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Role of TET enzymes in DNA methylation, development, and cancer

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High-resolution TADs reveal DNA sequences underlying genome organization in flies

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Targeted in situ genome-wide profiling with high efficiency for low cell numbers

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Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling

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Improved CUT&RUN chromatin profiling tools

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Towards a comprehensive catalogue of validated and target-linked human enhancers

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Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks

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Transcription shapes 3D chromatin organization by interacting with loop extrusion

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Profiling of Pluripotency Factors in Single Cells and Early Embryos

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Islands of retroelements are major components of Drosophila centromeres

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Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation

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DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo

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Z-DNA-forming sites identified by ChIP-Seq are associated with actively transcribed regions in the human genome

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Complex-dependent histone acetyltransferase activity of KAT8 determines its role in transcription and cellular homeostasis

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A map of direct TF–DNA interactions in the human genome

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Convolutional neural networks (CNNs): concepts and applications in pharmacogenomics

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A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis

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Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression

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TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells

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Production of Spliced Long Noncoding RNAs Specifies Regions with Increased Enhancer Activity

Gil, N., & Ulitsky, I. (2018) · Cell Systems · doi:10.1016/j.cels.2018.10.009 · Cited by 88

Epigenome Regulation by Dynamic Nucleosome Unwrapping

Brahma, S., & Henikoff, S. (2019) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2019.09.003 · Cited by 91

CBP Regulates Recruitment and Release of Promoter-Proximal RNA Polymerase II

Boija, A., Mahat, D. B., Zare, A., Holmqvist, P.-H., Philip, P., Meyers, D. J., Cole, P. A., Lis, J. T., Stenberg, P., & Mannervik, M. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.09.031 · Cited by 83

LIM domain–binding 1 maintains the terminally differentiated state of pancreatic β cells

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Genome-wide measurement of local nucleosome array regularity and spacing by nanopore sequencing

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In vivo binding of PRDM9 reveals interactions with noncanonical genomic sitesPreprint

Grey, C., Clément, J. A. J., Buard, J., Leblanc, B., Gut, I. G., Gut, M. O., Duret, L., & de Massy, B. (2017) · Genome Research · doi:10.1101/gr.217240.116 · Cited by 76

Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs

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Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators

Kwon, S. Y., Grisan, V., Jang, B., Herbert, J. M. J., & Badenhorst, P. W. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1005969 · Cited by 70

HOT or not: examining the basis of high-occupancy target regions

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Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding

Bonocora, R. P., Smith, C., Lapierre, P., & Wade, J. T. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005552 · Cited by 60

Cofactor squelching: Artifact or fact?

Schmidt, S. F., Larsen, B. D., Loft, A., & Mandrup, S. (2016) · BioEssays · doi:10.1002/bies.201600034 · Cited by 56

DamID as a versatile tool for understanding gene regulation

Aughey, G., Cheetham, S. W., & Southall, T. D. (2019) · Development · doi:10.1242/dev.173666 · Cited by 56

Mapping transcription factor occupancy using minimal numbers of cells in vitro and in vivoPreprint

Tosti, L., Ashmore, J., Tan, B. S. N., Carbone, B., Mistri, T. K., Wilson, V. A., Tomlinson, S. R., & Kaji, K. (2018) · Genome Research · doi:10.1101/gr.227124.117 · Cited by 54

NF-Y and SP transcription factors — New insights in a long-standing liaison

Suske, G. (2016) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2016.08.011 · Cited by 52

Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding

Shen, N., Zhao, J., Schipper, J. L., Zhang, Y., Bepler, T., Leehr, D., Bradley, J., Horton, J., Lapp, H., & Gordân, R. (2018) · Cell Systems · doi:10.1016/j.cels.2018.02.009 · Cited by 50

Transcriptional repression by FEZF2 restricts alternative identities of cortical projection neurons

Tsyporin, J., Tastad, D., Ma, X., Nehme, A., Finn, T. S., Huebner, L., Liu, G., Gallardo, D., Makhamreh, A. K., Roberts, J. M., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109269 · Cited by 51

Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression

Sasse, S. K., Gruca, M., Allen, M. A., Kadiyala, V., Song, T., Gally, F., Gupta, A., Pufall, M. A., Dowell, R. D., & Gerber, A. N. (2019) · Genome Research · doi:10.1101/gr.248187.119 · Cited by 44

Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors

Yus, E., Lloréns‐Rico, V., Martínez, S., Gallo, C., Eilers, H., Blötz, C., Stülke, J., Lluch‐Senar, M., & Serrano, L. G. (2019) · Cell Systems · doi:10.1016/j.cels.2019.07.001 · Cited by 51

Identification of plant transcription factor target sequences

Franco‐Zorrilla, J. M., & Solano, R. (2016) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2016.05.001 · Cited by 46

Facultative dosage compensation of developmental genes on autosomes in Drosophila and mouse embryonic stem cells

Valsecchi, C. I. K., Basilicata, M. F., Semplicio, G., Georgiev, P., Gutierrez, N. M., & Akhtar, A. (2018) · Nature Communications · doi:10.1038/s41467-018-05642-2 · Cited by 40

Innovation of heterochromatin functions drives rapid evolution of essential ZAD-ZNF genes in Drosophila

Kasinathan, B., Colmenares, S. U., McConnell, H., Young, J. M., Karpen, G. H., & Malik, H. S. (2020) · eLife · doi:10.7554/elife.63368 · Cited by 41

High-intensity UV laser ChIP-seq for the study of protein-DNA interactions in living cells

Steube, A., Schenk, T., Tretyakov, A. N., & Saluz, H. P. (2017) · Nature Communications · doi:10.1038/s41467-017-01251-7 · Cited by 41

Chromatin organizer SATB1 controls the cell identity of CD4+ CD8+ double-positive thymocytes by regulating the activity of super-enhancers

Feng, D., Chen, Y., Dai, R., Bian, S., Xue, W., Zhu, Y., Li, Z., Yang, Y., Zhang, Y., Zhang, J., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33333-6 · Cited by 40

The MUC5B-associated variant rs35705950 resides within an enhancer subject to lineage- and disease-dependent epigenetic remodeling

Gally, F., Sasse, S. K., Kurche, J. S., Gruca, M. A., Cardwell, J., Okamoto, T., Chu, H. W., Hou, X., Poirion, O., Buchanan, J., et al. (2020) · JCI Insight · doi:10.1172/jci.insight.144294 · Cited by 35

Regulation of the BMP Signaling-Responsive Transcriptional Network in the Drosophila Embryo

Deignan, L., Pinheiro, M. T., Sutcliffe, C., Saunders, A., Wilcockson, S. G., Zeef, L. A. H., Donaldson, I. J., & Ashe, H. L. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006164 · Cited by 39

CHRAC/ACF contribute to the repressive ground state of chromatin

Scacchetti, A., Brueckner, L., Jain, D. S., Schauer, T., Zhang, X., Schnorrer, F., van Steensel, B., Straub, T., & Becker, P. B. (2018) · Life Science Alliance · doi:10.26508/lsa.201800024 · Cited by 35

Unexpected conformational variations of the human centromeric chromatin complexPreprint

Thakur, J., & Henikoff, S. (2018) · Genes & Development · doi:10.1101/gad.307736.117 · Cited by 34

Central control of dynamic gene circuits governs T cell rest and activation

Arce, M. M., Umhoefer, J. M., Arang, N., Kasinathan, S., Freimer, J. W., Steinhart, Z., Shen, H., Pham, M. T. N., Ota, M., Wadhera, A., et al. (2024) · Nature · doi:10.1038/s41586-024-08314-y · Cited by 38

Past Roadblocks and New Opportunities in Transcription Factor Network Mapping

Brent, M. R. (2016) · Trends in Genetics · doi:10.1016/j.tig.2016.08.009 · Cited by 34

Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content

Colombo, D., Burger, L., Baubec, T., & Schübeler, D. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1007102 · Cited by 32

Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associationsPreprint

Ramaker, R. C., Hardigan, A. A., Goh, S.-T., Partridge, E. C., Wold, B. J., Cooper, S. J., & Myers, R. (2020) · Genome Research · doi:10.1101/gr.260463.119 · Cited by 35

Gawky modulates MTF-1-mediated transcription activation and metal discrimination

Jia, R., Song, Z., Lin, J., Li, Z., Shan, G., & Huang, C. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab474 · Cited by 30

Establishment of H3K9me3-dependent heterochromatin during embryogenesis in Drosophila miranda

Wei, K. H.-C., Chan, C., & Bachtrog, D. (2021) · eLife · doi:10.7554/elife.55612 · Cited by 29

Putative Causal Variants Are Enriched in Annotated Functional Regions From Six Bovine Tissues

Prowse-Wilkins, C., Wang, J., Xiang, R., Garner, J. B., Goddard, M. E., & Chamberlain, A. J. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.664379 · Cited by 29

The Genome-Wide Binding Profile for Human RE1 Silencing Transcription Factor Unveils a Unique Genetic Circuitry in Hippocampus

McGann, J. C., Spinner, M. A., Garg†, S. K., Müllendorff, K., Woltjer, R. L., & Mandel, G. (2021) · Journal of Neuroscience · doi:10.1523/jneurosci.2059-20.2021 · Cited by 27

Genome-wide studies reveal novel and distinct biological pathways regulated by SIN3 isoforms

Saha, N., Liu, M., Gajan, A., & Pile, L. A. (2016) · BMC Genomics · doi:10.1186/s12864-016-2428-5 · Cited by 27

MS2-TRIBE Evaluates Both Protein-RNA Interactions and Nuclear Organization of Transcription by RNA Editing

Biswas, J., Rahman, R., Gupta, V., Rosbash, M., & Singer, R. H. (2020) · iScience · doi:10.1016/j.isci.2020.101318 · Cited by 27

A large-scale benchmark for network inference from single-cell perturbation data

Chevalley, M., Roohani, Y. H., Mehrjou, A., Leskovec, J., & Schwab, P. (2025) · Communications Biology · doi:10.1038/s42003-025-07764-y · Cited by 26

Lessons from eRNAs: understanding transcriptional regulation through the lens of nascent RNAs

Cardiello, J. F., Sanchez, G. J., Allen, M. A., & Dowell, R. D. (2019) · Transcription · doi:10.1080/21541264.2019.1704128 · Cited by 24

Dynamic enhancer function in the chromatin context

Goldstein, I., & Hager, G. L. (2018) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1390 · Cited by 25

Assaying epigenome functions of PRMTs and their substrates

Rakow, S., Pullamsetti, S. S., Bauer, U., & Bouchard, C. (2019) · Methods · doi:10.1016/j.ymeth.2019.09.014 · Cited by 24

Genome-wide variability in recombination activity is associated with meiotic chromatin organizationPreprint

Jin, X., Fudenberg, G., & Pollard, K. S. (2021) · Genome Research · doi:10.1101/gr.275358.121 · Cited by 25

What to do about those immunoprecipitation blues

Marx, V. (2019) · Nature Methods · doi:10.1038/s41592-019-0365-3 · Cited by 23

Implications of CpG islands on chromosomal architectures and modes of global gene regulation

Beck, S., Rhee, C., Song, J., Lee, B., LeBlanc, L., Cannon, L., & Kim, J. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky147 · Cited by 22

Chromatin reprogramming in breast cancer

Swinstead, E. E., Paakinaho, V., & Hager, G. L. (2018) · Endocrine Related Cancer · doi:10.1530/erc-18-0033 · Cited by 24

Differential cytokine sensitivities of STAT5-dependent enhancers rely onStat5autoregulation

Willi, M., Yoo, K. H., Wang, C., Trajanoski, Z., & Hennighausen, L. G. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw844 · Cited by 22

Enzymatic methods for genome-wide profiling of protein binding sites

Policastro, R. A., & Zentner, G. E. (2017) · Briefings in Functional Genomics · doi:10.1093/bfgp/elx030 · Cited by 22

DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP

Mitra, S., Biswas, A., & Narlikar, L. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006090 · Cited by 19

To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq

Xu, J., Kudron, M. M., Victorsen, A., Gao, J., Ammouri, H., Navarro, F. C. P., Gevirtzman, L., Waterston, R., White, K. P., Reinke, V., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1155 · Cited by 19

Cell-specific and shared regulatory elements control a multigene locus active in mammary and salivary glands

Lee, H., Willi, M., Liu, C., & Hennighausen, L. G. (2023) · Nature Communications · doi:10.1038/s41467-023-40712-0 · Cited by 24

Retrieving Chromatin Patterns from Deep Sequencing Data Using Correlation Functions

Molitor, J., Mallm, J., Rippe, K., & Erdel, F. (2017) · Biophysical Journal · doi:10.1016/j.bpj.2017.01.001 · Cited by 17

Dissecting chromatin-mediated gene regulation and epigenetic memory through mathematical modelling

Ringrose, L., & Howard, M. (2017) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2017.02.003 · Cited by 16

CUT&RUN Profiling of the Budding Yeast Epigenome

Brahma, S., & Henikoff, S. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2257-5_9 · Cited by 15

Lineage-Specific and Non-specific Cytokine-Sensing Genes Respond Differentially to the Master Regulator STAT5

Zeng, X., Willi, M., Shin, H. Y., Hennighausen, L. G., & Wang, C. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.11.079 · Cited by 16

Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis

Mahmud, A. K. M. F., Nilsson, K. L., Fahlgren, A., Navais, R., Choudhury, R., Avican, K., & Fällman, M. (2020) · mSystems · doi:10.1128/msystems.01006-20 · Cited by 16

normR: Regime enrichment calling for ChIP-seq dataPreprint

Helmuth, J., Li, N., Arrigoni, L., Gianmoena, K., Cadenas, C., Gasparoni, G., Sinha, A. N., Rosenstiel, P. C., Walter, J., Hengstler, J. G., et al. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/082263 · Cited by 18

Cell-type specific profiling of histone post-translational modifications in the adult mouse striatum

Carpenter, M. D., Fischer, D. K., Zhang, S., Bond, A. M., Czarnecki, K. S., Woolf, M. T., Song, H., & Heller, E. A. (2022) · Nature Communications · doi:10.1038/s41467-022-35384-1 · Cited by 14

A role for tuned levels of nucleosome remodeler subunit ACF1 during Drosophila oogenesis

Börner, K., Jain, D. S., Vázquez‐Pianzola, P., Vengadasalam, S., Steffen, N., Fyodorov, D. V., Tomančák, P., Konev, A. Y., Suter, B., & Becker, P. B. (2016) · Developmental Biology · doi:10.1016/j.ydbio.2016.01.039 · Cited by 14

A Quantitative Proteomic Analysis of In Vitro Assembled Chromatin

Völker-Albert, M. C., Pusch, M. C., Fedisch, A., Schilcher, P., Schmidt, A., & Imhof, A. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m115.053553 · Cited by 14

ChIPulate: A comprehensive ChIP-seq simulation pipeline

Datta, V., Hannenhalli, S. S., & Siddharthan, R. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006921 · Cited by 13

Alternative Oxidase Transcription Factors AOD2 and AOD5 of Neurospora crassa Control the Expression of Genes Involved in Energy Production and Metabolism

Qi, Z., Smith, K. M., Bredeweg, E. L., Bosnjak, N., Freitag, M., & Nargang, F. E. (2017) · G3 Genes|Genomes|Genetics · doi:10.1534/g3.116.035402 · Cited by 12

Factors and Methods for the Detection of Gene Expression Regulation

Wang, M., Li, Q., & Liu, L. (2023) · Biomolecules · doi:10.3390/biom13020304 · Cited by 15

Comparison of genotoxic versus nongenotoxic stabilization of p53 provides insight into parallel stress-responsive transcriptional networks

Catizone, A. N., Good, C. R., Alexander, K. A., Berger, S. L., & Sammons, M. A. (2019) · Cell Cycle · doi:10.1080/15384101.2019.1593643 · Cited by 12

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Grünberg, S., & Zentner, G. E. (2017) · Journal of Visualized Experiments · doi:10.3791/55836 · Cited by 10

Biomimetic mimicry of formaldehyde-induced DNA–protein crosslinks in the confined space of a metal–organic framework

Wei, Y., Luo, D., Xiong, X., Huang, Y., Xie, M., Lu, W., & Li, D. (2022) · Chemical Science · doi:10.1039/d2sc00188h · Cited by 9

An improved CUT&RUN method for regulation network reconstruction of low abundance transcription factor

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