The DOI matches its Crossref record; 105 of the 105 references it cites were found in a registry or an index.
H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency
Open accessAbstract
Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to mark the transcription start sites of active genes. Here, we show that H3K4me3 domains that spread more broadly over genes in a given cell type preferentially mark genes that are essential for the identity and function of that cell type. Using the broadest H3K4me3 domains as a discovery tool in neural progenitor cells, we identify novel regulators of these cells. Machine learning models reveal that the broadest H3K4me3 domains represent a distinct entity, characterized by increased marks of elongation. The broadest H3K4me3 domains also have more paused polymerase at their promoters, suggesting a unique transcriptional output. Indeed, genes marked by the broadest H3K4me3 domains exhibit enhanced transcriptional consistency and [corrected] increased transcriptional levels, and perturbation of H3K4me3 breadth leads to changes in transcriptional consistency. Thus, H3K4me3 breadth contains information that could ensure transcriptional precision at key cell identity/function genes.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Interestingly, H3K4me3 domains vary in breadth in a locus- and cell-type-specific manner (Benayoun et al., 2014; Chen et al., 2015), and these differences could provide clues about the context-dependent roles of this mark during aging.”
From The Aging Epigenome (2016) · cites this paper as Benayoun et al., 2014
In the citing paper
“The breadth of the H3K4me3 mark has been previously linked to cell identity, gene expression and transcriptional consistency across a variety of cell types30.”
From Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues (2021) · cites this paper as [30]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
1 retracted
Fasano, C. A., Dimos, J. T., Ivanova, N. B., Lowry, N. A., Lemischka, I. R., & Temple, S. (2007) · Cell stem cell · doi:10.1016/j.stem.2007.04.001 · Cited by 308
RetractedSystematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890
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
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
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
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
Self-citationTrapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn923 · Cited by 14,108
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
Bioconductor: open software development for computational biology and bioinformatics
Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., et al. (2004) · Genome biology · doi:10.1186/gb-2004-5-10-r80 · Cited by 12,082
Flagged first, then by citations
Cited by
Sorted by citations
Histone post-translational modifications - cause and consequence of genome function
Millán-Zambrano, G., Burton, A., Bannister, A. J., & Schneider, R. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00468-7 · Cited by 1,116
Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos
Liu, X., Wang, C., Liu, W., Li, J., Li, C., Kou, X., Chen, J., Zhao, Y., Gao, H., Wang, H., et al. (2016) · Nature · doi:10.1038/nature19362 · Cited by 746
Histone Methylation Dynamics and Gene Regulation Occur through the Sensing of One-Carbon Metabolism
Mentch, S. J., Mehrmohamadi, M., Huang, L., Liu, X., Gupta, D., Mattocks, D. A. L., Padilla, P. G., Ables, G. P., Bamman, M. M., Thalacker‐Mercer, A. E., et al. (2015) · Cell Metabolism · doi:10.1016/j.cmet.2015.08.024 · Cited by 706
Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition
Dahl, J. A., Jung, I., Aanes, H., Greggains, G. D., Manaf, A., Lerdrup, M., Li, G., Kuan, S., Li, B., Lee, A. Y., et al. (2016) · Nature · doi:10.1038/nature19360 · Cited by 650
Epigenetic regulation of ageing: linking environmental inputs to genomic stability
Benayoun, B. A., Pollina, E. A., & Brunet, A. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm4048 · Cited by 610
Self-citationThe impact of cellular metabolism on chromatin dynamics and epigenetics
Reid, M. A., Dai, Z., & Locasale, J. W. (2017) · Nature Cell Biology · doi:10.1038/ncb3629 · Cited by 515
Booth, L. N., & Brunet, A. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.05.013 · Cited by 499
Self-citationIs H3K4me3 instructive for transcription activation?
Howe, F. S., Fischl, H., Murray, S. C., & Mellor, J. (2016) · BioEssays · doi:10.1002/bies.201600095 · Cited by 533
Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues
Bartosovic, M., Kabbe, M., & Castelo-Branco, G. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00869-9 · Cited by 483
One‐carbon metabolism and epigenetics: understanding the specificity
Mentch, S. J., & Locasale, J. W. (2015) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.12956 · Cited by 510
Epigenetic mechanisms in breast cancer therapy and resistance
Garcia-Martinez, L., Zhang, Y., Nakata, Y., Chan, H. L., & Morey, L. (2021) · Nature Communications · doi:10.1038/s41467-021-22024-3 · Cited by 485
Direct cell reprogramming: approaches, mechanisms and progress
Wang, H., Yang, Y., Liu, J., & Li, Q. (2021) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00335-z · Cited by 463
Benayoun, B. A., Pollina, E. A., Singh, P. P., Mahmoudi, S., Harel, I., Casey, K. M., Dulken, B. W., Kundaje, A., & Brunet, A. (2019) · Genome Research · doi:10.1101/gr.240093.118 · Cited by 360
Self-citationChen, K., Chen, Z., Wu, D., Zhang, L., Lin, X., Su, J., Rodriguez, B., Xi, Y., Xia, Z., Chen, X., et al. (2015) · Nature Genetics · doi:10.1038/ng.3385 · Cited by 373
Heterogeneity in old fibroblasts is linked to variability in reprogramming and wound healing
Mahmoudi, S., Mancini, E., Xu, L., Moore, A., Jahanbani, F., Hebestreit, K., Srinivasan, R., Li, X., Devarajan, K., Prélot, L., et al. (2019) · Nature · doi:10.1038/s41586-019-1658-5 · Cited by 285
Self-citationSuper-Enhancer-Mediated RNA Processing Revealed by Integrative MicroRNA Network Analysis
Suzuki, H. I., Young, R. A., & Sharp, P. A. (2017) · Cell · doi:10.1016/j.cell.2017.02.015 · Cited by 284
Inhibition of fatty acid oxidation enables heart regeneration in adult mice
Li, X., Wu, F., Günther, S., Looso, M., Kuenne, C. T., Zhang, T., Wiesnet, M., Klatt, S., Zukunft, S., Fleming, I., et al. (2023) · Nature · doi:10.1038/s41586-023-06585-5 · Cited by 270
Regulation of Stem Cell Aging by Metabolism and Epigenetics
Ren, R., Ocampo, A., Liu, G., & Belmonte, J. C. I. (2017) · Cell Metabolism · doi:10.1016/j.cmet.2017.07.019 · Cited by 286
Hinohara, K., Wu, H.-J., Vigneau, S., McDonald, T. O., Igarashi, K. J., Yamamoto, K. N., Madsen, T., Fassl, A., Egri, S. B., Papanastasiou, M., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.10.014 · Cited by 255
The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes
Beacon, T. H., Delcuve, G. P., Lopez, C. L., Nardocci, G., Kovalchuk, I., van Wijnen, A. J., & Davie, J. (2021) · Clinical Epigenetics · doi:10.1186/s13148-021-01126-1 · Cited by 267
Park, S. H., Kang, K., Γιαννοπούλου, Ε., Qiao, Y., Kang, K., Kim, G., Park‐Min, K., & Ivashkiv, L. B. (2017) · Nature Immunology · doi:10.1038/ni.3818 · Cited by 247
Mutations in the histone methyltransferase gene KMT2B cause complex early-onset dystonia
Meyer, E., Study, D. D. D., Carss, K., Rankin, J., Nichols, J. M. E., Grozeva, D., Joseph, A. P., Mencacci, N. E., Papandreou, A., Ng, J., et al. (2016) · Nature Genetics · doi:10.1038/ng.3740 · Cited by 245
Long Noncoding RNA MANTIS Facilitates Endothelial Angiogenic Function
Leisegang, M. S., Fork, C., Josipovic, I., Richter, F. M., Preussner, J., Hu, J., Miller, M. J., Epah, J., Hofmann, P., Günther, S., et al. (2017) · Circulation · doi:10.1161/circulationaha.116.026991 · Cited by 242
A Platform for Rapid Exploration of Aging and Diseases in a Naturally Short-Lived Vertebrate
Harel, I., Benayoun, B. A., Machado, B., Singh, P. P., Hu, C.-K., Pech, M. F., Valenzano, D. R., Zhang, E., Sharp, S. C., Artandi, S. E., et al. (2015) · Cell · doi:10.1016/j.cell.2015.01.038 · Cited by 232
Self-citationIntratumoral Heterogeneity: More Than Just Mutations
Hinohara, K., & Polyák, K. (2019) · Trends in Cell Biology · doi:10.1016/j.tcb.2019.03.003 · Cited by 241
Epigenome in Early Mammalian Development: Inheritance, Reprogramming and Establishment
Xu, Q., & Xie, W. (2017) · Trends in Cell Biology · doi:10.1016/j.tcb.2017.10.008 · Cited by 224
Killaars, A. R., Grim, J. C., Walker, C. J., Hushka, E. A., Brown, T. E., & Anseth, K. S. (2018) · Advanced Science · doi:10.1002/advs.201801483 · Cited by 209
Determinants of Histone H3K4 Methylation Patterns
Soares, L. M., He, P. C., Chun, Y., Suh, H., Kim, T., & Buratowski, S. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.10.013 · Cited by 209
Kareta, M. S., Gorges, L. L., Hafeez, S., Benayoun, B. A., Marro, S. G., Zmoos, A., Cecchini, M. J., Spacek, D. V., Batista, L. F. Z., O’Brien, M., et al. (2014) · Cell stem cell · doi:10.1016/j.stem.2014.10.019 · Cited by 204
Self-citationDnmt3a and Dnmt3b Associate with Enhancers to Regulate Human Epidermal Stem Cell Homeostasis
Rinaldi, L., Datta, D., Serrat, J., Morey, L., Solanas, G., Avgustinova, A., Blanco, E., Pons, J., Matallanas, D., von Kriegsheim, A., et al. (2016) · Cell stem cell · doi:10.1016/j.stem.2016.06.020 · Cited by 201
Histone H3 lysine K4 methylation and its role in learning and memory
Collins, B. E., Greer, C. B., Coleman, B. C., & Sweatt, J. D. (2019) · Epigenetics & Chromatin · doi:10.1186/s13072-018-0251-8 · Cited by 209
A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity
D’Alessio, A. C., Fan, Z. P., Wert, K. J., Baranov, P., Cohen, M. A., Saini, J. S., Cohick, E., Charniga, C., Dadon, D., Hannett, N. M., et al. (2015) · Stem Cell Reports · doi:10.1016/j.stemcr.2015.09.016 · Cited by 172
Roles of H3K4 methylation in biology and disease
Wang, H., & Helin, K. (2024) · Trends in Cell Biology · doi:10.1016/j.tcb.2024.06.001 · Cited by 177
The Polycomb-Dependent Epigenome Controls β Cell Dysfunction, Dedifferentiation, and Diabetes
Lu, T. T.-H., Heyne, S., Dror, E., Casas, E., Leonhardt, L., Boenke, T., Yang, C.-H., Sagar, Arrigoni, L., Dalgaard, K., et al. (2018) · Cell Metabolism · doi:10.1016/j.cmet.2018.04.013 · Cited by 151
Mellén, M., Ayata, P., & Heintz, N. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1708044114 · Cited by 151
Policarpi, C., Munafò, M., Tsagkris, S., Carlini, V., & Hackett, J. A. (2024) · Nature Genetics · doi:10.1038/s41588-024-01706-w · Cited by 163
EZH2-H3K27me3 mediated KRT14 upregulation promotes TNBC peritoneal metastasis
Verma, A., Singh, A., Singh, M. P., Nengroo, M. A., Saini, K. K., Satrusal, S. R., Khan, M. A., Chaturvedi, P., Sinha, A., Meena, S., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-35059-x · Cited by 148
MLL4 Is Required to Maintain Broad H3K4me3 Peaks and Super-Enhancers at Tumor Suppressor Genes
Dhar, S. S., Zhao, D., Lin, T., Gu, B., Pal, K., Wu, S. J., Alam, H., Lv, J., Yun, K., Gopalakrishnan, V., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.04.028 · Cited by 142
Editing the Epigenome: Reshaping the Genomic Landscape
Holtzman, L., & Gersbach, C. A. (2018) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083117-021632 · Cited by 147
Methylation across the central dogma in health and diseases: new therapeutic strategies
Liu, R., Zhao, E., Yu, H., Yuan, C., Abbas, M. N., & Cui, H. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01528-y · Cited by 155
Morey, L., Santanach, A., Blanco, E., Aloia, L., Nora, E. P., Bruneau, B. G., & Croce, L. D. (2015) · Cell stem cell · doi:10.1016/j.stem.2015.08.009 · Cited by 151
Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation
Hughes, A. L., Kelley, J. R., & Klose, R. J. (2020) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2020.194567 · Cited by 139
Fan, Z., Zhu, P., Wu, J., Wu, J., 朱潇潇, Zhu, X., Wang, Y., Xiong, Z., Fan, D., Guo, H., et al. (2022) · Cell Research · doi:10.1038/s41422-022-00645-7 · Cited by 137
Methionine metabolism influences genomic architecture and gene expression through H3K4me3 peak width
Dai, Z., Mentch, S. J., Gao, X., Nichenametla, S. N., & Locasale, J. W. (2018) · Nature Communications · doi:10.1038/s41467-018-04426-y · Cited by 138
Loft, A., Alfaro, A. J., Schmidt, S. F., Pedersen, F. B., Terkelsen, M. K., Puglia, M., Chow, K. K., Feuchtinger, A., Troullinaki, M., Maida, A., et al. (2021) · Cell Metabolism · doi:10.1016/j.cmet.2021.06.005 · Cited by 129
Kang, J., Lienhard, M., Pastor, W. A., Chawla, A., Novotny, M., Tsagaratou, A., Lasken, R. S., Thompson, E. C., Surani, M. A., Koralov, S. B., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1510510112 · Cited by 126
G-quadruplex DNA structures in human stem cells and differentiation
Zyner, K. G., Simeone, A., Flynn, S. M., Doyle, C., Marsico, G., Adhikari, S., Portella, G., Tannahill, D., & Balasubramanian, S. (2022) · Nature Communications · doi:10.1038/s41467-021-27719-1 · Cited by 124
KDM5B is a master regulator of the H3K4-methylome in stem cells, development and cancer
Xhabija, B., & Kidder, B. L. (2018) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2018.11.001 · Cited by 120
Hörmanseder, E., Simeone, A., Allen, G. E., Bradshaw, C. R., Figlmüller, M., Gurdon, J. B., & Jullien, J. (2017) · Cell stem cell · doi:10.1016/j.stem.2017.03.003 · Cited by 120
Tome, J. M., Tippens, N. D., & Lis, J. T. (2018) · Nature Genetics · doi:10.1038/s41588-018-0234-5 · Cited by 118
Resolving Heart Regeneration by Replacement Histone Profiling
Goldman, J., Kuzu, G., Lee, N., Karasik, J., Gemberling, M. P., Foglia, M. J., Karra, R., Dickson, A. L., Sun, F., Tolstorukov, M. Y., et al. (2017) · Developmental Cell · doi:10.1016/j.devcel.2017.01.013 · Cited by 121
ATX3, ATX4, and ATX5 Encode Putative H3K4 Methyltransferases and Are Critical for Plant Development
Chen, L., Luo, J., Cui, Z., Xue, M., Wang, L., Zhang, X., Pawlowski, W. P., & He, Y. (2017) · PLANT PHYSIOLOGY · doi:10.1104/pp.16.01944 · Cited by 118
NAD(+)-SIRT1 control of H3K4 trimethylation through circadian deacetylation of MLL1
Aguilar-Arnal, L., Katada, S., Orozco-Solis, R., & Sassone-Corsi, P. (2015) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2990 · Cited by 117
EPOP Interacts with Elongin BC and USP7 to Modulate the Chromatin Landscape
Liefke, R., Karwacki-Neisius, V., & Shi, Y. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.10.019 · Cited by 123
Epigenome profiling and editing of neocortical progenitor cells during development
Albert, M., Kalebic, N., Florio, M., Lakshmanaperumal, N., Haffner, C., Brandl, H., Henry, I., & Huttner, W. Β. (2017) · The EMBO Journal · doi:10.15252/embj.201796764 · Cited by 118
Examining the Roles of H3K4 Methylation States with Systematically Characterized Antibodies
Shah, R. N., Grzybowski, A. T., Cornett, E. M., Johnstone, A. L., Dickson, B. M., Boone, B. A., Cheek, M. A., Cowles, M. W., Maryanski, D. N., Meiners, M. J., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.08.015 · Cited by 121
The role of DNA methylation in directing the functional organization of the cancer epigenomePreprint
Lay, F. D., Liu, Y., Kelly, T. K., Witt, H. N., Farnham, P., Jones, P. A., & Berman, B. P. (2015) · Genome Research · doi:10.1101/gr.183368.114 · Cited by 111
Lee, K.-W., Yeo, S.-Y., Gong, J.-R., Koo, O.-J., Sohn, I., Lee, W. Y., Kim, H. C., Yun, S. H., Cho, Y. B., Choi, M.-A., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30484-4 · Cited by 103
Pnueli, L., Rudnizky, S., Yosefzon, Y., & Melamed, P. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1414841112 · Cited by 109
DUBs, the regulation of cell identity and disease
Heideker, J., & Wertz, I. E. (2014) · Biochemical Journal · doi:10.1042/bj20140496 · Cited by 108
Brusslan, J. A., Bonora, G., Alvarez-Canterbury, A. M. R., Tariq, F., Jaroszewicz, A., & Pellegrini, M. A. (2015) · PLANT PHYSIOLOGY · doi:10.1104/pp.114.252999 · Cited by 101
Xiong, H., Luo, Y., Wang, Q., Yu, X., & He, A. (2021) · Nature Methods · doi:10.1038/s41592-021-01129-z · Cited by 100
Genetics and Pathogenesis of Dystonia
Thomsen, M., Lange, L. M., Zech, M., & Lohmann, K. (2023) · Annual Review of Pathology Mechanisms of Disease · doi:10.1146/annurev-pathmechdis-051122-110756 · Cited by 98
Gopi, L. K., & Kidder, B. L. (2021) · Nature Communications · doi:10.1038/s41467-021-21707-1 · Cited by 101
The Genomic Landscape of Position Effects on Protein Expression Level and Noise in Yeast
Chen, X., & Zhang, J. (2016) · Cell Systems · doi:10.1016/j.cels.2016.03.009 · Cited by 101
Systematic Analysis of the Determinants of Gene Expression Noise in Embryonic Stem Cells
Faure, A. J., Schmiedel, J. M., & Lehner, B. (2017) · Cell Systems · doi:10.1016/j.cels.2017.10.003 · Cited by 92
Quiescence Entry, Maintenance, and Exit in Adult Stem Cells
Mohammad, K., Dakik, P., Medkour, Y., Mitrofanova, D., & Titorenko, V. I. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20092158 · Cited by 94
Quevedo, M., Meert, L., Dekker, M. R., Dekkers, D. H. W., Brandsma, J. H., van den Berg, D. L. C., Özgür, Z., van IJcken, W. F. J., Demmers, J., Fornerod, M. W. J., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10502-8 · Cited by 95
González, A. J., Setty, M. N., & Leslie, C. S. (2015) · Nature Genetics · doi:10.1038/ng.3402 · Cited by 85
Kerry, J., Godfrey, L., Repapi, E., Tapia, M. C., Blackledge, N. P., Ma, H., Ballabio, E., O’Byrne, S., Ponthan, F., Heidenreich, O. T., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2016.12.054 · Cited by 79
Broad domains of histone H3 lysine 4 trimethylation in transcriptional regulation and disease
Park, S., Kim, G. W., Kwon, S. H., & Lee, J. (2020) · FEBS Journal · doi:10.1111/febs.15219 · Cited by 88
State of the art technologies to explore long non‐coding RNAs in cancer
Salehi, S., Taheri, M. N., Azarpira, N., Zare, A., & Behzad‐Behbahani, A. (2017) · Journal of Cellular and Molecular Medicine · doi:10.1111/jcmm.13238 · Cited by 84
Grzybowski, A. T., Chen, Z., & Ruthenburg, A. J. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.04.022 · Cited by 84
Cao, F., Fang, Y., Tan, H. K., Goh, Y., Choy, J. Y. H., Koh, B. T. H., Hao Tan, J., Bertin, N., Ramadass, A., Hunter, E., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-02257-3 · Cited by 80
Epigenetic regulation of ACE2, the receptor of the SARS-CoV-2 virus1
Beacon, T. H., Delcuve, G. P., & Davie, J. (2020) · Genome · doi:10.1139/gen-2020-0124 · Cited by 76
Variation is function: Are single cell differences functionally important?
Dueck, H., Eberwine, J. H., & Kim, J. (2015) · BioEssays · doi:10.1002/bies.201500124 · Cited by 84
Multiomics reveals glutathione metabolism as a driver of bimodality during stem cell aging
Benjamin, D. I., Brett, J. O., Both, P., Benjamin, J. S., Ishak, H. D., Kang, J., Kim, S., Chung, M., Arjona, M., Nutter, C. W., et al. (2023) · Cell Metabolism · doi:10.1016/j.cmet.2023.02.001 · Cited by 80
Self-citationInteraction between epigenetic and metabolism in aging stem cells
Brunet, A., & Rando, T. A. (2017) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2016.12.009 · Cited by 79
Self-citationGlobal H3.3 dynamic deposition defines its bimodal role in cell fate transition
Fang, H., Farran, C. A. E., Xing, Q. R., Zhang, L., Li, H., Lim, B., & Loh, Y. (2018) · Nature Communications · doi:10.1038/s41467-018-03904-7 · Cited by 71
Dhar, S. S., & Lee, M. G. (2021) · Oncotarget · doi:10.18632/oncotarget.27988 · Cited by 73
Ponnaluri, V. K. C., Ehrlich, K. C., Zhang, G., Lacey, M. R., Johnston, D. A., Pradhan, S., & Ehrlich, M. (2016) · Epigenetics · doi:10.1080/15592294.2016.1265713 · Cited by 77
Browne, G., Dragon, J. A., Hong, D., Messier, T., Gordon, J. A. R., Farina, N. H., Boyd, J. R., VanOudenhove, J., Perez, A. W., Zaidi, S. K., et al. (2016) · Tumor Biology · doi:10.1007/s13277-015-4710-6 · Cited by 70
Dincer, A., Gavin, D. P., Xu, K., Zhang, B., Dudley, J. T., Schadt, E. E., & Akbarian, S. (2015) · Translational Psychiatry · doi:10.1038/tp.2015.169 · Cited by 65
Dpy30 is critical for maintaining the identity and function of adult hematopoietic stem cells
Yang, Z., Shah, K. K., Khodadadi-Jamayran, A., & Jiang, H. (2016) · The Journal of Experimental Medicine · doi:10.1084/jem.20160185 · Cited by 69
van de Leemput, J., Hess, J., Glatt, S. J., & Tsuang, M. T. (2016) · Advances in genetics · doi:10.1016/bs.adgen.2016.08.001 · Cited by 71
Coordinated regulation of cellular identity–associated H3K4me3 breadth by the COMPASS family
Sze, C. C., Ozark, P. A., Cao, K., Ugarenko, M., Das, S., Wang, L., Marshall, S. A., Rendleman, E. J., Ryan, C., Zha, D., et al. (2020) · Science Advances · doi:10.1126/sciadv.aaz4764 · Cited by 70
Navarro‐Costa, P., McCarthy, A., Prudêncio, P., Greer, C., Guilgur, L. G., Becker, J. D., Secombe, J., Rangan, P., & Martinho, R. G. (2016) · Nature Communications · doi:10.1038/ncomms12331 · Cited by 71
Aleksic, T., Gray, N., Wu, X., Rieunier, G., Osher, E. L., Mills, J. V., Verrill, C. L., Bryant, R. J., Han, C., Hutchinson, K., et al. (2018) · Cancer Research · doi:10.1158/0008-5472.can-17-3498 · Cited by 67
Independent regulation of gene expression level and noise by histone modifications
Wu, S., Li, K., Li, Y., Zhao, T., Li, T., Yang, Y., & Qian, W. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005585 · Cited by 62
Cildir, G., Toubia, J., Yip, K. H., Zhou, M., Pant, H., Hissaria, P., Zhang, J., Hong, W., Robinson, N., Grimbaldeston, M. A., et al. (2019) · Immunity · doi:10.1016/j.immuni.2019.09.021 · Cited by 65
Rahane, C. S., Kutzner, A., & Heese, K. (2018) · Journal of Neuro-Oncology · doi:10.1007/s11060-018-03029-3 · Cited by 65
Zhang, Z., Shi, L., Dawany, N. B., Kelsen, J. R., Petri, M., & Sullivan, K. E. (2016) · Clinical Epigenetics · doi:10.1186/s13148-016-0179-4 · Cited by 64
The Role of H3K4me3 in Transcriptional Regulation Is Altered in Huntington’s Disease
Dong, X., Tsuji, J., Labadorf, A. T., Roussos, P., Chen, J., Myers, R. H., Akbarian, S., & Weng, Z. (2015) · PLoS ONE · doi:10.1371/journal.pone.0144398 · Cited by 67
WDR5 represents a therapeutically exploitable target for cancer stem cells in glioblastomaPreprint
Mitchell, K., Sprowls, S. A., Arora, S., Shakya, S., Silver, D. J., Goins, C. M., Wallace, L. C., Roversi, G. A., Schafer, R., Kay, K. E., et al. (2023) · Genes & Development · doi:10.1101/gad.349803.122 · Cited by 62
Epigenomic Landscape of Human Fetal Brain, Heart, and Liver
Yan, L., Guo, H., Hu, B., Li, R., Yong, J., Zhao, Y., Zhi, X., Fan, X., Guo, F., Wang, X., et al. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.672931 · Cited by 59
The complex activities of the SET1/MLL complex core subunits in development and disease
Jiang, H. (2020) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2020.194560 · Cited by 58
Esnault, C., Gualdrini, F., Horswell, S. D., Kelly, G. P., Stewart, A., East, P., Matthews, N., & Treisman, R. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.02.005 · Cited by 55
Epigenetic modulation of brain gene networks for cocaine and alcohol abuse
Farris, S. P., Harris, R. A., & Ponomarev, I. (2015) · Frontiers in Neuroscience · doi:10.3389/fnins.2015.00176 · Cited by 57
The roles of chromatin-remodelers and epigenetic modifiers in kidney cancer
Liao, L., Testa, J. R., & Yang, H. (2015) · Cancer Genetics · doi:10.1016/j.cancergen.2015.02.008 · Cited by 58
Li, T., Zheng, Q., An, J., Wu, M., Li, H., Gui, X., Pu, H., & Lu, D. (2015) · Molecular Therapy · doi:10.1038/mt.2015.208 · Cited by 57
Retracted
Metadata
- Authors
- Benayoun, B. A., Pollina, E. A., Ucar, D., Mahmoudi, S., Karra, K., Wong, E. D., Devarajan, K., Daugherty, A. C., Kundaje, A. B., Mancini, E., Hitz, B. C., Gupta, R., Rando, T. A., Baker, J. C., Snyder, M. P., Cherry, J. M., & Brunet, A.
- Affiliations
- Stanford University (US)
- Stanford Medicine (US)
- VA Palo Alto Health Care System (US)
- Corresponding author
- Brunet, Anne
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2014-07
- Volume
- 158
- Issue
- 3
- Pages
- 673-688
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC4137894
- OpenAlex
- W1984173288
- Cited by
- 536
- References
- 105
- Citations by year
- 2026: 28 · 2025: 53 · 2024: 52 · 2023: 50 · 2022: 41 · 2021: 57 · 2020: 40 · 2019: 44 · 2018: 32 · 2017: 51 · 2016: 47 · 2015: 38 · 2014: 3
- FWCI
- 4.36
- Type
- journal article
- Language
- en
- Update notices
- erratum (2015-11-19)
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
- Funders
- National Institute on Aging (F31AG043232, DP1AG044848, P01AG036695)
- National Cancer Institute (T32CA009302)
- National Institute of General Medical Sciences (P01GM099130, R01GM103787, T32GM007790)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- H3K4me3, histone trimethylation, chromatin modification, transcription start sites, cell identity, neural progenitor cells, gene expression regulation, RNA polymerase II elongation, cell type-specific genes, machine learning
- MeSH terms
- Animals, Artificial Intelligence, Cells, Histones, Humans, Lysine, Methylation, Mice, Inbred C57BL, RNA Polymerase II, Transcription, Genetic, Genomics, Histone Code, Neural Stem Cells
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review