HepG2, and endoderm-derived iPSC. In each case, the relative levels of housekeeping transcripts defined a particular cell fate. Interestingly, we find that three transcripts, LDHA, NONO, and ACTB, contribute the most to this diversity and together serve to segregate all six cell types. Overall, this suggests that levels of housekeeping transcripts, which are expressed within all cells, can be leveraged to distinguish between human cell types and thus may serve as important biomarkers for stem cell biology and other disciplines.

    View details for DOI 10.1002/stem.1009

    View details for Web of Science ID 000300611400025

    View details for PubMedID 22162332

  • Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage NATURE BIOTECHNOLOGY Amps, K., Andrews, P. W., Anyfantis, G., Armstrong, L., Avery, S., Baharvand, H., Baker, J., Baker, D., Munoz, M. B., Beil, S., Benvenisty, N., Ben-Yosef, D., Biancotti, J., Bosman, A., Brena, R. M., Brison, D., Caisander, G., Camarasa, M. V., Chen, J., Chiao, E., Choi, Y. M., Choo, A. B., Collins, D., Colman, A., Crook, J. M., Daley, G. Q., Dalton, A., De Sousa, P. A., Denning, C., Downie, J., Dvorak, P., Montgomery, K. D., Feki, A., Ford, A., Fox, V., Fraga, A. M., Frumkin, T., Ge, L., Gokhale, P. J., Golan-Lev, T., Gourabi, H., Gropp, M., Lu Guangxiu, G. X., Hampl, A., Harron, K., Healy, L., Herath, W., Holm, F., Hovatta, O., Hyllner, J., Inamdar, M. S., Irwanto, A. K., Ishii, T., Jaconi, M., Jin, Y., Kimber, S., Kiselev, S., Knowles, B. B., Kopper, O., Kukharenko, V., Kuliev, A., Lagarkova, M. A., Laird, P. W., Lako, M., Laslett, A. L., Lavon, N., Lee, D. R., Lee, J. E., Li, C., Lim, L. S., Ludwig, T. E., Ma, Y., Maltby, E., Mateizel, I., Mayshar, Y., Mileikovsky, M., Minger, S. L., Miyazaki, T., Moon, S. Y., Moore, H., Mummery, C., Nagy, A., Nakatsuji, N., Narwani, K., Oh, S. K., Oh, S. K., Olson, C., Otonkoski, T., Pan, F., Park, I., Pells, S., Pera, M. F., Pereira, L. V., Qi, O., Raj, G. S., Reubinoff, B., Robins, A., Robson, P., Rossant, J., Salekdeh, G. H., Schulz, T. C., Sermon, K., Mohamed, J. S., Shen, H., Sherrer, E., Sidhu, K., Sivarajah, S., Skottman, H., Spits, C., Stacey, G. N., Strehl, R., Strelchenko, N., Suemori, H., Sun, B., Suuronen, R., Takahashi, K., Tuuri, T., Venu, P., Verlinsky, Y., Ward-van Oostwaard, D., Weisenberger, D. J., Wu, Y., Yamanaka, S., Young, L., Zhou, Q. 2011; 29 (12): 1132-U113

    Abstract

    The International Stem Cell Initiative analyzed 125 human embryonic stem (ES) cell lines and 11 induced pluripotent stem (iPS) cell lines, from 38 laboratories worldwide, for genetic changes occurring during culture. Most lines were analyzed at an early and late passage. Single-nucleotide polymorphism (SNP) analysis revealed that they included representatives of most major ethnic groups. Most lines remained karyotypically normal, but there was a progressive tendency to acquire changes on prolonged culture, commonly affecting chromosomes 1, 12, 17 and 20. DNA methylation patterns changed haphazardly with no link to time in culture. Structural variants, determined from the SNP arrays, also appeared sporadically. No common variants related to culture were observed on chromosomes 1, 12 and 17, but a minimal amplicon in chromosome 20q11.21, including three genes expressed in human ES cells, ID1, BCL2L1 and HM13, occurred in >20% of the lines. Of these genes, BCL2L1 is a strong candidate for driving culture adaptation of ES cells.

    View details for DOI 10.1038/nbt.2051

    View details for Web of Science ID 000298038700025

    View details for PubMedID 22119741

    View details for PubMedCentralID PMC3454460

  • Global hormone profiling of murine placenta reveals Secretin expression PLACENTA Knox, K., Leuenberger, D., Penn, A. A., Baker, J. C. 2011; 32 (11): 811-816

    Abstract

    To elucidate and categorize the murine placental hormones expressed across gestation, including the expression of hormones with previously undescribed roles.Expression levels of all genes with known or predicted hormone activity expressed in two separate tissues, the placenta and maternal decidua, were assessed across a timecourse spanning the full lifetime of the placenta. Novel expression patterns were confirmed by in situ hybridization and protein level measurements.A combination of temporal and spatial information defines five groups that can accurately predict the patterns of uncharacterized hormones. Our analysis identified Secretin, a novel placental hormone that is expressed specifically by the trophoblast at levels many times greater than in any other tissue.The characteristics of Secretin fit the paradigm of known placental hormones and suggest that it may play an important role during pregnancy.

    View details for DOI 10.1016/j.placenta.2011.08.013

    View details for Web of Science ID 000297906600003

    View details for PubMedID 21944867

  • Chromatin and transcriptional signatures for Nodal signaling during endoderm formation in hESCs DEVELOPMENTAL BIOLOGY Kim, S. W., Yoon, S., Chuong, E., Oyolu, C., Wills, A. E., Gupta, R., Baker, J. 2011; 357 (2): 492-504

    Abstract

    The first stages of embryonic differentiation are driven by signaling pathways hardwired to induce particular fates. Endoderm commitment is controlled by the TGF-β superfamily member, Nodal, which utilizes the transcription factors, SMAD2/3, SMAD4 and FOXH1, to drive target gene expression. While the role of Nodal is well defined within the context of endoderm commitment, mechanistically it is unknown how this signal interacts with chromatin on a genome wide scale to trigger downstream responses. To elucidate the Nodal transcriptional network that governs endoderm formation, we used ChIP-seq to identify genomic targets for SMAD2/3, SMAD3, SMAD4, FOXH1 and the active and repressive chromatin marks, H3K4me3 and H3K27me3, in human embryonic stem cells (hESCs) and derived endoderm. We demonstrate that while SMAD2/3, SMAD4 and FOXH1 associate with DNA in a highly dynamic fashion, there is an optimal bivalent signature at 32 gene loci for driving endoderm commitment. Initially, this signature is marked by both H3K4me3 and H3K27me3 as a very broad bivalent domain in hESCs. Within the first 24h, SMAD2/3 accumulation coincides with H3K27me3 reduction so that these loci become monovalent marked by H3K4me3. JMJD3, a histone demethylase, is simultaneously recruited to these promoters, suggesting a conservation of mechanism at multiple promoters genome-wide. The correlation between SMAD2/3 binding, monovalent formation and transcriptional activation suggests a mechanism by which SMAD proteins coordinate with chromatin at critical promoters to drive endoderm specification.

    View details for DOI 10.1016/j.ydbio.2011.06.009

    View details for Web of Science ID 000294834400019

    View details for PubMedID 21741376

  • HEB and E2A function as SMAD/FOXH1 cofactors GENES & DEVELOPMENT Yoon, S., Wills, A. E., Chuong, E., Gupta, R., Baker, J. C. 2011; 25 (15): 1654-1661

    Abstract

    Nodal signaling, mediated through SMAD transcription factors, is necessary for pluripotency maintenance and endoderm commitment. We identified a new motif, termed SMAD complex-associated (SCA), that is bound by SMAD2/3/4 and FOXH1 in human embryonic stem cells (hESCs) and derived endoderm. We demonstrate that two basic helix-loop-helix (bHLH) proteins-HEB and E2A-bind the SCA motif at regions overlapping SMAD2/3 and FOXH1. Furthermore, we show that HEB and E2A associate with SMAD2/3 and FOXH1, suggesting they form a complex at critical target regions. This association is biologically important, as E2A is critical for mesendoderm specification, gastrulation, and Nodal signal transduction in Xenopus tropicalis embryos. Taken together, E proteins are novel Nodal signaling cofactors that associate with SMAD2/3 and FOXH1 and are necessary for mesendoderm differentiation.

    View details for DOI 10.1101/gad.16800511

    View details for Web of Science ID 000293700900011

    View details for PubMedID 21828274

    View details for PubMedCentralID PMC3182016

  • A New FACS Approach Isolates hESC Derived Endoderm Using Transcription Factors PLOS ONE Pan, Y., Ouyang, Z., Wong, W. H., Baker, J. C. 2011; 6 (3)

    Abstract

    We show that high quality microarray gene expression profiles can be obtained following FACS sorting of cells using combinations of transcription factors. We use this transcription factor FACS (tfFACS) methodology to perform a genomic analysis of hESC-derived endodermal lineages marked by combinations of SOX17, GATA4, and CXCR4, and find that triple positive cells have a much stronger definitive endoderm signature than other combinations of these markers. Additionally, SOX17(+) GATA4(+) cells can be obtained at a much earlier stage of differentiation, prior to expression of CXCR4(+) cells, providing an important new tool to isolate this earlier definitive endoderm subtype. Overall, tfFACS represents an advancement in FACS technology which broadly crosses multiple disciplines, most notably in regenerative medicine to redefine cellular populations.

    View details for DOI 10.1371/journal.pone.0017536

    View details for Web of Science ID 000288170900026

    View details for PubMedID 21408072

    View details for PubMedCentralID PMC3052315

  • Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver GENOME RESEARCH Brunner, A. L., Johnson, D. S., Kim, S. W., Valouev, A., Reddy, T. E., Neff, N. F., Anton, E., Medina, C., Nguyen, L., Chiao, E., Oyolu, C. B., Schroth, G. P., Absher, D. M., Baker, J. C., Myers, R. M. 2009; 19 (6): 1044-1056

    Abstract

    To investigate the role of DNA methylation during human development, we developed Methyl-seq, a method that assays DNA methylation at more than 90,000 regions throughout the genome. Performing Methyl-seq on human embryonic stem cells (hESCs), their derivatives, and human tissues allowed us to identify several trends during hESC and in vivo liver differentiation. First, differentiation results in DNA methylation changes at a minimal number of assayed regions, both in vitro and in vivo (2%-11%). Second, in vitro hESC differentiation is characterized by both de novo methylation and demethylation, whereas in vivo fetal liver development is characterized predominantly by demethylation. Third, hESC differentiation is uniquely characterized by methylation changes specifically at H3K27me3-occupied regions, bivalent domains, and low density CpG promoters (LCPs), suggesting that these regions are more likely to be involved in transcriptional regulation during hESC differentiation. Although both H3K27me3-occupied domains and LCPs are also regions of high variability in DNA methylation state during human liver development, these regions become highly unmethylated, which is a distinct trend from that observed in hESCs. Taken together, our results indicate that hESC differentiation has a unique DNA methylation signature that may not be indicative of in vivo differentiation.

    View details for DOI 10.1101/gr.088773.108

    View details for Web of Science ID 000266521500010

    View details for PubMedID 19273619

    View details for PubMedCentralID PMC2694474

  • The E3 ubiquitin ligase GREUL1 anteriorizes ectoderm during Xenopus development DEVELOPMENTAL BIOLOGY Borchers, A. G., Hufton, A. L., Eldridge, A. G., Jackson, P. K., Harland, R. M., Baker, J. C. 2002; 251 (2): 395-408

    Abstract

    We have identified a family of RING finger proteins that are orthologous to Drosophila Goliath (G1, Gol). One of the members, GREUL1 (Goliath Related E3 Ubiquitin Ligase 1), can convert Xenopus ectoderm into XAG-1- and Otx2-expressing cells in the absence of both neural tissue and muscle. This activity, combined with the finding that XGREUL1 is expressed within the cement gland, suggests a role for GREUL1 in the generation of anterior ectoderm. Although GREUL1 is not a direct inducer of neural tissue, it can activate the formation of ectopic neural cells within the epidermis of intact embryos. This suggests that GREUL1 can sensitize ectoderm to neuralizing signals. In this paper, we provide evidence that GREUL1 is an E3 ubiquitin ligase. Using a biochemical assay, we show that GREUL1 catalyzes the addition of polyubiquitin chains. These events are mediated by the RING domain since a mutation in two of the cysteines abolishes ligase activity. Mutation of these cysteines also compromises GREUL1's ability to induce cement gland. Thus, GREUL1's RING domain is necessary for both the ubiquitination of substrates and for the conversion of ectoderm to an anterior fate.

    View details for DOI 10.1006/dbio.2002.0814

    View details for Web of Science ID 000179377900015

    View details for PubMedID 12435366

  • Wnt signaling in Xenopus embryos inhibits Bmp4 expression and activates neural development GENES & DEVELOPMENT Baker, J. C., Beddington, R. S., Harland, R. M. 1999; 13 (23): 3149-3159

    Abstract

    We report a new role for Wnt signaling in the vertebrate embryo: the induction of neural tissue from ectoderm. Early expression of mouse wnt8, Xwnt8, beta-catenin, or dominant-negative GSK3 induces the expression of neural-specific markers and inhibits the expression of Bmp4 in Xenopus ectoderm. We show that Wnt8, but not the BMP antagonist Noggin, can inhibit Bmp4 expression at early gastrula stages. Furthermore, inhibition of beta-catenin activity in the neural ectoderm of whole embryos by a truncated TCF results in a decrease in neural development. Therefore, we suggest that a cleavage-stage Wnt signal normally contributes to an early repression of Bmp4 on the dorsal side of the embryo and sensitizes the ectoderm to respond to neural inducing signals from the organizer. The Wnt targets Xnr3 and siamois have been shown previously to have neuralizing activity when overexpressed. However, antagonists of Wnt signaling, dnXwnt8 and Nxfrz8, inhibit Wnt-mediated Xnr3 and siamois induction, but not neural induction, suggesting an alternative mechanism for Bmp repression and neuralization. Conversely, dnTCF blocks both Wnt-mediated Xnr3 and neural induction, suggesting that both pathways require this transcription factor.

    View details for Web of Science ID 000084287900011

    View details for PubMedID 10601040

  • From receptor to nucleus: the Smad pathway CURRENT OPINION IN GENETICS & DEVELOPMENT Baker, J. C., Harland, R. M. 1997; 7 (4): 467-473

    Abstract

    The transforming growth factor-beta (TGF-beta) superfamily plays a central role in the specification and patterning of cells in the early embryo. Several years ago, the TGF-beta s were shown to signal through serine/threonine receptor kinases. Now, with the identification of Smad proteins, we can trace the TGF-beta signal transduction pathway from the receptors into the nucleus.

    View details for Web of Science ID A1997XU02500004

    View details for PubMedID 9309176

  • A novel mesoderm inducer, Madr2 functions in the activin signal transduction pathway GENES & DEVELOPMENT Baker, J. C., Harland, R. M. 1996; 10 (15): 1880-1889

    Abstract

    A functional assay to clone mouse mesoderm inducers has identified the mouse gene Mad related 2 (Madr2). Madr2 induces dorsal mesoderm from Xenopus ectoderm and can mimic the organizer in recruiting neighboring cells into a second axis. By analyzing the expression of a lacZ/Madr2 fusion protein, we find Madr2 confined to the nucleus in the deep, anterior cells of the second axis, whereas in epidermal and more posterior cells the protein is cytoplasmically localized. This context-dependent nuclear localization suggests that in certain regions of the embryo, Madr2 responds to a localized signal and amplifies this signal to form the second axis. Furthermore, although Madr2 remains unlocalized in ectodermal explants, addition of activin enhances the concentration of Madr2 in the nucleus. Significantly, a functional lacZ fusion to a carboxy-terminal portion of Madr2 is nuclear localized even in the absence of activin. This indicates that Madr2 contains a domain that can activate downstream components and a repressive domain that anchors the protein in the cytoplasm. Nuclear localization of Madr2 in response to activin, and the activin-like phenotypes induced by overexpression of Madr2, indicate that Madr2 is a signal transduction component that mediates the activity of activin.

    View details for Web of Science ID A1996VB85000004

    View details for PubMedID 8756346

  • A human Mad protein acting as a BMP-regulated transcriptional activator Nature J. C. Baker, Liu, F., A. Hata, J. Doody, J. Carcamo, R. M. Harland, J. Massague 1996; 381