The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
The genomic landscape of histone modifications in human T cells
Open accessAbstract
To understand the molecular basis that supports the dynamic gene expression programs unique to T cells, we investigated the genomic landscape of activating histone modifications, including histone H3 K9/K14 diacetylation (H3K9acK14ac), H3 K4 trimethylation (H3K4me3), and the repressive histone modification H3 K27 trimethylation (H3K27me3) in primary human T cells. We show that H3K9acK14ac and H3K4me3 are associated with active genes required for T cell function and development, whereas H3K27me3 is associated with silent genes that are involved in development in other cell types. Unexpectedly, we find that 3,330 gene promoters are associated with all of these histone modifications. The gene expression levels are correlated with both the absolute and relative levels of the activating H3K4me3 and the repressive H3K27me3 modifications. Our data reveal that rapidly inducible genes are associated with the H3 acetylation and H3K4me3 modifications, suggesting they assume a chromatin structure poised for activation. In addition, we identified a subpopulation of chromatin regions that are associated with high levels of H3K4me3 and H3K27me3 but low levels of H3K9acK14ac. Therefore, these regions have a distinctive chromatin modification pattern and thus may represent a distinct class of chromatin domains.
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.
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
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
Bernstein, B. E., Mikkelsen, T. S., Xie, X., Kamal, M., Huebert, D. J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.041 · Cited by 5,361
A gene atlas of the mouse and human protein-encoding transcriptomes
Su, A. I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K. A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0400782101 · Cited by 3,475
Transcriptional regulation by calcium, calcineurin, and NFAT
Hogan, P. G., Chen, L., Nardone, J., & Rao, A. (2003) · Genes & Development · doi:10.1101/gad.1102703 · Cited by 1,991
CpG islands as gene markers in the human genome
Larsen, F., Gundersen, G., Lopez, R., & Prydz, H. (1992) · Genomics · doi:10.1016/0888-7543(92)90024-m · Cited by 922
Histone acetylation and deacetylation in yeast
Kurdistani, S. K., & Grunstein, M. (2003) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1075 · Cited by 677
Cited by
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
Self-citationCpG islands and the regulation of transcription
Deaton, A. M., & Bird, A. (2011) · Genes & Development · doi:10.1101/gad.2037511 · Cited by 3,187
Combinatorial patterns of histone acetylations and methylations in the human genome
Wang, Z., Zang, C., Rosenfeld, J. A., Schones, D. E., Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Peng, W., Zhang, M. Q., et al. (2008) · Nature Genetics · doi:10.1038/ng.154 · Cited by 2,331
Self-citationBernstein, B. E., Meissner, A., & Lander, E. S. (2007) · Cell · doi:10.1016/j.cell.2007.01.033 · Cited by 2,086
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
De Santa, F., Totaro, M. G., Prosperini, E., Notarbartolo, S., Testa, G., & Natoli, G. (2007) · Cell · doi:10.1016/j.cell.2007.08.019 · Cited by 965
A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers
De Santa, F., Barozzi, I., Mietton, F., Ghisletti, S., Polletti, S., Tusi, B. K., Muller, H., Ragoussis, J., Wei, C.-L., & Natoli, G. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000384 · Cited by 934
Whole-Genome Analysis of Histone H3 Lysine 4 and Lysine 27 Methylation in Human Embryonic Stem Cells
Pan, G., Tian, S., Nie, J., Yang, C., Ruotti, V., Wei, H., Jonsdottir, G. A., Stewart, R., & Thomson, J. A. (2007) · Cell Stem Cell · doi:10.1016/j.stem.2007.08.003 · Cited by 711
Cuddapah, S., Jothi, R., Schones, D. E., Roh, T.-Y., Cui, K., & Zhao, K. (2009) · Genome Research · doi:10.1101/gr.082800.108 · Cited by 637
Chromatin modifiers and remodellers: regulators of cellular differentiation
Chen, T., & Dent, S. Y. R. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3607 · Cited by 619
Shah, P. P., Donahue, G., Otte, G. L., Capell, B. C., Nelson, D. M., Cao, K., Aggarwala, V., Cruickshanks, H. A., Rai, T. S., McBryan, T., et al. (2013) · Genes & Development · doi:10.1101/gad.223834.113 · Cited by 550
Deconstructing repression: evolving models of co-repressor action
Perissi, V., Jepsen, K., Glass, C. K., & Rosenfeld, M. G. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2736 · Cited by 532
Danko, C. G., Hah, N., Luo, X., Martins, A. L., Core, L., Lis, J. T., Siepel, A., & Kraus, W. L. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.02.015 · Cited by 333
Hypoxia induces a novel signature of chromatin modifications and global repression of transcription
Johnson, A. B., Denko, N., & Barton, M. C. (2008) · Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis · doi:10.1016/j.mrfmmm.2008.01.001 · Cited by 250
Nongenetic inheritance and transgenerational epigenetics
Szyf, M. (2015) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2014.12.004 · Cited by 238
Epigenomic consequences of immortalized plant cell suspension culture
Tanurdzic, M., Vaughn, M. W., Jiang, H., Lee, T.-J., Slotkin, R. K., Sosinski, B., Thompson, W. F., Doerge, R. W., & Martienssen, R. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060302 · Cited by 218
Genomic location analysis by ChIP‐Seq
Barski, A., & Zhao, K. (2009) · Journal of Cellular Biochemistry · doi:10.1002/jcb.22077 · Cited by 169
Self-citationGenome-Wide Analysis of KAP1 Binding Suggests Autoregulation of KRAB-ZNFs
O'Geen, H., Squazzo, S. L., Iyengar, S., Blahnik, K., Rinn, J. L., Chang, H. Y., Green, R., & Farnham, P. J. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030089 · Cited by 178
Genome-wide analysis of histone modifications in human pancreatic islets
Bhandare, R., Schug, J., Le Lay, J., Fox, A., Smirnova, O., Liu, C., Naji, A., & Kaestner, K. H. (2010) · Genome Research · doi:10.1101/gr.102038.109 · Cited by 136
Hoffman, B. G., Robertson, G., Zavaglia, B., Beach, M., Cullum, R., Lee, S., Soukhatcheva, G., Li, L., Wederell, E. D., Thiessen, N., et al. (2010) · Genome Research · doi:10.1101/gr.104356.109 · Cited by 115
“Cis-regulatory regions are associated with diverse histone modifications that include acetylations and methylations of histone tails (Bernstein et al. 2006; Roh et al. 2006; Barski et al. 2007; Heintzman et al. 2007; Robertson et al. 2008; Wang et al. 2008).”
BackgroundCharacterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro
Zhang, B., Srivastava, A., Mimitou, E., Stuart, T., Raimondi, I., Hao, Y., Smibert, P., & Satija, R. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01250-0 · Cited by 104
Bam, M., Yang, X., Zhou, J., Ginsberg, J. P., Leyden, Q., Nagarkatti, P. S., & Nagarkatti, M. (2016) · Journal of Neuroimmune Pharmacology · doi:10.1007/s11481-015-9643-8 · Cited by 103
Rush, M., Appanah, R., Lee, S., Lam, L. L., Goyal, P., & Lorincz, M. C. (2009) · Epigenetics · doi:10.4161/epi.4.6.9392 · Cited by 83
Epigenetics, a key for unlocking complex CNS disorders? Therapeutic implications
Szyf, M. (2015) · European Neuropsychopharmacology · doi:10.1016/j.euroneuro.2014.01.009 · Cited by 76
Epigenetic regulation of matrix metalloproteinases and their collagen substrates in cancer
Chernov, A. V., & Strongin, A. Y. (2011) · bmc · doi:10.1515/bmc.2011.017 · Cited by 69
Simulated microgravity‐induced epigenetic changes in human lymphocytes
Singh, K. P., Kumari, R., & DuMond, J. W. (2010) · Journal of Cellular Biochemistry · doi:10.1002/jcb.22674 · Cited by 64
Polycomb proteins in hematologic malignancies
Martin-Perez, D., Piris, M. A., & Sanchez-Beato, M. (2010) · Blood · doi:10.1182/blood-2010-05-267096 · Cited by 65
Duel of the fates: the role of transcriptional circuits and noise in CD4+ cells
Hebenstreit, D., Deonarine, A., Babu, M. M., & Teichmann, S. A. (2012) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2012.03.007 · Cited by 20
Metadata
- Authors
- Roh, T.-Y., Cuddapah, S., Cui, K., & Zhao, K.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2006-10-24
- Volume
- 103
- Issue
- 43
- Pages
- 15782-15787
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W1978104691
- Cited by
- 496
- References
- 5
- FWCI
- 14.00
- Type
- journal article
- Language
- en
- Open access
- bronze
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
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
