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

BEDTools: a flexible suite of utilities for comparing genomic features

Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437 · see citing works

Model-based Analysis of ChIP-Seq (MACS)

Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386 · see citing works

An integrated encyclopedia of DNA elements in the human genome

The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072 · see citing works

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y. C., Laslo, P., Cheng, J. X., Murre, C., Singh, H., & Glass, C. K. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.05.004 · Cited by 13,382 · see citing works

High-Resolution Profiling of Histone Methylations in the Human Genome

Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845 · see citing works

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007) · Science · doi:10.1126/science.1141319 · Cited by 2,927 · see citing works

CUT&Tag for efficient epigenomic profiling of small samples and single cells

Kaya-Okur, H. S., Wu, S. J., Codomo, C. A., Pledger, E. S., Bryson, T. D., Henikoff, J. G., Ahmad, K., & Henikoff, S. (2019) · Nature Communications · doi:10.1038/s41467-019-09982-5 · Cited by 2,187 · see citing works

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

Skene, P. J., & Henikoff, S. (2017) · eLife · doi:10.7554/elife.21856 · Cited by 1,737 · see citing works

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

Robertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., Zeng, T., Euskirchen, G., Bernier, B., Varhol, R., Delaney, A., et al. (2007) · Nature Methods · doi:10.1038/nmeth1068 · Cited by 1,454 · see citing works

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

Skene, P. J., Henikoff, J. G., & Henikoff, S. (2018) · Nature Protocols · doi:10.1038/nprot.2018.015 · Cited by 803 · see citing works

Dynamic regulation of transcriptional states by chromatin and transcription factors

Voss, T. C., & Hager, G. L. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3623 · Cited by 504 · see citing works

Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures.

Solomon, M. J., & Varshavsky, A. J. (1985) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.82.19.6470 · Cited by 462 · see citing works

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

Teytelman, L., Thurtle, D. M., Rine, J., & van Oudenaarden, A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1316064110 · Cited by 389 · see citing works

Transcription factor binding dynamics during human ES cell differentiation

Tsankov, A. M., Gu, H., Akopian, V., Ziller, M. J., Donaghey, J., Amit, I., Gnirke, A., & Meissner, A. (2015) · Nature · doi:10.1038/nature14233 · Cited by 349 · see citing works

Use Model-Based Analysis of ChIP-Seq (MACS) to Analyze Short Reads Generated by Sequencing Protein–DNA Interactions in Embryonic Stem Cells

Liu, T. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-0512-6_4 · Cited by 283 · see citing works

Active promoters give rise to false positive ‘Phantom Peaks’ in ChIP-seq experiments

Jain, D., Baldi, S., Zabel, A., Straub, T., & Becker, P. B. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv637 · Cited by 156 · see citing works

Widespread Misinterpretable ChIP-seq Bias in Yeast

Park, D., Lee, Y., Bhupindersingh, G., & Iyer, V. R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0083506 · Cited by 144 · see citing works

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

Nakato, R., & Shirahige, K. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw023 · Cited by 141 · see citing works

Transcription and Remodeling Produce Asymmetrically Unwrapped Nucleosomal Intermediates

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.11.015 · Cited by 135 · see citing works

Features that define the best ChIP-seq peak calling algorithms

Thomas, R., Thomas, S., Holloway, A. K., & Pollard, K. S. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw035 · Cited by 112 · see citing works

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

Janssens, D. H., Wu, S. J., Sarthy, J. F., Meers, M. P., Myers, C. H., Olson, J. M., Ahmad, K., & Henikoff, S. (2018) · Epigenetics & Chromatin · doi:10.1186/s13072-018-0243-8 · Cited by 73 · see citing works

Efficient low-cost chromatin profiling with CUT&Tag

Kaya-Okur, H. S., Janssens, D. H., Henikoff, J. G., Ahmad, K., & Henikoff, S. (2020) · Nature Protocols · doi:10.1038/s41596-020-0373-x · Cited by 425 · see citing works

Hexokinase 2-mediated gene expression via histone lactylation is required for hepatic stellate cell activation and liver fibrosis

Rho, H., Terry, A. R., Chronis, C., & Hay, N. (2023) · Cell Metabolism · doi:10.1016/j.cmet.2023.06.013 · Cited by 421 · see citing works

Establishment, maintenance, and recall of inflammatory memory

Larsen, S. B., Cowley, C. J., Sajjath, S. M., Barrows, D., Yang, Y., Carroll, T. S., & Fuchs, E. V. (2021) · Cell stem cell · doi:10.1016/j.stem.2021.07.001 · Cited by 321 · see citing works

Adipose tissue retains an epigenetic memory of obesity after weight loss

Hinte, L. C., Castellano‐Castillo, D., Ghosh, A., Melrose, K., Gasser, E., Noé, F., Massier, L., Dong, H., Sun, W., Hoffmann, A., et al. (2024) · Nature · doi:10.1038/s41586-024-08165-7 · Cited by 298 · see citing works

Transcription factors interact with RNA to regulate genes

Oksuz, O., Henninger, J. E., Warneford-Thomson, R., Zheng, M. M., Erb, H., Vancura, A., Overholt, K. J., Hawken, S. W., Banani, S. F., Lauman, R., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.06.012 · Cited by 275 · see citing works

H3K18 lactylation marks tissue-specific active enhancers

Galle, E., Wong, C.-W., Ghosh, A., Desgeorges, T., Melrose, K., Hinte, L. C., Castellano‐Castillo, D., Engl, M., de Sousa, J. A., Ruiz‐Ojeda, F. J., et al. (2022) · Genome biology · doi:10.1186/s13059-022-02775-y · Cited by 242 · see citing works

Thymic epithelial cells co-opt lineage-defining transcription factors to eliminate autoreactive T cells

Michelson, D. A., Hase, K., Kaisho, T., Benoist, C. O., & Mathis, D. J. (2022) · Cell · doi:10.1016/j.cell.2022.05.018 · Cited by 208 · see citing works

Reversible phase separation of HSF1 is required for an acute transcriptional response during heat shock

Zhang, H., Shao, S., Zeng, Y., Wang, X., Qin, Y., Ren, Q., Xiang, S., Wang, Y., Xiao, J., & Sun, Y. (2022) · Nature Cell Biology · doi:10.1038/s41556-022-00846-7 · Cited by 185 · see citing works

BATF regulates progenitor to cytolytic effector CD8+ T cell transition during chronic viral infection

Chen, Y., Zander, R., Wu, X., Schauder, D., Kasmani, M. Y., Shen, J., Zheng, S., Burns, R., Taparowsky, E. J., & Cui, W. (2021) · Nature Immunology · doi:10.1038/s41590-021-00965-7 · Cited by 177 · see citing works

The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data

Reiff, S. B., Schroeder, A. J., Kırlı, K., Cosolo, A., Bakker, C., Mercado, L., Lee, S., Veit, A. D., Balashov, A. K., Vitzthum, C. M., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29697-4 · Cited by 173 · see citing works

Molecular Co-occupancy Identifies Transcription Factor Binding Cooperativity In Vivo

Sönmezer, C., Kleinendorst, R., Imanci, D., Barzaghi, G., Villacorta, L., Schübeler, D., Benes, V., Molina, N., & Krebs, A. R. (2021) · Molecular Cell · doi:10.1016/j.molcel.2020.11.015 · Cited by 162 · see citing works

Single-cell multi-cohort dissection of the schizophrenia transcriptome

Ruzicka, W. B., Mohammadi, S., Fullard, J. F., Dávila-Velderrain, J., Subburaju, S., Tso, D. R., Hourihan, M., Jiang, S., Lee, H.-C., Bendl, J. M., et al. (2024) · Science · doi:10.1126/science.adg5136 · Cited by 155 · see citing works

Transcriptional repression of estrogen receptor alpha by YAP reveals the Hippo pathway as therapeutic target for ER+ breast cancer

Ma, S., Tang, T. T.-L., Probst, G. D., Konradi, A. W., Jin, C., Li, F., Gutkind, J. S., Fu, X., & Guan, K. (2022) · Nature Communications · doi:10.1038/s41467-022-28691-0 · Cited by 145 · see citing works

The transcription factor IRF2 drives interferon-mediated CD8+ T cell exhaustion to restrict anti-tumor immunity

Lukhele, S., Abd-Rabbo, D., Guo, M., Shen, J., Elsaesser, H. J., Quevedo, R., Carew, M., Gadalla, R., Snell, L. M., Mahesh, L., et al. (2022) · Immunity · doi:10.1016/j.immuni.2022.10.020 · Cited by 135 · see citing works

A NPAS4–NuA4 complex couples synaptic activity to DNA repair

Pollina, E. A., Gilliam, D. T., Landau, A. T., Lin, C., Pajarillo, N., Davis, C. P., Harmin, D. A., Yap, E.-L., Vogel, I. R., Griffith, E. C., et al. (2023) · Nature · doi:10.1038/s41586-023-05711-7 · Cited by 125 · see citing works

Dual-specificity RNA aptamers enable manipulation of target-specific O-GlcNAcylation and unveil functions of O-GlcNAc on β-catenin

Zhu, Y., & Hart, G. W. (2023) · Cell · doi:10.1016/j.cell.2022.12.016 · Cited by 123 · see citing works

SOX17 enables immune evasion of early colorectal adenomas and cancers

Goto, N., Westcott, P. M. K., Goto, S., Imada, S., Taylor, M. S., Eng, G. M., Braverman, J., Deshpande, V., Jacks, T., Agudo, J., et al. (2024) · Nature · doi:10.1038/s41586-024-07135-3 · Cited by 116 · see citing works

Smarca4 Inactivation Promotes Lineage-Specific Transformation and Early Metastatic Features in the Lung

Concepcion, C. P., Ma, S., LaFave, L. M., Bhutkar, A. J., Liu, M., DeAngelo, L. P., Kim, J. Y., Priore, I. S. D., Schoenfeld, A. J., Miller, M., et al. (2021) · Cancer Discovery · doi:10.1158/2159-8290.cd-21-0248 · Cited by 116 · see citing works

RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis

Zhang, S., Übelmesser, N., Josipović, N., Forte, G., Slotman, J. A., Chiang, M., Gothe, H. J., Gusmao, E. G., Becker, C., Altmüller, J., et al. (2021) · Science Advances · doi:10.1126/sciadv.abg8205 · Cited by 114 · see citing works

Nutrient-driven histone code determines exhausted CD8 + T cell fates

Ma, S., Dahabieh, M. S., Mann, T. H., Zhao, S., McDonald, B., Song, W., Chung, H., Farsakoglu, Y., Garcia-Rivera, L., Hoffmann, F. A., et al. (2024) · Science · doi:10.1126/science.adj3020 · Cited by 109 · see citing works

Multifactorial profiling of epigenetic landscapes at single-cell resolution using MulTI-Tag

Meers, M. P., Llagas, G., Janssens, D. H., Codomo, C. A., & Henikoff, S. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01522-9 · Cited by 103 · see citing works

Genome-wide mapping of i-motifs reveals their association with transcription regulation in live human cells

Zanin, I., Ruggiero, E., Nicoletto, G., Lago, S., Maurizio, I., Gallina, I., & Richter, S. N. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad626 · Cited by 101 · see citing works

CRISPR screens decode cancer cell pathways that trigger γδ T cell detection

Mamedov, M. R., Vedova, S., Freimer, J. W., Sahu, A. D., Ramesh, A., Arce, M. M., Meringa, A. D., Ota, M., Chen, P. A., Hanspers, K., et al. (2023) · Nature · doi:10.1038/s41586-023-06482-x · Cited by 100 · see citing works

TASOR is a pseudo-PARP that directs HUSH complex assembly and epigenetic transposon control

Douse, C. H., Tchasovnikarova, I. A., Timms, R. T., Protasio, A. V., Seczyńska, M., Prigozhin, D. M., Albecka, A., Wagstaff, J. L., Williamson, J. C., Freund, S. M. V., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18761-6 · Cited by 99 · see citing works

Interferon subverts an AHR–JUN axis to promote CXCL13+ T cells in lupus

Law, C., Wacleche, V. S., Cao, Y., Pillai, A., Sowerby, J. M., Hancock, B. L., Horisberger, A., Bracero, S., Skidanova, V., Li, Z., et al. (2024) · Nature · doi:10.1038/s41586-024-07627-2 · Cited by 99 · see citing works

Regulation of human trophoblast gene expression by endogenous retroviruses

Frost, J. M., Amante, S. M., Okae, H., Jones, E. M., Ashley, B., Lewis, R. M., Cleal, J. K., Caley, M. P., Arima, T., Maffucci, T., et al. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-00960-6 · Cited by 94 · see citing works

Comprehensive interactome profiling of the human Hsp70 network highlights functional differentiation of J domains

Piette, B. L., Alerasool, N., Lin, Z., Lacoste, J., Lam, M. H. Y., Qian, W. W., Tran, S., Larsen, B. G., Campos, E. I., Peng, J., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.04.012 · Cited by 91 · see citing works

Cooperation between melanoma cell states promotes metastasis through heterotypic cluster formation

Campbell, N. R., Rao, A. N., Hunter, M., Sznurkowska, M. K., Briker, L., Zhang, M., Baron, M., Heilmann, S., Déforet, M., Kenny, C., et al. (2021) · Developmental Cell · doi:10.1016/j.devcel.2021.08.018 · Cited by 90 · see citing works

The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes

Brahma, S., & Henikoff, S. (2023) · Nature Genetics · doi:10.1038/s41588-023-01603-8 · Cited by 89 · see citing works

Automated CUT&Tag profiling of chromatin heterogeneity in mixed-lineage leukemia

Janssens, D. H., Meers, M. P., Wu, S. J., Babaeva, E., Meshinchi, S., Sarthy, J. F., Ahmad, K., & Henikoff, S. (2021) · Nature Genetics · doi:10.1038/s41588-021-00941-9 · Cited by 88 · see citing works

A chromosome-scale epigenetic map of the <i>Hydra</i> genome reveals conserved regulators of cell state

Cazet, J. F., Siebert, S., Little, H. M., Bertemes, P., Primack, A. S., Ladurner, P., Achrainer, M., Fredriksen, M. T., Moreland, R. T., Singh, S., et al. (2023) · Genome Research · doi:10.1101/gr.277040.122 · Cited by 66 · see citing works

Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat

Zhao, L., Yang, Y., Chen, J., Lin, X., Zhang, H., Wang, H., Wang, H., Bie, X., Jiang, J., Feng, X., et al. (2023) · Genome biology · doi:10.1186/s13059-022-02844-2 · Cited by 87 · see citing works

Lung dendritic-cell metabolism underlies susceptibility to viral infection in diabetes

Nobs, S. P., Kolodziejczyk, A. A., Adler, L. N., Horesh, N., Botscharnikow, C., Herzog, E., Mohapatra, G., Hejndorf, S., Hodgetts, R. J., Spivak, I., et al. (2023) · Nature · doi:10.1038/s41586-023-06803-0 · Cited by 86 · see citing works

Single-cell mapping of DNA G-quadruplex structures in human cancer cells

Hui, W. W. I., Simeone, A., Zyner, K. G., Tannahill, D., & Balasubramanian, S. (2021) · Scientific Reports · doi:10.1038/s41598-021-02943-3 · Cited by 85 · see citing works

Class I HDAC inhibitors enhance antitumor efficacy and persistence of CAR-T cells by activation of the Wnt pathway

Zhu, M., Han, Y., Gu, T., Wang, R. Y., Si, X., Kong, D., Zhao, P., Wang, X., Li, J., Zhai, X., et al. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114065 · Cited by 83 · see citing works

MITF reprograms the extracellular matrix and focal adhesion in melanoma

Dilshat, R., Fock, V., Kenny, C., Gerritsen, I., Lasseur, R. M. J., Trávníčková, J., Eichhoff, O. M., Cerny, P., Möller, K., Sigurbjörnsdóttir, S., et al. (2021) · eLife · doi:10.7554/elife.63093 · Cited by 82 · see citing works

Comparison of tumor-associated YAP1 fusions identifies a recurrent set of functions critical for oncogenesisPreprint

Szulzewsky, F., Arora, S., Hoellerbauer, P., King, C., Nathan, E., Chan, M., Cimino, P. J., Ozawa, T., Kawauchi, D., Pajtler, K. W., et al. (2020) · Genes & Development · doi:10.1101/gad.338681.120 · Cited by 81 · see citing works

GAGA-associated factor fosters loop formation in the Drosophila genome

Li, X., Tang, X., Bing, X., Catalano, C., Li, T., Dolsten, G. A., Wu, C., & Levine, M. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.03.011 · Cited by 77 · see citing works

BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2

Samelson, A. J., Tran, Q. D., Robinot, R., Carrau, L., Rezelj, V. V., Kain, A. M., Chen, M., Ramadoss, G. N., Guo, X., Lim, S. A., et al. (2022) · Nature Cell Biology · doi:10.1038/s41556-021-00821-8 · Cited by 76 · see citing works

Nucleosome Patterns in Circulating Tumor DNA Reveal Transcriptional Regulation of Advanced Prostate Cancer Phenotypes

Sarkar, N. D., Patton, R. D., Doebley, A.-L., Hanratty, B. P., Kreitzman, A. J., Sarthy, J. F., Ko, M., Adil, M., Brahma, S., Meers, M. P., et al. (2022) · Cancer Discovery · doi:10.1158/2159-8290.cd-22-0692 · Cited by 75 · see citing works

H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function

Pal, D., Patel, M., Boulet, F., Jayakumar, S., Grant, O. A., Branco, M. R., Basu, S., Santos, S. D. M., Zabet, N. R., Scaffidi, P., et al. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01016-5 · Cited by 74 · see citing works

The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates

Yang, Y., Gomez, N. C., Infarinato, N. R., Adam, R. C., Sribour, M., Baek, I., Laurin, M., & Fuchs, E. V. (2023) · Nature Cell Biology · doi:10.1038/s41556-023-01184-y · Cited by 74 · see citing works

Targeting PIM1-Mediated Metabolism in Myeloid Suppressor Cells to Treat Cancer

Xin, G., Yao, C., Topchyan, P., Kasmani, M. Y., Burns, R., Volberding, P. J., Wu, X., Cohn, A., Chen, Y., Lin, C., et al. (2021) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-20-0433 · Cited by 73 · see citing works

TBX20 Improves Contractility and Mitochondrial Function During Direct Human Cardiac Reprogramming

Tang, Y., Aryal, S., Geng, X., Zhou, X., Fast, V. G., Zhang, J. J., Lu, R., & Zhou, Y. (2022) · Circulation · doi:10.1161/circulationaha.122.059713 · Cited by 71 · see citing works

Single-Cell Dissection of Schizophrenia Reveals Neurodevelopmental-Synaptic Link and Transcriptional Resilience Associated Cellular State

Ruzicka, B., Mohammadi, S., Dávila-Velderrain, J., Subburaju, S., Tso, D. R., Hourihan, M., & Kellis, M. (2021) · Biological Psychiatry · doi:10.1016/j.biopsych.2021.02.273 · Cited by 70 · see citing works

Histone deposition pathways determine the chromatin landscapes of H3.1 and H3.3 K27M oncohistones

Sarthy, J. F., Meers, M. P., Janssens, D. H., Henikoff, J. G., Feldman, H. M., Paddison, P. J., Lockwood, C. M., Vitanza, N. A., Olson, J. M., Ahmad, K., et al. (2020) · eLife · doi:10.7554/elife.61090 · Cited by 69 · see citing works

Histone lactylation in macrophages is predictive for gene expression changes during ischemia induced-muscle regeneration

Desgeorges, T., Galle, E., Zhang, J., von Meyenn, F., & Bock, K. D. (2024) · Molecular Metabolism · doi:10.1016/j.molmet.2024.101923 · Cited by 69 · see citing works

Acetyl-CoA metabolism maintains histone acetylation for syncytialization of human placental trophoblast stem cells

Yu, X., Wu, H., Su, J., Liu, X., Liang, K., Li, Q., Yu, R., Shao, X., Wang, H., Wang, Y.-L., et al. (2024) · Cell stem cell · doi:10.1016/j.stem.2024.07.003 · Cited by 66 · see citing works

Nucleosome conformation dictates the histone code

Marunde, M. R., Fuchs, H. A., Burg, J. M., Popova, I. K., Vaidya, A., Hall, N. W., Weinzapfel, E. N., Meiners, M. J., Watson, R., Gillespie, Z. B., et al. (2024) · eLife · doi:10.7554/elife.78866 · Cited by 65 · see citing works

CUT&RUNTools 2.0: a pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis

Yu, F., Sankaran, V. G., & Yuan, G. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab507 · Cited by 64 · see citing works

A reversible epigenetic memory of inflammatory injury controls lineage plasticity and tumor initiation in the mouse pancreas

Falvo, D. J., Grimont, A., Zumbo, P., Fall, W. B., Yang, J. L., Osterhoudt, A., Pan, G., Rendeiro, A. F., Meng, Y., Wilkinson, J. E., et al. (2023) · Developmental Cell · doi:10.1016/j.devcel.2023.11.008 · Cited by 64 · see citing works

Vitamin A resolves lineage plasticity to orchestrate stem cell lineage choices

Tierney, M. T., Polak, L., Yang, Y., Abdusselamoglu, M. D., Baek, I., Stewart, K. S., & Fuchs, E. V. (2024) · Science · doi:10.1126/science.adi7342 · Cited by 64 · see citing works

CTCF is a barrier for 2C-like reprogramming

Olbrich, T., Vega-Sendino, M., Tillo, D., Wu, W., Zolnerowich, N., Pavani, R., Tran, A. D., Domingo, C. N., Franco, M., Markiewicz-Potoczny, M., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25072-x · Cited by 63 · see citing works

Single-cell profiling of transcriptome and histone modifications with EpiDamID

Rang, F. J., de Luca, K. L., de Vries, S. S., Valdes‐Quezada, C., Boele, E., Nguyen, P. D., Guerreiro, I. M., Sato, Y., Kimurâ, H., Bakkers, J., et al. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.03.009 · Cited by 63 · see citing works

The CUT&RUN suspect list of problematic regions of the genome

Nordin, A., Zambanini, G., Pagella, P., & Cantù, C. (2023) · Genome biology · doi:10.1186/s13059-023-03027-3 · Cited by 63 · see citing works

ZNF683 marks a CD8+ T cell population associated with anti-tumor immunity following anti-PD-1 therapy for Richter syndrome

Parry, E. M., Lemvigh, C. K., Deng, S., Dangle, N. J., Ruthen, N. G., Knisbacher, B. A., Broséus, J., Hergalant, S., Guièze, R., Li, S., et al. (2023) · Cancer Cell · doi:10.1016/j.ccell.2023.08.013 · Cited by 63 · see citing works

Methylation and gene expression differences between reproductive and sterile bumblebee workers

Marshall, H., Lonsdale, Z. N., & Mallon, E. B. (2019) · Evolution Letters · doi:10.1002/evl3.129 · Cited by 63 · see citing works

Sox2 Controls Neural Stem Cell Self-Renewal Through a Fos -Centered Gene Regulatory Network

Pagin, M., Pernebrink, M., Giubbolini, S., Barone, C., Sambruni, G., Zhu, Y., Chiara, M., Ottolenghi, S., Pavesi, G., Wei, C., et al. (2021) · Stem Cells · doi:10.1002/stem.3373 · Cited by 61 · see citing works

Nuclear RIPK1 promotes chromatin remodeling to mediate inflammatory response

Li, W., Shan, B., Zou, C., Wang, H., Zhang, M., Zhu, H., Naito, M. G., Xu, D., Manuel, V. J., Mifflin, L., et al. (2022) · Cell Research · doi:10.1038/s41422-022-00673-3 · Cited by 60 · see citing works

Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer–promoter interactions

Wang, K., Escobar, M., Li, J., Mahata, B., Goell, J., Shah, S. T., Cluck, M., & Hilton, I. B. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac582 · Cited by 60 · see citing works

CUT&Tag2for1: a modified method for simultaneous profiling of the accessible and silenced regulome in single cells

Janssens, D. H., Otto, D. J., Meers, M. P., Setty, M. N., Ahmad, K., & Henikoff, S. (2022) · Genome biology · doi:10.1186/s13059-022-02642-w · Cited by 57 · see citing works

Zinc finger protein SALL4 functions through an AT-rich motif to regulate gene expression

Kong, N. R., Bassal, M. A., Tan, H. K., Kurland, J. V., Yong, K. J., Young, J. J., Yang, Y., Li, F., Lee, J. D., Liu, Y., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2020.108574 · Cited by 56 · see citing works

Ybx1 fine-tunes PRC2 activities to control embryonic brain development

Evans, M. K., Matsui, Y., Xu, B., Willis, C., Loome, J. F., Milburn, L., Fan, Y., Pagala, V., & Peng, J. C. (2020) · Nature Communications · doi:10.1038/s41467-020-17878-y · Cited by 53 · see citing works

C/EBPB-dependent adaptation to palmitic acid promotes tumor formation in hormone receptor negative breast cancer

Liu, X., Rulina, A., Choi, M. H., Pedersen, L., Lepland, J., Takle, S. T., Madeleine, N., Peters, S. D., Wogsland, C. E., Grøndal, S. M., et al. (2022) · Nature Communications · doi:10.1038/s41467-021-27734-2 · Cited by 53 · see citing works

GoPeaks: histone modification peak calling for CUT&Tag

Yashar, W. M., Kong, G., VanCampen, J., Curtiss, B. M., Coleman, D. J., Carbone, L., Yardımcı, G. G., Maxson, J. E., & Braun, T. P. (2022) · Genome biology · doi:10.1186/s13059-022-02707-w · Cited by 53 · see citing works

ARID1A orchestrates SWI/SNF-mediated sequential binding of transcription factors with ARID1A loss driving pre-memory B cell fate and lymphomagenesis

Barišić, D., Chin, C. R., Meydan, C., Teater, M. R., Tsialta, I., Mlynarczyk, C., Chadburn, A., Wang, X., Sarkozy, M., Xia, M., et al. (2024) · Cancer Cell · doi:10.1016/j.ccell.2024.02.010 · Cited by 51 · see citing works

RNA polymerase II at histone genes predicts outcome in human cancer

Henikoff, S., Zheng, Y., Paranal, R. M., Xu, Y., Greene, J. E., Henikoff, J. G., Russell, Z. R., Szulzewsky, F., Thirimanne, H. N., Kugel, S., et al. (2025) · Science · doi:10.1126/science.ads2169 · Cited by 50 · see citing works

Structure and functional mapping of the KRAB‐KAP1 repressor complex

Stoll, G. A., Pandiloski, N., Douse, C. H., & Modis, Y. (2022) · The EMBO Journal · doi:10.15252/embj.2022111179 · Cited by 50 · see citing works

ONECUT2 acts as a lineage plasticity driver in adenocarcinoma as well as neuroendocrine variants of prostate cancer

Qian, C., Yang, Q., Rotinen, M., Huang, R., Kim, H., Gallent, B., Yan, Y., Cadaneanu, R. M., Zhang, B., Kaochar, S., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae547 · Cited by 49 · see citing works

Altered DNA methylation underlies monocyte dysregulation and immune exhaustion memory in sepsis

Caldwell, B. A., Wu, Y., Wang, J., & Li, L. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.113894 · Cited by 48 · see citing works

Changes in gene body methylation do not correlate with changes in gene expression in Anthozoa or Hexapoda

Dixon, G., & Matz, M. V. (2022) · BMC Genomics · doi:10.1186/s12864-022-08474-z · Cited by 47 · see citing works

RUNX1 isoform disequilibrium promotes the development of trisomy 21–associated myeloid leukemia

Gialesaki, S., Bräuer-Hartmann, D., Issa, H., Bhayadia, R., Alejo-Valle, O., Verboon, L., Schmell, A. L., Laszig, S., Regényi, E., Schuschel, K., et al. (2022) · Blood · doi:10.1182/blood.2022017619 · Cited by 47 · see citing works

High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq)

Bartlett, D. A., Dileep, V., Handa, T., Ohkawa, Y., Kimurâ, H., Henikoff, S., & Gilbert, D. M. (2021) · The Journal of Cell Biology · doi:10.1083/jcb.202103078 · Cited by 46 · see citing works

The primitive endoderm supports lineage plasticity to enable regulative development

Linneberg-Agerholm, M., Sell, A. C., Riveiro, A. R., Perera, M., Proks, M., Knudsen, T. E., Barral, A., Manzanares, M., & Brickman, J. M. (2024) · Cell · doi:10.1016/j.cell.2024.05.051 · Cited by 45 · see citing works

Epigenome Programming by H3.3K27M Mutation Creates a Dependence of Pediatric Glioma on SMARCA4

Mo, Y., Duan, S., Zhang, X., Hua, X., Zhou, H., Wei, H.-J., Watanabe, J., McQuillan, N., Su, Z., Gu, W. J., et al. (2022) · Cancer Discovery · doi:10.1158/2159-8290.cd-21-1492 · Cited by 44 · see citing works

Mutant p53 exploits enhancers to elevate immunosuppressive chemokine expression and impair immune checkpoint inhibitors in pancreatic cancer

Mahat, D. B., Kumra, H., Castro, S. A., Metcalf, E., Nguyen, K. B., Morisue, R., Ho, W. W., Chen, I. X., Sullivan, B., Yim, L., et al. (2025) · Immunity · doi:10.1016/j.immuni.2025.06.005 · Cited by 43 · see citing works

Transcription factor chromatin profiling genome-wide using uliCUT&RUN in single cells and individual blastocysts

Patty, B. J., & Hainer, S. J. (2021) · Nature Protocols · doi:10.1038/s41596-021-00516-2 · Cited by 42 · see citing works

SMYD5 catalyzes histone H3 lysine 36 trimethylation at promoters

Zhang, Y., Fang, Y., Tang, Y., Han, S., Jia, J., Wan, X., Chen, J., Yuan, Y., Zhao, B., & Dong, F. (2022) · Nature Communications · doi:10.1038/s41467-022-30940-1 · Cited by 42 · see citing works

Regulation of chromatin accessibility by the histone chaperone CAF-1 sustains lineage fidelity

Franklin, R., Guo, Y., He, S., Chen, M., Ji, F., Zhou, X., Frankhouser, D. E., Do, B. T., Chiem, C., Jang, M., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29730-6 · Cited by 41 · see citing works

cLoops2: a full-stack comprehensive analytical tool for chromatin interactions

Cao, Y., Liu, S., Ren, G., Tang, Q., & Zhao, K. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab1233 · Cited by 41 · see citing works

Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer

Grillo, G., Keshavarzian, T., Linder, S., Arlidge, C., Mout, L., Nand, A., Teng, M., Qamra, A., Zhou, S., Kron, K. J., et al. (2023) · Cancer Discovery · doi:10.1158/2159-8290.cd-23-0331 · Cited by 40 · see citing works

Stem cells tightly regulate dead cell clearance to maintain tissue fitness

Stewart, K. S., Abdusselamoglu, M. D., Tierney, M. T., Gola, A., Hur, Y. H., Gonzales, K. A. U., Yuan, S., Bonny, A. R., Yang, Y., Infarinato, N. R., et al. (2024) · Nature · doi:10.1038/s41586-024-07855-6 · Cited by 40 · see citing works

Extensive NEUROG3 occupancy in the human pancreatic endocrine gene regulatory network

Schreiber, V., Mercier, R., Jiménez, S., Ye, T., García-Sánchez, E., Klein, A.-C., Meunier, A., Ghimire, S., Birck, C., Jost, B., et al. (2021) · bioRxiv · doi:10.1016/j.molmet.2021.101313 · Cited by 34 · see citing works

Aging is associated with increased chromatin accessibility and reduced polymerase pausing in liver

Bozukova, M., Nikopoulou, C., Kleinenkuhnen, N., Grbavac, D., Goetsch, K., & Tessarz, P. (2022) · Molecular Systems Biology · doi:10.15252/msb.202211002 · Cited by 39 · see citing works

NEUROD1 reinforces endocrine cell fate acquisition in pancreatic development

Bohuslavová, R., Fabriciova, V., Smolík, O., Lebrón‐Mora, L., Abaffy, P., Benesova, S., Žucha, D., Valihrach, L., Berková, Z., Saudek, F., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-41306-6 · Cited by 39 · see citing works

Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape

Boddu, P. C., Gupta, A. K., Roy, R., Avalos, B. D. L. P., Olazabal‐Herrero, A., Neuenkirchen, N., Zimmer, J. T., Chandhok, N. S., King, D. P., Nannya, Y., et al. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.02.032 · Cited by 39 · see citing works

The long non-coding RNA HOTAIR contributes to joint-specific gene expression in rheumatoid arthritis

Elhaï, M., Micheroli, R., Houtman, M., Mirrahimi, M., Moser, L., Pauli, C., Bürki, K., Laimbacher, A., Kania, G., Klein, K., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-44053-w · Cited by 38 · see citing works

The megakaryocytic transcription factor ARID3A suppresses leukemia pathogenesis

Alejo-Valle, O., Weigert, K., Bhayadia, R., Ng, M. S. W., Issa, H., Beyer, C., Emmrich, S., Schuschel, K., Ihling, C. H., Sinz, A., et al. (2021) · Blood · doi:10.1182/blood.2021012231 · Cited by 37 · see citing works

Pervasive structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs

Xie, T., Danieli‐Mackay, A., Buccarelli, M., Barbieri, M., Papadionysiou, I., D’Alessandris, Q. G., Robens, C., Übelmesser, N., Vinchure, O. S., Lauretti, L., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-48053-2 · Cited by 36 · see citing works

Parity-induced changes to mammary epithelial cells control NKT cell expansion and mammary oncogenesis

Somasundara, A. V. H., Moss, M. A., Feigman, M. J., Chen, C., Cyrill, S. L., Ciccone, M. F., Trousdell, M. C., Vollbrecht, M., Li, S., Kendall, J., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.110099 · Cited by 36 · see citing works

Histone demethylase KDM5 regulates cardiomyocyte maturation by promoting fatty acid oxidation, oxidative phosphorylation, and myofibrillar organization

Deogharia, M., Venegas-Zamora, L., Agrawal, A., Shi, M., Jain, A. K., McHugh, K. J., Altamirano, F. J., Marian, A. J., & Gurha, P. (2024) · Cardiovascular Research · doi:10.1093/cvr/cvae014 · Cited by 35 · see citing works

Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content

Olagunju, T., Rosen, B. D., Neibergs, H. L., Becker, G. M., Davenport, K. M., Elsik, C. G., Hadfield, T. S., Koren, S., Kuhn, K. L., Rhie, A., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-52384-5 · Cited by 35 · see citing works

Epigenetic control of melanoma cell invasiveness by the stem cell factor SALL4

Diener, J., Baggiolini, A., Pernebrink, M., Dalcher, D., Lerra, L., Cheng, P. F., Varum, S., Häusel, J., Stierli, S., Treier, M., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25326-8 · Cited by 34 · see citing works

Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages

Simonis, A., Theobald, S. J., Koch, A. E., Mummadavarapu, R., Mudler, J. M., Pouikli, A., Göbel, U., Acton, R., Winter, S., Albus, A., et al. (2025) · Molecular Systems Biology · doi:10.1038/s44320-025-00093-6 · Cited by 33 · see citing works

Hippo-Yap Signaling Maintains Sinoatrial Node Homeostasis

Zheng, M., Li, G., Song, J., Zhao, X., Tang, L., Erhardt, S., Chen, W., Nguyen, B. H., Li, X., Li, M., et al. (2022) · Circulation · doi:10.1161/circulationaha.121.058777 · Cited by 33 · see citing works

Loss of MLL3/4 decouples enhancer H3K4 monomethylation, H3K27 acetylation, and gene activation during embryonic stem cell differentiation

Boileau, R. M., Chen, K. X., & Blelloch, R. H. (2023) · Genome biology · doi:10.1186/s13059-023-02883-3 · Cited by 33 · see citing works

CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks

Abbasova, L., Urbanaviciute, P., Hu, D., Ismail, J. N., Schilder, B. M., Nott, A., Skene, N., & Marzi, S. J. (2025) · Nature Communications · doi:10.1038/s41467-025-58137-2 · Cited by 32 · see citing works

MacroH2A restricts inflammatory gene expression in melanoma cancer-associated fibroblasts by coordinating chromatin looping

Filipescu, D., Carcamo, S., Agarwal, A., Tung, N., Humblin, É., Goldberg, M. S., Vyas, N. S., Beaumont, K. G., Demircioğlu, D., Sridhar, S., et al. (2023) · Nature Cell Biology · doi:10.1038/s41556-023-01208-7 · Cited by 32 · see citing works

Single-cell analysis reveals transcriptomic and epigenomic impacts on the maternal–fetal interface following SARS-CoV-2 infection

Gao, L., Mathur, V., Tam, S. K. M., Zhou, X., Cheung, M. F., Chan, L. Y., Estrada-Gutiérrez, G., Leung, B. W., Moungmaithong, S., Wang, C. C., et al. (2023) · Nature Cell Biology · doi:10.1038/s41556-023-01169-x · Cited by 31 · see citing works

Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans

Feng, Y., Xie, N., Inoue, F., Fan, S., Saskin, J., Zhang, C., Zhang, F., Hansen, M. E. B., Nyambo, T., Mpoloka, S. W., et al. (2024) · Nature Genetics · doi:10.1038/s41588-023-01626-1 · Cited by 31 · see citing works

MOESM1 of Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling

Meers, M. P., Tenenbaum, D., & Henikoff, S. (2019) · Figshare · doi:10.6084/m9.figshare.8867351

Benchmarking CUT&RUN analysis using motif enrichmentPreprint

Tan, L., Viner, C., Li, X. H., Wrana, M., Ishak, C. A., Shen, S. Y., Carvalho, D. D. D., Hainer, S. J., & Hoffman, M. M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.09.09.749495

OroujiLab/CUTandRun_Peak_Calling: Benchmarking Peak Calling Methods for CUT&RUN

Aminnn, & OroujiLab (2025) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.15208150

MOESM2 of Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling

Meers, M. P., Tenenbaum, D., & Henikoff, S. (2019) · Figshare · doi:10.6084/m9.figshare.8867357

Benchmarking peak calling methods for CUT&RUN

Nooranikhojasteh, A., Tavallaee, G., & Orouji, E. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf375 · Cited by 3 · see citing works