Histone editing elucidates the functional roles of H3K27 methylation and acetylation in mammals.
Journal
Nature genetics
ISSN: 1546-1718
Titre abrégé: Nat Genet
Pays: United States
ID NLM: 9216904
Informations de publication
Date de publication:
06 2022
06 2022
Historique:
received:
16
02
2021
accepted:
04
05
2022
pubmed:
7
6
2022
medline:
18
6
2022
entrez:
6
6
2022
Statut:
ppublish
Résumé
Posttranslational modifications of histones (PTMs) are associated with specific chromatin and gene expression states
Identifiants
pubmed: 35668298
doi: 10.1038/s41588-022-01091-2
pii: 10.1038/s41588-022-01091-2
doi:
Substances chimiques
Chromatin
0
Histones
0
Polycomb Repressive Complex 2
EC 2.1.1.43
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
754-760Subventions
Organisme : NCI NIH HHS
ID : P30 CA008748
Pays : United States
Commentaires et corrections
Type : CommentIn
Informations de copyright
© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.
Références
Lawrence, M., Daujat, S. & Schneider, R. Lateral thinking: how histone modifications regulate gene expression. Trends Genet. 32, 42–56 (2016).
pubmed: 26704082
doi: 10.1016/j.tig.2015.10.007
Zhao, Y. & Garcia, B. A. Comprehensive catalog of currently documented histone modifications. Cold Spring Harb. Perspect. Biol. 7, a025064 (2015).
pubmed: 26330523
pmcid: 4563710
doi: 10.1101/cshperspect.a025064
Pengelly, A. R., Copur, O., Jackle, H., Herzig, A. & Muller, J. A histone mutant reproduces the phenotype caused by loss of histone-modifying factor Polycomb. Science 339, 698–699 (2013).
pubmed: 23393264
doi: 10.1126/science.1231382
Pengelly, A. R., Kalb, R., Finkl, K. & Muller, J. Transcriptional repression by PRC1 in the absence of H2A monoubiquitylation. Genes Dev. 29, 1487–1492 (2015).
pubmed: 26178786
pmcid: 4526733
doi: 10.1101/gad.265439.115
McKay, D. J. et al. Interrogating the function of metazoan histones using engineered gene clusters. Dev. Cell 32, 373–386 (2015).
pubmed: 25669886
pmcid: 4385256
doi: 10.1016/j.devcel.2014.12.025
Ogryzko, V. V., Schiltz, R. L., Russanova, V., Howard, B. H. & Nakatani, Y. The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell 87, 953–959 (1996).
pubmed: 8945521
doi: 10.1016/S0092-8674(00)82001-2
Laugesen, A., Hojfeldt, J. W. & Helin, K. Molecular mechanisms directing PRC2 recruitment and H3K27 methylation. Mol. Cell 74, 8–18 (2019).
pubmed: 30951652
pmcid: 6452890
doi: 10.1016/j.molcel.2019.03.011
Allis, C. D. & Jenuwein, T. The molecular hallmarks of epigenetic control. Nat. Rev. Genet. 17, 487–500 (2016).
pubmed: 27346641
doi: 10.1038/nrg.2016.59
Husmann, D. & Gozani, O. Histone lysine methyltransferases in biology and disease. Nat. Struct. Mol. Biol. 26, 880–889 (2019).
pubmed: 31582846
pmcid: 6951022
doi: 10.1038/s41594-019-0298-7
Cornett, E. M., Ferry, L., Defossez, P. A. & Rothbart, S. B. Lysine methylation regulators moonlighting outside the epigenome. Mol. Cell 75, 1092–1101 (2019).
pubmed: 31539507
pmcid: 6756181
doi: 10.1016/j.molcel.2019.08.026
Leatham-Jensen, M. et al. Lysine 27 of replication-independent histone H3.3 is required for Polycomb target gene silencing but not for gene activation. PLoS Genet. 15, e1007932 (2019).
pubmed: 30699116
pmcid: 6370247
doi: 10.1371/journal.pgen.1007932
Wang, Z. F. et al. Characterization of the mouse histone gene cluster on chromosome 13: 45 histone genes in three patches spread over 1Mb. Genome Res 6, 688–701 (1996).
pubmed: 8858344
doi: 10.1101/gr.6.8.688
Weinert, B. T. et al. Time-resolved analysis reveals rapid dynamics and broad scope of the CBP/p300 acetylome. Cell 174, 231–244 (2018).
pubmed: 29804834
pmcid: 6078418
doi: 10.1016/j.cell.2018.04.033
Lavarone, E., Barbieri, C. M. & Pasini, D. Dissecting the role of H3K27 acetylation and methylation in PRC2 mediated control of cellular identity. Nat. Commun. 10, 1679 (2019).
pubmed: 30976011
pmcid: 6459869
doi: 10.1038/s41467-019-09624-w
Raisner, R. et al. Enhancer activity requires CBP/P300 bromodomain-dependent histone H3K27 acetylation. Cell Rep. 24, 1722–1729 (2018).
pubmed: 30110629
doi: 10.1016/j.celrep.2018.07.041
Creyghton, M. P. et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl Acad. Sci. USA 107, 21931–21936 (2010).
pubmed: 21106759
pmcid: 3003124
doi: 10.1073/pnas.1016071107
Shvedunova, M. & Akhtar, A. Modulation of cellular processes by histone and non-histone protein acetylation.Nat. Rev. Mol. Cell Biol. 23, 329–349 (2022).
pubmed: 35042977
doi: 10.1038/s41580-021-00441-y
Zhang, T., Zhang, Z., Dong, Q., Xiong, J. & Zhu, B. Histone H3K27 acetylation is dispensable for enhancer activity in mouse embryonic stem cells. Genome Biol. 21, 45 (2020).
pubmed: 32085783
pmcid: 7035716
doi: 10.1186/s13059-020-01957-w
Gaudelli, N. M. et al. Programmable base editing of A*T to G*C in genomic DNA without DNA cleavage. Nature 551, 464–471 (2017).
pubmed: 29160308
pmcid: 5726555
doi: 10.1038/nature24644
Li, B., Ren, N., Yang, L., Liu, J. & Huang, Q. A qPCR method for genome editing efficiency determination and single-cell clone screening in human cells. Sci. Rep. 9, 18877 (2019).
pubmed: 31827197
pmcid: 6906436
doi: 10.1038/s41598-019-55463-6
Sawicka, A. & Seiser, C. Sensing core histone phosphorylation: a matter of perfect timing. Biochim. Biophys. Acta 1839, 711–718 (2014).
pubmed: 24747175
pmcid: 4103482
doi: 10.1016/j.bbagrm.2014.04.013
Martire, S. et al. Phosphorylation of histone H3.3 at serine 31 promotes p300 activity and enhancer acetylation. Nat. Genet. 51, 941–946 (2019).
pubmed: 31152160
pmcid: 6598431
doi: 10.1038/s41588-019-0428-5
Banaszynski, L. A. et al. Hira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells. Cell 155, 107–120 (2013).
pubmed: 24074864
doi: 10.1016/j.cell.2013.08.061
Pasini, D., Bracken, A. P., Jensen, M. R., Lazzerini Denchi, E. & Helin, K. Suz12 is essential for mouse development and for EZH2 histone methyltransferase activity. EMBO J. 23, 4061–4071 (2004).
pubmed: 15385962
pmcid: 524339
doi: 10.1038/sj.emboj.7600402
O’Carroll, D. et al. The polycomb-group gene Ezh2 is required for early mouse development. Mol. Cell. Biol. 21, 4330–4336 (2001).
pubmed: 11390661
pmcid: 87093
doi: 10.1128/MCB.21.13.4330-4336.2001
Faust, C., Schumacher, A., Holdener, B. & Magnuson, T. The eed mutation disrupts anterior mesoderm production in mice. Development 121, 273–285 (1995).
pubmed: 7768172
doi: 10.1242/dev.121.2.273
Pasini, D., Bracken, A. P., Hansen, J. B., Capillo, M. & Helin, K. The polycomb group protein Suz12 is required for embryonic stem cell differentiation. Mol. Cell. Biol. 27, 3769–3779 (2007).
pubmed: 17339329
pmcid: 1899991
doi: 10.1128/MCB.01432-06
Kagey, M. H. et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 467, 430–435 (2010).
pubmed: 20720539
pmcid: 2953795
doi: 10.1038/nature09380
Whyte, W. A. et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307–319 (2013).
pubmed: 23582322
pmcid: 3653129
doi: 10.1016/j.cell.2013.03.035
Hojfeldt, J. W. et al. Accurate H3K27 methylation can be established de novo by SUZ12-directed PRC2. Nat. Struct. Mol. Biol. 25, 225–232 (2018).
pubmed: 29483650
pmcid: 5842896
doi: 10.1038/s41594-018-0036-6
Chamberlain, S. J., Yee, D. & Magnuson, T. Polycomb repressive complex 2 is dispensable for maintenance of embryonic stem cell pluripotency. Stem Cells 26, 1496–1505 (2008).
pubmed: 18403752
pmcid: 2630378
doi: 10.1634/stemcells.2008-0102
Hayashi, K., Ohta, H., Kurimoto, K., Aramaki, S. & Saitou, M. Reconstitution of the mouse germ cell specification pathway in culture by pluripotent stem cells. Cell 146, 519–532 (2011).
pubmed: 21820164
doi: 10.1016/j.cell.2011.06.052
Buecker, C. et al. Reorganization of enhancer patterns in transition from naive to primed pluripotency. Cell Stem Cell 14, 838–853 (2014).
pubmed: 24905168
pmcid: 4491504
doi: 10.1016/j.stem.2014.04.003
Sun, Z. et al. The long noncoding RNA Lncenc1 maintains naive states of mouse ESCs by promoting the glycolysis pathway. Stem Cell Rep. 11, 741–755 (2018).
doi: 10.1016/j.stemcr.2018.08.001
Pasini, D. et al. Characterization of an antagonistic switch between histone H3 lysine 27 methylation and acetylation in the transcriptional regulation of Polycomb group target genes. Nucleic Acids Res. 38, 4958–4969 (2010).
pubmed: 20385584
pmcid: 2926606
doi: 10.1093/nar/gkq244
Fang, F. et al. Coactivators p300 and CBP maintain the identity of mouse embryonic stem cells by mediating long-range chromatin structure. Stem Cells 32, 1805–1816 (2014).
pubmed: 24648406
doi: 10.1002/stem.1705
Wang, Z. et al. Prediction of histone post-translational modification patterns based on nascent transcription data. Nat. Genet. 54, 295–305 (2022).
pubmed: 35273399
doi: 10.1038/s41588-022-01026-x
Martin, B. J. E. et al. Transcription shapes genome-wide histone acetylation patterns. Nat. Commun. 12, 210 (2021).
pubmed: 33431884
pmcid: 7801501
doi: 10.1038/s41467-020-20543-z
Anzalone, A. V., Koblan, L. W. & Liu, D. R. Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors. Nat. Biotechnol. 38, 824–844 (2020).
pubmed: 32572269
doi: 10.1038/s41587-020-0561-9
Martin Gonzalez, J. et al. Embryonic stem cell culture conditions support distinct states associated with different developmental stages and potency. Stem Cell Rep. 7, 177–191 (2016).
doi: 10.1016/j.stemcr.2016.07.009
dos Santos, R. L. et al. MBD3/NuRD facilitates induction of pluripotency in a context-dependent manner. Cell Stem Cell 15, 102–110 (2014).
pubmed: 24835571
pmcid: 4082719
doi: 10.1016/j.stem.2014.04.019
Gilbert, L. A. et al. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159, 647–661 (2014).
pubmed: 25307932
pmcid: 4253859
doi: 10.1016/j.cell.2014.09.029
Heckl, D. et al. Generation of mouse models of myeloid malignancy with combinatorial genetic lesions using CRISPR-Cas9 genome editing. Nat. Biotechnol. 32, 941–946 (2014).
pubmed: 24952903
pmcid: 4160386
doi: 10.1038/nbt.2951
Lewis, P. W. et al. Inhibition of PRC2 activity by a gain-of-function H3 mutation found in pediatric glioblastoma. Science 340, 857–861 (2013).
pubmed: 23539183
pmcid: 3951439
doi: 10.1126/science.1232245
Madi, E. et al. Gene silencing triggers polycomb repressive complex 2 recruitment to CpG islands genome wide. Mol. Cell 55, 347–360 (2014).
doi: 10.1016/j.molcel.2014.06.005
Lerdrup, M., Johansen, J. V., Agrawal-Singh, S. & Hansen, K. An interactive environment for agile analysis and visualization of ChIP-sequencing data. Nat. Struct. Mol. Biol. 23, 349–357 (2016).
pubmed: 26926434
doi: 10.1038/nsmb.3180
Yu, G., Wang, L. G., Han, Y. & He, Q. Y. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16, 284–287 (2012).
pubmed: 22455463
pmcid: 3339379
doi: 10.1089/omi.2011.0118
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. U S A 102, 15545–15550 (2005).
pubmed: 16199517
pmcid: 1239896
doi: 10.1073/pnas.0506580102