Rongxin Fang

All Publications

• Three-dimensional single-cell transcriptome imaging of thick tissues. eLife Fang, R., Halpern, A., Rahman, M. M., Huang, Z., Lei, Z., Hell, S. J., Dulac, C., Zhuang, X. 2024; 12

  Abstract

  Multiplexed error-robust fluorescence in situ hybridization (MERFISH) allows genome-scale imaging of RNAs in individual cells in intact tissues. To date, MERFISH has been applied to image thin-tissue samples of ~10 µm thickness. Here, we present a thick-tissue three-dimensional (3D) MERFISH imaging method, which uses confocal microscopy for optical sectioning, deep learning for increasing imaging speed and quality, as well as sample preparation and imaging protocol optimized for thick samples. We demonstrated 3D MERFISH on mouse brain tissue sections of up to 200 µm thickness with high detection efficiency and accuracy. We anticipate that 3D thick-tissue MERFISH imaging will broaden the scope of questions that can be addressed by spatial genomics.

  View details for DOI 10.7554/eLife.90029

  View details for PubMedID 39727221

  View details for PubMedCentralID PMC11677232

• Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH. Science (New York, N.Y.) Fang, R., Xia, C., Close, J. L., Zhang, M., He, J., Huang, Z., Halpern, A. R., Long, B., Miller, J. A., Lein, E. S., Zhuang, X. 2022; 377 (6601): 56-62

  Abstract

  The human cerebral cortex has tremendous cellular diversity. How different cell types are organized in the human cortex and how cellular organization varies across species remain unclear. In this study, we performed spatially resolved single-cell profiling of 4000 genes using multiplexed error-robust fluorescence in situ hybridization (MERFISH), identified more than 100 transcriptionally distinct cell populations, and generated a molecularly defined and spatially resolved cell atlas of the human middle and superior temporal gyrus. We further explored cell-cell interactions arising from soma contact or proximity in a cell type-specific manner. Comparison of the human and mouse cortices showed conservation in the laminar organization of cells and differences in somatic interactions across species. Our data revealed human-specific cell-cell proximity patterns and a markedly increased enrichment for interactions between neurons and non-neuronal cells in the human cortex.

  View details for DOI 10.1126/science.abm1741

  View details for PubMedID 35771910

  View details for PubMedCentralID PMC9262715

• Comprehensive analysis of single cell ATAC-seq data with SnapATAC. Nature communications Fang, R., Preissl, S., Li, Y., Hou, X., Lucero, J., Wang, X., Motamedi, A., Shiau, A. K., Zhou, X., Xie, F., Mukamel, E. A., Zhang, K., Zhang, Y., Behrens, M. M., Ecker, J. R., Ren, B. 2021; 12 (1): 1337

  Abstract

  Identification of the cis-regulatory elements controlling cell-type specific gene expression patterns is essential for understanding the origin of cellular diversity. Conventional assays to map regulatory elements via open chromatin analysis of primary tissues is hindered by sample heterogeneity. Single cell analysis of accessible chromatin (scATAC-seq) can overcome this limitation. However, the high-level noise of each single cell profile and the large volume of data pose unique computational challenges. Here, we introduce SnapATAC, a software package for analyzing scATAC-seq datasets. SnapATAC dissects cellular heterogeneity in an unbiased manner and map the trajectories of cellular states. Using the Nyström method, SnapATAC can process data from up to a million cells. Furthermore, SnapATAC incorporates existing tools into a comprehensive package for analyzing single cell ATAC-seq dataset. As demonstration of its utility, SnapATAC is applied to 55,592 single-nucleus ATAC-seq profiles from the mouse secondary motor cortex. The analysis reveals ~370,000 candidate regulatory elements in 31 distinct cell populations in this brain region and inferred candidate cell-type specific transcriptional regulators.

  View details for DOI 10.1038/s41467-021-21583-9

  View details for PubMedID 33637727

  View details for PubMedCentralID PMC7910485

• Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nature neuroscience Preissl, S., Fang, R., Huang, H., Zhao, Y., Raviram, R., Gorkin, D. U., Zhang, Y., Sos, B. C., Afzal, V., Dickel, D. E., Kuan, S., Visel, A., Pennacchio, L. A., Zhang, K., Ren, B. 2018; 21 (3): 432-439

  Abstract

  Analysis of chromatin accessibility can reveal transcriptional regulatory sequences, but heterogeneity of primary tissues poses a significant challenge in mapping the precise chromatin landscape in specific cell types. Here we report single-nucleus ATAC-seq, a combinatorial barcoding-assisted single-cell assay for transposase-accessible chromatin that is optimized for use on flash-frozen primary tissue samples. We apply this technique to the mouse forebrain through eight developmental stages. Through analysis of more than 15,000 nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell types. We further define cell-type-specific transcriptional regulatory sequences, infer potential master transcriptional regulators and delineate developmental changes in forebrain cellular composition. Our results provide insight into the molecular and cellular dynamics that underlie forebrain development in the mouse and establish technical and analytical frameworks that are broadly applicable to other heterogeneous tissues.

  View details for DOI 10.1038/s41593-018-0079-3

  View details for PubMedID 29434377

  View details for PubMedCentralID PMC5862073

• A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells. Nature methods Diao, Y., Fang, R., Li, B., Meng, Z., Yu, J., Qiu, Y., Lin, K. C., Huang, H., Liu, T., Marina, R. J., Jung, I., Shen, Y., Guan, K. L., Ren, B. 2017; 14 (6): 629-635

  Abstract

  Millions of cis-regulatory elements are predicted to be present in the human genome, but direct evidence for their biological function is scarce. Here we report a high-throughput method, cis-regulatory element scan by tiling-deletion and sequencing (CREST-seq), for the unbiased discovery and functional assessment of cis-regulatory sequences in the genome. We used it to interrogate the 2-Mb POU5F1 locus in human embryonic stem cells, and identified 45 cis-regulatory elements. A majority of these elements have active chromatin marks, DNase hypersensitivity, and occupancy by multiple transcription factors, which confirms the utility of chromatin signatures in cis-element mapping. Notably, 17 of them are previously annotated promoters of functionally unrelated genes, and like typical enhancers, they form extensive spatial contacts with the POU5F1 promoter. These results point to the commonality of enhancer-like promoters in the human genome.

  View details for DOI 10.1038/nmeth.4264

  View details for PubMedID 28417999

  View details for PubMedCentralID PMC5490986

• Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Cell research Fang, R., Yu, M., Li, G., Chee, S., Liu, T., Schmitt, A. D., Ren, B. 2016; 26 (12): 1345-1348

  View details for DOI 10.1038/cr.2016.137

  View details for PubMedID 27886167

  View details for PubMedCentralID PMC5143423

• Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues. Nature structural & molecular biology Yu, M., Zemke, N. R., Chen, Z., Juric, I., Hu, R., Raviram, R., Abnousi, A., Fang, R., Zhang, Y., Gorkin, D. U., Li, Y. E., Zhao, Y., Lee, L., Mishra, S., Schmitt, A. D., Qiu, Y., Dickel, D. E., Visel, A., Pennacchio, L. A., Hu, M., Ren, B. 2024

  Abstract

  While a rich set of putative cis-regulatory sequences involved in mouse fetal development have been annotated recently on the basis of chromatin accessibility and histone modification patterns, delineating their role in developmentally regulated gene expression continues to be challenging. To fill this gap, here we mapped chromatin contacts between gene promoters and distal sequences across the genome in seven mouse fetal tissues and across six developmental stages of the forebrain. We identified 248,620 long-range chromatin interactions centered at 14,138 protein-coding genes and characterized their tissue-to-tissue variations and developmental dynamics. Integrative analysis of the interactome with previous epigenome and transcriptome datasets from the same tissues revealed a strong correlation between the chromatin contacts and chromatin state at distal enhancers, as well as gene expression patterns at predicted target genes. We predicted target genes of 15,098 candidate enhancers and used them to annotate target genes of homologous candidate enhancers in the human genome that harbor risk variants of human diseases. We present evidence that schizophrenia and other adult disease risk variants are frequently found in fetal enhancers, providing support for the hypothesis of fetal origins of adult diseases.

  View details for DOI 10.1038/s41594-024-01431-2

  View details for PubMedID 39681766

  View details for PubMedCentralID 4556168

• Single nucleus multi-omics identifies human cortical cell regulatory genome diversity. Cell genomics Luo, C., Liu, H., Xie, F., Armand, E. J., Siletti, K., Bakken, T. E., Fang, R., Doyle, W. I., Stuart, T., Hodge, R. D., Hu, L., Wang, B. A., Zhang, Z., Preissl, S., Lee, D. S., Zhou, J., Niu, S. Y., Castanon, R., Bartlett, A., Rivkin, A., Wang, X., Lucero, J., Nery, J. R., Davis, D. A., Mash, D. C., Satija, R., Dixon, J. R., Linnarsson, S., Lein, E., Behrens, M. M., Ren, B., Mukamel, E. A., Ecker, J. R. 2022; 2 (3)

  Abstract

  Single-cell technologies measure unique cellular signatures but are typically limited to a single modality. Computational approaches allow the fusion of diverse single-cell data types, but their efficacy is difficult to validate in the absence of authentic multi-omic measurements. To comprehensively assess the molecular phenotypes of single cells, we devised single-nucleus methylcytosine, chromatin accessibility, and transcriptome sequencing (snmCAT-seq) and applied it to postmortem human frontal cortex tissue. We developed a cross-validation approach using multi-modal information to validate fine-grained cell types and assessed the effectiveness of computational data fusion methods. Correlation analysis in individual cells revealed distinct relations between methylation and gene expression. Our integrative approach enabled joint analyses of the methylome, transcriptome, chromatin accessibility, and conformation for 63 human cortical cell types. We reconstructed regulatory lineages for cortical cell populations and found specific enrichment of genetic risk for neuropsychiatric traits, enabling the prediction of cell types that are associated with diseases.

  View details for DOI 10.1016/j.xgen.2022.100107

  View details for PubMedID 35419551

  View details for PubMedCentralID PMC9004682

• Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature Bakken, T. E., Jorstad, N. L., Hu, Q., Lake, B. B., Tian, W., Kalmbach, B. E., Crow, M., Hodge, R. D., Krienen, F. M., Sorensen, S. A., Eggermont, J., Yao, Z., Aevermann, B. D., Aldridge, A. I., Bartlett, A., Bertagnolli, D., Casper, T., Castanon, R. G., Crichton, K., Daigle, T. L., Dalley, R., Dee, N., Dembrow, N., Diep, D., Ding, S. L., Dong, W., Fang, R., Fischer, S., Goldman, M., Goldy, J., Graybuck, L. T., Herb, B. R., Hou, X., Kancherla, J., Kroll, M., Lathia, K., van Lew, B., Li, Y. E., Liu, C. S., Liu, H., Lucero, J. D., Mahurkar, A., McMillen, D., Miller, J. A., Moussa, M., Nery, J. R., Nicovich, P. R., Niu, S. Y., Orvis, J., Osteen, J. K., Owen, S., Palmer, C. R., Pham, T., Plongthongkum, N., Poirion, O., Reed, N. M., Rimorin, C., Rivkin, A., Romanow, W. J., Sedeño-Cortés, A. E., Siletti, K., Somasundaram, S., Sulc, J., Tieu, M., Torkelson, A., Tung, H., Wang, X., Xie, F., Yanny, A. M., Zhang, R., Ament, S. A., Behrens, M. M., Bravo, H. C., Chun, J., Dobin, A., Gillis, J., Hertzano, R., Hof, P. R., Höllt, T., Horwitz, G. D., Keene, C. D., Kharchenko, P. V., Ko, A. L., Lelieveldt, B. P., Luo, C., Mukamel, E. A., Pinto-Duarte, A., Preissl, S., Regev, A., Ren, B., Scheuermann, R. H., Smith, K., Spain, W. J., White, O. R., Koch, C., Hawrylycz, M., Tasic, B., Macosko, E. Z., McCarroll, S. A., Ting, J. T., Zeng, H., Zhang, K., Feng, G., Ecker, J. R., Linnarsson, S., Lein, E. S. 2021; 598 (7879): 111-119

  Abstract

  The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch-seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.

  View details for DOI 10.1038/s41586-021-03465-8

  View details for PubMedID 34616062

  View details for PubMedCentralID PMC8494640

• An atlas of gene regulatory elements in adult mouse cerebrum. Nature Li, Y. E., Preissl, S., Hou, X., Zhang, Z., Zhang, K., Qiu, Y., Poirion, O. B., Li, B., Chiou, J., Liu, H., Pinto-Duarte, A., Kubo, N., Yang, X., Fang, R., Wang, X., Han, J. Y., Lucero, J., Yan, Y., Miller, M., Kuan, S., Gorkin, D., Gaulton, K. J., Shen, Y., Nunn, M., Mukamel, E. A., Behrens, M. M., Ecker, J. R., Ren, B. 2021; 598 (7879): 129-136

  Abstract

  The mammalian cerebrum performs high-level sensory perception, motor control and cognitive functions through highly specialized cortical and subcortical structures1. Recent surveys of mouse and human brains with single-cell transcriptomics2-6 and high-throughput imaging technologies7,8 have uncovered hundreds of neural cell types distributed in different brain regions, but the transcriptional regulatory programs that are responsible for the unique identity and function of each cell type remain unknown. Here we probe the accessible chromatin in more than 800,000 individual nuclei from 45 regions that span the adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei, and use the resulting data to map the state of 491,818 candidate cis-regulatory DNA elements in 160 distinct cell types. We find high specificity of spatial distribution for not only excitatory neurons, but also most classes of inhibitory neurons and a subset of glial cell types. We characterize the gene regulatory sequences associated with the regional specificity within these cell types. We further link a considerable fraction of the cis-regulatory elements to putative target genes expressed in diverse cerebral cell types and predict transcriptional regulators that are involved in a broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Our results provide a foundation for comprehensive analysis of gene regulatory programs of the mammalian brain and assist in the interpretation of noncoding risk variants associated with various neurological diseases and traits in humans.

  View details for DOI 10.1038/s41586-021-03604-1

  View details for PubMedID 34616068

  View details for PubMedCentralID PMC8494637

• A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature Yao, Z., Liu, H., Xie, F., Fischer, S., Adkins, R. S., Aldridge, A. I., Ament, S. A., Bartlett, A., Behrens, M. M., Van den Berge, K., Bertagnolli, D., de Bézieux, H. R., Biancalani, T., Booeshaghi, A. S., Bravo, H. C., Casper, T., Colantuoni, C., Crabtree, J., Creasy, H., Crichton, K., Crow, M., Dee, N., Dougherty, E. L., Doyle, W. I., Dudoit, S., Fang, R., Felix, V., Fong, O., Giglio, M., Goldy, J., Hawrylycz, M., Herb, B. R., Hertzano, R., Hou, X., Hu, Q., Kancherla, J., Kroll, M., Lathia, K., Li, Y. E., Lucero, J. D., Luo, C., Mahurkar, A., McMillen, D., Nadaf, N. M., Nery, J. R., Nguyen, T. N., Niu, S. Y., Ntranos, V., Orvis, J., Osteen, J. K., Pham, T., Pinto-Duarte, A., Poirion, O., Preissl, S., Purdom, E., Rimorin, C., Risso, D., Rivkin, A. C., Smith, K., Street, K., Sulc, J., Svensson, V., Tieu, M., Torkelson, A., Tung, H., Vaishnav, E. D., Vanderburg, C. R., van Velthoven, C., Wang, X., White, O. R., Huang, Z. J., Kharchenko, P. V., Pachter, L., Ngai, J., Regev, A., Tasic, B., Welch, J. D., Gillis, J., Macosko, E. Z., Ren, B., Ecker, J. R., Zeng, H., Mukamel, E. A. 2021; 598 (7879): 103-110

  Abstract

  Single-cell transcriptomics can provide quantitative molecular signatures for large, unbiased samples of the diverse cell types in the brain1-3. With the proliferation of multi-omics datasets, a major challenge is to validate and integrate results into a biological understanding of cell-type organization. Here we generated transcriptomes and epigenomes from more than 500,000 individual cells in the mouse primary motor cortex, a structure that has an evolutionarily conserved role in locomotion. We developed computational and statistical methods to integrate multimodal data and quantitatively validate cell-type reproducibility. The resulting reference atlas-containing over 56 neuronal cell types that are highly replicable across analysis methods, sequencing technologies and modalities-is a comprehensive molecular and genomic account of the diverse neuronal and non-neuronal cell types in the mouse primary motor cortex. The atlas includes a population of excitatory neurons that resemble pyramidal cells in layer 4 in other cortical regions4. We further discovered thousands of concordant marker genes and gene regulatory elements for these cell types. Our results highlight the complex molecular regulation of cell types in the brain and will directly enable the design of reagents to target specific cell types in the mouse primary motor cortex for functional analysis.

  View details for DOI 10.1038/s41586-021-03500-8

  View details for PubMedID 34616066

  View details for PubMedCentralID PMC8494649

• Single-cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes risk. Nature genetics Chiou, J., Zeng, C., Cheng, Z., Han, J. Y., Schlichting, M., Miller, M., Mendez, R., Huang, S., Wang, J., Sui, Y., Deogaygay, A., Okino, M. L., Qiu, Y., Sun, Y., Kudtarkar, P., Fang, R., Preissl, S., Sander, M., Gorkin, D. U., Gaulton, K. J. 2021; 53 (4): 455-466

  Abstract

  Single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) creates new opportunities to dissect cell type-specific mechanisms of complex diseases. Since pancreatic islets are central to type 2 diabetes (T2D), we profiled 15,298 islet cells by using combinatorial barcoding snATAC-seq and identified 12 clusters, including multiple alpha, beta and delta cell states. We cataloged 228,873 accessible chromatin sites and identified transcription factors underlying lineage- and state-specific regulation. We observed state-specific enrichment of fasting glucose and T2D genome-wide association studies for beta cells and enrichment for other endocrine cell types. At T2D signals localized to islet-accessible chromatin, we prioritized variants with predicted regulatory function and co-accessibility with target genes. A causal T2D variant rs231361 at the KCNQ1 locus had predicted effects on a beta cell enhancer co-accessible with INS and genome editing in embryonic stem cell-derived beta cells affected INS levels. Together our findings demonstrate the power of single-cell epigenomics for interpreting complex disease genetics.

  View details for DOI 10.1038/s41588-021-00823-0

  View details for PubMedID 33795864

  View details for PubMedCentralID PMC9037575

• Chromothripsis drives the evolution of gene amplification in cancer. Nature Shoshani, O., Brunner, S. F., Yaeger, R., Ly, P., Nechemia-Arbely, Y., Kim, D. H., Fang, R., Castillon, G. A., Yu, M., Li, J. S., Sun, Y., Ellisman, M. H., Ren, B., Campbell, P. J., Cleveland, D. W. 2021; 591 (7848): 137-141

  Abstract

  Focal chromosomal amplification contributes to the initiation of cancer by mediating overexpression of oncogenes1-3, and to the development of cancer therapy resistance by increasing the expression of genes whose action diminishes the efficacy of anti-cancer drugs. Here we used whole-genome sequencing of clonal cell isolates that developed chemotherapeutic resistance to show that chromothripsis is a major driver of circular extrachromosomal DNA (ecDNA) amplification (also known as double minutes) through mechanisms that depend on poly(ADP-ribose) polymerases (PARP) and the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs). Longitudinal analyses revealed that a further increase in drug tolerance is achieved by structural evolution of ecDNAs through additional rounds of chromothripsis. In situ Hi-C sequencing showed that ecDNAs preferentially tether near chromosome ends, where they re-integrate when DNA damage is present. Intrachromosomal amplifications that formed initially under low-level drug selection underwent continuing breakage-fusion-bridge cycles, generating amplicons more than 100 megabases in length that became trapped within interphase bridges and then shattered, thereby producing micronuclei whose encapsulated ecDNAs are substrates for chromothripsis. We identified similar genome rearrangement profiles linked to localized gene amplification in human cancers with acquired drug resistance or oncogene amplifications. We propose that chromothripsis is a primary mechanism that accelerates genomic DNA rearrangement and amplification into ecDNA and enables rapid acquisition of tolerance to altered growth conditions.

  View details for DOI 10.1038/s41586-020-03064-z

  View details for PubMedID 33361815

  View details for PubMedCentralID PMC7933129

• Spatiotemporal DNA methylome dynamics of the developing mouse fetus. Nature He, Y., Hariharan, M., Gorkin, D. U., Dickel, D. E., Luo, C., Castanon, R. G., Nery, J. R., Lee, A. Y., Zhao, Y., Huang, H., Williams, B. A., Trout, D., Amrhein, H., Fang, R., Chen, H., Li, B., Visel, A., Pennacchio, L. A., Ren, B., Ecker, J. R. 2020; 583 (7818): 752-759

  Abstract

  Cytosine DNA methylation is essential for mammalian development but understanding of its spatiotemporal distribution in the developing embryo remains limited1,2. Here, as part of the mouse Encyclopedia of DNA Elements (ENCODE) project, we profiled 168 methylomes from 12 mouse tissues or organs at 9 developmental stages from embryogenesis to adulthood. We identified 1,808,810 genomic regions that showed variations in CG methylation by comparing the methylomes of different tissues or organs from different developmental stages. These DNA elements predominantly lose CG methylation during fetal development, whereas the trend is reversed after birth. During late stages of fetal development, non-CG methylation accumulated within the bodies of key developmental transcription factor genes, coinciding with their transcriptional repression. Integration of genome-wide DNA methylation, histone modification and chromatin accessibility data enabled us to predict 461,141 putative developmental tissue-specific enhancers, the human orthologues of which were enriched for disease-associated genetic variants. These spatiotemporal epigenome maps provide a resource for studies of gene regulation during tissue or organ progression, and a starting point for investigating regulatory elements that are involved in human developmental disorders.

  View details for DOI 10.1038/s41586-020-2119-x

  View details for PubMedID 32728242

  View details for PubMedCentralID PMC7398276

• Joint profiling of DNA methylation and chromatin architecture in single cells. Nature methods Li, G., Liu, Y., Zhang, Y., Kubo, N., Yu, M., Fang, R., Kellis, M., Ren, B. 2019; 16 (10): 991-993

  Abstract

  We report a molecular assay, Methyl-HiC, that can simultaneously capture the chromosome conformation and DNA methylome in a cell. Methyl-HiC reveals coordinated DNA methylation status between distal genomic segments that are in spatial proximity in the nucleus, and delineates heterogeneity of both the chromatin architecture and DNA methylome in a mixed population. It enables simultaneous characterization of cell-type-specific chromatin organization and epigenome in complex tissues.

  View details for DOI 10.1038/s41592-019-0502-z

  View details for PubMedID 31384045

  View details for PubMedCentralID PMC6765429

• Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells. Nature genetics Zhang, Y., Li, T., Preissl, S., Amaral, M. L., Grinstein, J. D., Farah, E. N., Destici, E., Qiu, Y., Hu, R., Lee, A. Y., Chee, S., Ma, K., Ye, Z., Zhu, Q., Huang, H., Fang, R., Yu, L., Izpisua Belmonte, J. C., Wu, J., Evans, S. M., Chi, N. C., Ren, B. 2019; 51 (9): 1380-1388

  Abstract

  Chromatin architecture has been implicated in cell type-specific gene regulatory programs, yet how chromatin remodels during development remains to be fully elucidated. Here, by interrogating chromatin reorganization during human pluripotent stem cell (hPSC) differentiation, we discover a role for the primate-specific endogenous retrotransposon human endogenous retrovirus subfamily H (HERV-H) in creating topologically associating domains (TADs) in hPSCs. Deleting these HERV-H elements eliminates their corresponding TAD boundaries and reduces the transcription of upstream genes, while de novo insertion of HERV-H elements can introduce new TAD boundaries. The ability of HERV-H to create TAD boundaries depends on high transcription, as transcriptional repression of HERV-H elements prevents the formation of boundaries. This ability is not limited to hPSCs, as these actively transcribed HERV-H elements and their corresponding TAD boundaries also appear in pluripotent stem cells from other hominids but not in more distantly related species lacking HERV-H elements. Overall, our results provide direct evidence for retrotransposons in actively shaping cell type- and species-specific chromatin architecture.

  View details for DOI 10.1038/s41588-019-0479-7

  View details for PubMedID 31427791

  View details for PubMedCentralID PMC6722002

• MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. PLoS computational biology Juric, I., Yu, M., Abnousi, A., Raviram, R., Fang, R., Zhao, Y., Zhang, Y., Qiu, Y., Yang, Y., Li, Y., Ren, B., Hu, M. 2019; 15 (4): e1006982

  Abstract

  Hi-C and chromatin immunoprecipitation (ChIP) have been combined to identify long-range chromatin interactions genome-wide at reduced cost and enhanced resolution, but extracting information from the resulting datasets has been challenging. Here we describe a computational method, MAPS, Model-based Analysis of PLAC-seq and HiChIP, to process the data from such experiments and identify long-range chromatin interactions. MAPS adopts a zero-truncated Poisson regression framework to explicitly remove systematic biases in the PLAC-seq and HiChIP datasets, and then uses the normalized chromatin contact frequencies to identify significant chromatin interactions anchored at genomic regions bound by the protein of interest. MAPS shows superior performance over existing software tools in the analysis of chromatin interactions from multiple PLAC-seq and HiChIP datasets centered on different transcriptional factors and histone marks. MAPS is freely available at https://github.com/ijuric/MAPS.

  View details for DOI 10.1371/journal.pcbi.1006982

  View details for PubMedID 30986246

  View details for PubMedCentralID PMC6483256

• Hyper-Editing of Cell-Cycle Regulatory and Tumor Suppressor RNA Promotes Malignant Progenitor Propagation. Cancer cell Jiang, Q., Isquith, J., Zipeto, M. A., Diep, R. H., Pham, J., Delos Santos, N., Reynoso, E., Chau, J., Leu, H., Lazzari, E., Melese, E., Ma, W., Fang, R., Minden, M., Morris, S., Ren, B., Pineda, G., Holm, F., Jamieson, C. 2019; 35 (1): 81-94.e7

  Abstract

  Adenosine deaminase associated with RNA1 (ADAR1) deregulation contributes to therapeutic resistance in many malignancies. Here we show that ADAR1-induced hyper-editing in normal human hematopoietic progenitors impairs miR-26a maturation, which represses CDKN1A expression indirectly via EZH2, thereby accelerating cell-cycle transit. However, in blast crisis chronic myeloid leukemia progenitors, loss of EZH2 expression and increased CDKN1A oppose cell-cycle transit. Moreover, A-to-I editing of both the MDM2 regulatory microRNA and its binding site within the 3' UTR region stabilizes MDM2 transcripts, thereby enhancing blast crisis progenitor propagation. These data reveal a dual mechanism governing malignant transformation of progenitors that is predicated on hyper-editing of cell-cycle-regulatory miRNAs and the 3' UTR binding site of tumor suppressor miRNAs.

  View details for DOI 10.1016/j.ccell.2018.11.017

  View details for PubMedID 30612940

  View details for PubMedCentralID PMC6333511

• Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function. Cell Link, V. M., Duttke, S. H., Chun, H. B., Holtman, I. R., Westin, E., Hoeksema, M. A., Abe, Y., Skola, D., Romanoski, C. E., Tao, J., Fonseca, G. J., Troutman, T. D., Spann, N. J., Strid, T., Sakai, M., Yu, M., Hu, R., Fang, R., Metzler, D., Ren, B., Glass, C. K. 2018; 173 (7): 1796-1809.e17

  Abstract

  Non-coding genetic variation is a major driver of phenotypic diversity and allows the investigation of mechanisms that control gene expression. Here, we systematically investigated the effects of >50 million variations from five strains of mice on mRNA, nascent transcription, transcription start sites, and transcription factor binding in resting and activated macrophages. We observed substantial differences associated with distinct molecular pathways. Evaluating genetic variation provided evidence for roles of ∼100 TFs in shaping lineage-determining factor binding. Unexpectedly, a substantial fraction of strain-specific factor binding could not be explained by local mutations. Integration of genomic features with chromatin interaction data provided evidence for hundreds of connected cis-regulatory domains associated with differences in transcription factor binding and gene expression. This system and the >250 datasets establish a substantial new resource for investigation of how genetic variation affects cellular phenotypes.

  View details for DOI 10.1016/j.cell.2018.04.018

  View details for PubMedID 29779944

  View details for PubMedCentralID PMC6003872