I am a postdoctoral fellow in the lab of Alistair Boettiger in the Department of Developmental Biology. I have always been interested in understanding regulatory mechanisms that lead to tissue or cell type specific gene expression. During my PhD in the lab of Galit Lahav at Harvard Medical School, I studied how temporal dynamics of a tumor suppressor transcription factor, p53 regulate the dynamics of gene expression in response to DNA damage. In the Boettiger lab, I'm interested how specificity between enhancer-promoter interactions is achieved using super-resolution microscopy.

Honors & Awards

  • Walter V. and Idun Berry Postdoctoral Fellowship, Walter V. and Idun Berry Foundation (2018-2021)
  • Boehringer Ingelheim Fonds PhD Fellowship, Boehringer Ingelheim Fonds (2013-2016)
  • Lynch PhD Fellowship, Lynch foundation (2011-2013)
  • Excellence award for Master's degree, Ecole Polytechnique Federale de Lausanne (EPFL) (2010)
  • WISH Scholarship for Master project abroad, WISH foundation (EPFL) (2009)

Professional Education

  • Bachelor of Science, Ecole Polytechnique Federale de Lausanne, Life Sciences (2008)
  • Master of Science, Ecole Polytechnique Federale de Lausanne (EPFL), Bioengineering and Biotechnology (2010)
  • Doctor of Philosophy, Harvard University (2017)

Lab Affiliations

All Publications

  • The spatial organization of transcriptional control. Nature reviews. Genetics Hafner, A., Boettiger, A. 2022


    In animals, the sequences for controlling gene expression do not concentrate just at the transcription start site of genes, but are frequently thousands to millions of base pairs distal to it. The interaction of these sequences with one another and their transcription start sites is regulated by factors that shape the three-dimensional (3D) organization of the genome within the nucleus. Over the past decade, indirect tools exploiting high-throughput DNA sequencing have helped to map this 3D organization, have identified multiple key regulators of its structure and, in the process, have substantially reshaped our view of how 3D genome architecture regulates transcription. Now, new tools for high-throughput super-resolution imaging of chromatin have directly visualized the 3D chromatin organization, settling some debates left unresolved by earlier indirect methods, challenging some earlier models of regulatory specificity and creating hypotheses about the role of chromatin structure in transcriptional regulation.

    View details for DOI 10.1038/s41576-022-00526-0

    View details for PubMedID 36104547

  • A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation. Nature communications Llimos, G., Gardeux, V., Koch, U., Kribelbauer, J. F., Hafner, A., Alpern, D., Pezoldt, J., Litovchenko, M., Russeil, J., Dainese, R., Moia, R., Mahmoud, A. M., Rossi, D., Gaidano, G., Plass, C., Lutsik, P., Gerhauser, C., Waszak, S. M., Boettiger, A., Radtke, F., Deplancke, B. 2022; 13 (1): 2042


    Non-coding variants coordinate transcription factor (TF) binding and chromatin mark enrichment changes over regions spanning >100kb. These molecularly coordinated regions are named "variable chromatin modules" (VCMs), providing a conceptual framework of how regulatory variation might shape complex traits. To better understand the molecular mechanisms underlying VCM formation, here, we mechanistically dissect a VCM-modulating noncoding variant that is associated with reduced chronic lymphocytic leukemia (CLL) predisposition and disease progression. This common, germline variant constitutes a 5-bp indel that controls the activity of an AXIN2 gene-linked VCM by creating a MEF2 binding site, which, upon binding, activates a super-enhancer-like regulatory element. This triggers a large change in TF binding activity and chromatin state at an enhancer cluster spanning >150kb, coinciding with subtle, long-range chromatin compaction and robust AXIN2 up-regulation. Our results support a model in which the indel acts as an AXIN2 VCM-activating TF nucleation event, which modulates CLL pathology.

    View details for DOI 10.1038/s41467-022-29625-6

    View details for PubMedID 35440565

  • How subtle changes in 3D structure can create large changes in transcription. eLife Xiao, J. Y., Hafner, A., Boettiger, A. N. 2021; 10


    Animal genomes are organized into topologically associated domains (TADs). TADs are thought to contribute to gene regulation by facilitating enhancer-promoter (E-P) contacts within a TAD preventing these contacts across TAD borders. However, the absolute difference in contact frequency across TAD boundaries is usually less than two-fold, even though disruptions of TAD borders can change gene expression by ten-fold. Existing models fail to explain this hypersensitive response. Here, we propose a futile cycle model of enhancer-mediated regulation that can exhibit hypersensitivity through bistability and hysteresis. Consistent with recent experiments, this regulation does not exhibit strong correlation between enhancer-promoter contact and promoter activity, even though regulation occurs through contact. Through mathematical analysis and stochastic simulation, we show that this system can create an illusion of enhancer-promoter biochemical specificity and explain the importance of weak TAD boundaries. It also offers a mechanism to reconcile apparently contradictory results from recent global TAD disruption with local TAD boundary deletion experiments. Together, these analyses advance our understanding of cis-regulatory contacts in controlling gene expression, and suggest new experimental directions.

    View details for DOI 10.7554/eLife.64320

    View details for PubMedID 34240703

  • mSWI/SNF promotes Polycomb repression both directly and through genome-wide redistribution. Nature structural & molecular biology Weber, C. M., Hafner, A., Kirkland, J. G., Braun, S. M., Stanton, B. Z., Boettiger, A. N., Crabtree, G. R. 2021; 28 (6): 501-511


    The mammalian SWI/SNF complex, or BAF complex, has a conserved and direct role in antagonizing Polycomb-mediated repression. Yet, BAF also promotes repression by Polycomb in stem cells and cancer. How BAF both antagonizes and promotes Polycomb-mediated repression remains unknown. Here, we utilize targeted protein degradation to dissect the BAF-Polycomb axis in mouse embryonic stem cells on short timescales. We report that rapid BAF depletion redistributes Polycomb repressive complexes PRC1 and PRC2 from highly occupied domains, like Hox clusters, to weakly occupied sites normally opposed by BAF. Polycomb redistribution from highly repressed domains results in their decompaction, gain of active epigenomic features and transcriptional derepression. Surprisingly, through dose-dependent degradation of PRC1 and PRC2, we identify a conventional role for BAF in Polycomb-mediated repression, in addition to global Polycomb redistribution. These findings provide new mechanistic insight into the highly dynamic state of the Polycomb-Trithorax axis.

    View details for DOI 10.1038/s41594-021-00604-7

    View details for PubMedID 34117481

  • Quantifying the Central Dogma in the p53 Pathway in Live Single Cells. Cell systems Hafner, A., Reyes, J., Stewart-Ornstein, J., Tsabar, M., Jambhekar, A., Lahav, G. 2020


    Transcription factors (TFs) integrate signals to regulate target gene expression, but we generally lack a quantitative understanding of how changes in TF levels regulate mRNA and protein production. Here, we established a system to simultaneously monitor the levels of p53, a TF that shows oscillations following DNA damage, and the transcription and protein levels of its target p21 in individual cells. p21 transcription tracked p53 dynamics, while p21 protein steadily accumulated. p21 transcriptional activation showed bursts of mRNA production, with p53 levels regulating the probability but not magnitude of activation. Variations in p53 levels between cells contributed to heterogeneous p21 transcription while independent p21 alleles exhibited highly correlated behaviors. Pharmacologically elevating p53 increased the probability of p21 transcription with minor effects on its magnitude, leading to a strong increase in p21 protein levels. Our results reveal quantitative mechanisms by which TF dynamics can regulate protein levels of its targets. A record of this paper's transparent peer review process is included in the Supplemental Information.

    View details for DOI 10.1016/j.cels.2020.05.001

    View details for PubMedID 32533938

  • Identification of universal and cell-type specific p53 DNA binding. BMC molecular and cell biology Hafner, A., Kublo, L., Tsabar, M., Lahav, G., Stewart-Ornstein, J. 2020; 21 (1): 5


    BACKGROUND: The tumor suppressor p53 is a major regulator of the DNA damage response and has been suggested to selectively bind and activate cell-type specific gene expression programs. However recent studies and meta-analyses of genomic data propose largely uniform, and condition independent p53 binding and thus question the selective and cell-type dependent function of p53.RESULTS: To systematically assess the cell-type specificity of p53, we measured its association with DNA in 12 p53 wild-type cancer cell lines, from a range of epithelial linages, in response to ionizing radiation. We found that the majority of bound sites were occupied across all cell lines, however we also identified a subset of binding sites that were specific to one or a few cell lines. Unlike the shared p53-bound genome, which was not dependent on chromatin accessibility, the association of p53 with these atypical binding sites was well explained by chromatin accessibility and could be modulated by forcing cell state changes such as the epithelial-to-mesenchymal transition.CONCLUSIONS: Our study reconciles previous conflicting views in the p53 field, by demonstrating that although the majority of p53 DNA binding is conserved across cell types, there is a small set of cell line specific binding sites that depend on cell state.

    View details for DOI 10.1186/s12860-020-00251-8

    View details for PubMedID 32070277

  • A Comprehensive Drosophila melanogaster Transcription Factor Interactome. Cell reports Shokri, L., Inukai, S., Hafner, A., Weinand, K., Hens, K., Vedenko, A., Gisselbrecht, S. S., Dainese, R., Bischof, J., Furger, E., Feuz, J. D., Basler, K., Deplancke, B., Bulyk, M. L. 2019; 27 (3): 955-970.e7


    Combinatorial interactions among transcription factors (TFs) play essential roles in generating gene expression specificity and diversity in metazoans. Using yeast 2-hybrid (Y2H) assays on nearly all sequence-specific Drosophila TFs, we identified 1,983 protein-protein interactions (PPIs), more than doubling the number of currently known PPIs among Drosophila TFs. For quality assessment, we validated a subset of our interactions using MITOMI and bimolecular fluorescence complementation assays. We combined our interactome with prior PPI data to generate an integrated Drosophila TF-TF binary interaction network. Our analysis of ChIP-seq data, integrating PPI and gene expression information, uncovered different modes by which interacting TFs are recruited to DNA. We further demonstrate the utility of our Drosophila interactome in shedding light on human TF-TF interactions. This study reveals how TFs interact to bind regulatory elements in vivo and serves as a resource of Drosophila TF-TF binary PPIs for understanding tissue-specific gene regulation.

    View details for DOI 10.1016/j.celrep.2019.03.071

    View details for PubMedID 30995488

  • Visualizing DNA folding and RNA in embryos at single-cell resolution NATURE Mateo, L. J., Murphy, S. E., Hafner, A., Cinquini, I. S., Walker, C. A., Boettiger, A. N. 2019; 568 (7750): 49-+
  • The multiple mechanisms that regulate p53 activity and cell fate. Nature reviews. Molecular cell biology Hafner, A. n., Bulyk, M. L., Jambhekar, A. n., Lahav, G. n. 2019


    The tumour suppressor p53 has a central role in the response to cellular stress. Activated p53 transcriptionally regulates hundreds of genes that are involved in multiple biological processes, including in DNA damage repair, cell cycle arrest, apoptosis and senescence. In the context of DNA damage, p53 is thought to be a decision-making transcription factor that selectively activates genes as part of specific gene expression programmes to determine cellular outcomes. In this Review, we discuss the multiple molecular mechanisms of p53 regulation and how they modulate the induction of apoptosis or cell cycle arrest following DNA damage. Specifically, we discuss how the interaction of p53 with DNA and chromatin affects gene expression, and how p53 post-translational modifications, its temporal expression dynamics and its interactions with chromatin regulators and transcription factors influence cell fate. These multiple layers of regulation enable p53 to execute cellular responses that are appropriate for specific cellular states and environmental conditions.

    View details for PubMedID 30824861

  • p53 pulses lead to distinct patterns of gene expression albeit similar DNA-binding dynamics. Nature structural & molecular biology Hafner, A., Stewart-Ornstein, J., Purvis, J. E., Forrester, W. C., Bulyk, M. L., Lahav, G. 2017; 24 (10): 840-847


    The dynamics of transcription factors play important roles in a variety of biological systems. However, the mechanisms by which these dynamics are decoded into different transcriptional responses are not well understood. Here we focus on the dynamics of the tumor-suppressor protein p53, which exhibits a series of pulses in response to DNA damage. We performed time course RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) measurements to determine how p53 oscillations are linked with gene expression genome wide. We discovered multiple distinct patterns of gene expression in response to p53 pulses. Surprisingly, p53-binding dynamics were uniform across all genomic loci, even for genes that exhibited distinct mRNA dynamics. Using a mathematical model, supported by additional experimental measurements in response to sustained p53 input, we determined that p53 binds to and activates transcription of its target genes uniformly, whereas post-transcriptional mechanisms are responsible for the differences in gene expression dynamics.

    View details for DOI 10.1038/nsmb.3452

    View details for PubMedID 28825732

    View details for PubMedCentralID PMC5629117

  • A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks MOLECULAR SYSTEMS BIOLOGY Gubelmann, C., Waszak, S. M., Isakova, A., Holcombe, W., Hens, K., Iagovitina, A., Feuz, J., Raghav, S. K., Simicevic, J., Deplancke, B. 2013; 9


    The comprehensive mapping of gene promoters and enhancers has significantly improved our understanding of how the mammalian regulatory genome is organized. An important challenge is to elucidate how these regulatory elements contribute to gene expression by identifying their trans-regulatory inputs. Here, we present the generation of a mouse-specific transcription factor (TF) open-reading frame clone library and its implementation in yeast one-hybrid assays to enable large-scale protein-DNA interaction detection with mouse regulatory elements. Once specific interactions are identified, we then use a microfluidics-based method to validate and precisely map them within the respective DNA sequences. Using well-described regulatory elements as well as orphan enhancers, we show that this cross-platform pipeline characterizes known and uncovers many novel TF-DNA interactions. In addition, we provide evidence that several of these novel interactions are relevant in vivo and aid in elucidating the regulatory architecture of enhancers.

    View details for DOI 10.1038/msb.2013.38

    View details for Web of Science ID 000323940300001

    View details for PubMedID 23917988

    View details for PubMedCentralID PMC3779800

  • Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos NATURE METHODS Gisselbrecht, S. S., Barrera, L. A., Porsch, M., Aboukhalil, A., Estep, P. W., Vedenko, A., Palagi, A., Kim, Y., Zhu, X., Busser, B. W., Gamble, C. E., Iagovitina, A., Singhania, A., Michelson, A. M., Bulyk, M. L. 2013; 10 (8): 774-?


    Transcriptional enhancers are a primary mechanism by which tissue-specific gene expression is achieved. Despite the importance of these regulatory elements in development, responses to environmental stresses and disease, testing enhancer activity in animals remains tedious, with a minority of enhancers having been characterized. Here we describe 'enhancer-FACS-seq' (eFS) for highly parallel identification of active, tissue-specific enhancers in Drosophila melanogaster embryos. Analysis of enhancers identified by eFS as being active in mesodermal tissues revealed enriched DNA binding site motifs of known and putative, previously uncharacterized mesodermal transcription factors. Naive Bayes classifiers using transcription factor binding site motifs accurately predicted mesodermal enhancer activity. Application of eFS to other cell types and organisms should accelerate the cataloging of enhancers and understanding how transcriptional regulation is encoded in them.

    View details for DOI 10.1038/NMETH.2558

    View details for Web of Science ID 000322453600029

    View details for PubMedID 23852450

    View details for PubMedCentralID PMC3733245

  • Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo CHAOS Kim, Y., Iagovitina, A., Ishihara, K., Fitzgerald, K. M., Deplancke, B., Papatsenko, D., Shvartsman, S. Y. 2013; 23 (2)


    Terminal regions of the Drosophila embryo are patterned by the localized activation of Mitogen Activated Protein Kinase (MAPK), which induces zygotic genes through relief of their repression by transcriptional repressor Capicua. The levels of MAPK activation at the anterior and posterior termini are close to each other, but the expression patterns of MAPK-target genes, such as zerknüllt (zen) and tailless (tll), display strong anterior-posterior (AP) asymmetry. This region-specific response to MAPK activation provides a clear example of context-dependent interpretation of inductive signaling, a common developmental effect that remains poorly understood. In the past, the AP asymmetry of zen expression was attributed to a mechanism that depends on MAPK substrate competition. We present data suggesting that the asymmetric expression of tll is generated by a different mechanism, based on feedforward control and multiple enhancers of the tll gene. A simple mathematical model of this mechanism correctly predicts how the wild-type expression pattern of tll changes in mutants affecting the anterior, dorsoventral, and terminal patterning systems and some of their direct targets.

    View details for DOI 10.1063/1.4808157

    View details for Web of Science ID 000321146500038

    View details for PubMedID 23822503

    View details for PubMedCentralID PMC3689791

  • Automated protein-DNA interaction screening of Drosophila regulatory elements NATURE METHODS Hens, K., Feuz, J., Isakova, A., Iagovitina, A., Massouras, A., Bryois, J., Callaerts, P., Celniker, S. E., Deplanckeadenine, B. 2011; 8 (12): 1065-?


    Drosophila melanogaster has one of the best characterized metazoan genomes in terms of functionally annotated regulatory elements. To explore how these elements contribute to gene regulation, we need convenient tools to identify the proteins that bind to them. Here we describe the development and validation of a high-throughput yeast one-hybrid platform, which enables screening of DNA elements versus an array of full-length, sequence-verified clones containing over 85% of predicted Drosophila transcription factors. Using six well-characterized regulatory elements, we identified 33 transcription factor-DNA interactions of which 27 were previously unidentified. To simultaneously validate these interactions and locate the binding sites of involved transcription factors, we implemented a powerful microfluidics-based approach that enabled us to retrieve DNA-occupancy data for each transcription factor throughout the respective target DNA elements. Finally, we biologically validated several interactions and identified two new regulators of sine oculis gene expression and hence eye development.

    View details for DOI 10.1038/NMETH.1763

    View details for Web of Science ID 000297931700020

    View details for PubMedID 22037703

    View details for PubMedCentralID PMC3929264