Calcium modulates the tethering of BCOR-PRC1.1 enzymatic core to KDM2B via liquid-liquid phase separation.
Journal
Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179
Informations de publication
Date de publication:
10 Sep 2024
10 Sep 2024
Historique:
received:
23
01
2024
accepted:
31
08
2024
medline:
11
9
2024
pubmed:
11
9
2024
entrez:
10
9
2024
Statut:
epublish
Résumé
Recruitment of non-canonical BCOR-PRC1.1 to non-methylated CpG islands via KDM2B plays a fundamental role in transcription control during developmental processes and cancer progression. However, the mechanism is still largely unknown on how this recruitment is regulated. Here, we unveiled the importance of the Poly-D/E regions within the linker of BCOR for its binding to KDM2B. Interestingly, we also demonstrated that these negatively charged Poly-D/E regions on BCOR play autoinhibitory roles in liquid-liquid phase separation (LLPS) of BCOR
Identifiants
pubmed: 39256555
doi: 10.1038/s42003-024-06820-3
pii: 10.1038/s42003-024-06820-3
doi:
Substances chimiques
Proto-Oncogene Proteins
0
Repressor Proteins
0
Calcium
SY7Q814VUP
Jumonji Domain-Containing Histone Demethylases
EC 1.14.11.-
Polycomb Repressive Complex 1
EC 2.3.2.27
BCOR protein, human
0
KDM2A protein, human
EC 1.14.11.27
F-Box Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1112Informations de copyright
© 2024. The Author(s).
Références
Jaenisch, R. & Bird, A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat. Genet. 33, 245–254 (2003).
pubmed: 12610534
doi: 10.1038/ng1089
Kouzarides, T. Chromatin modifications and their function. Cell 128, 693–705 (2007).
pubmed: 17320507
doi: 10.1016/j.cell.2007.02.005
Blackledge, N. P. & Klose, R. J. The molecular principles of gene regulation by polycomb repressive complexes. Nat. Rev. Mol. Cell Biol. 22, 815–833 (2021).
pubmed: 34400841
pmcid: 7612013
doi: 10.1038/s41580-021-00398-y
Jaenisch, R. & Young, R. Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell 132, 567–582 (2008).
pubmed: 18295576
pmcid: 4142810
doi: 10.1016/j.cell.2008.01.015
Margueron, R. & Reinberg, D. The polycomb complex PRC2 and its mark in life. Nature 469, 343–349 (2011).
pubmed: 21248841
pmcid: 3760771
doi: 10.1038/nature09784
Sparmann, A. & van Lohuizen, M. Polycomb silencers control cell fate, development and cancer. Nat. Rev. Cancer 6, 846–856 (2006).
pubmed: 17060944
doi: 10.1038/nrc1991
Schuettengruber, B., Bourbon, H. M., Di Croce, L. & Cavalli, G. Genome regulation by polycomb and trithorax: 70 years and counting. Cell 171, 34–57 (2017).
pubmed: 28938122
doi: 10.1016/j.cell.2017.08.002
Simon, J. A. & Kingston, R. E. Occupying chromatin: polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put. Mol. Cell 49, 808–824 (2013).
pubmed: 23473600
pmcid: 3628831
doi: 10.1016/j.molcel.2013.02.013
Barbour, H., Daou, S., Hendzel, M. & Affar, E. B. Polycomb group-mediated histone H2A monoubiquitination in epigenome regulation and nuclear processes. Nat. Commun. 11, 5947 (2020).
pubmed: 33230107
pmcid: 7683540
doi: 10.1038/s41467-020-19722-9
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
Margueron, R. et al. Ezh1 and Ezh2 maintain repressive chromatin through different mechanisms. Mol. Cell 32, 503–518 (2008).
pubmed: 19026781
pmcid: 3641558
doi: 10.1016/j.molcel.2008.11.004
Chittock, E. C., Latwiel, S., Miller, T. C. & Muller, C. W. Molecular architecture of polycomb repressive complexes. Biochem. Soc. Trans. 45, 193–205 (2017).
pubmed: 28202673
pmcid: 5310723
doi: 10.1042/BST20160173
Gao, Z. et al. PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. Mol. Cell 45, 344–356 (2012).
pubmed: 22325352
pmcid: 3293217
doi: 10.1016/j.molcel.2012.01.002
Aranda, S., Mas, G. & Di Croce, L. Regulation of gene transcription by polycomb proteins. Sci. Adv. 1, e1500737 (2015).
pubmed: 26665172
pmcid: 4672759
doi: 10.1126/sciadv.1500737
Gil, J. & O’Loghlen, A. PRC1 complex diversity: where is it taking us? Trends Cell Biol. 24, 632–641 (2014).
pubmed: 25065329
doi: 10.1016/j.tcb.2014.06.005
Fursova, N. A. et al. Synergy between variant PRC1 complexes defines polycomb-mediated gene repression. Mol. Cell 74, 1020–1036 e8 (2019).
pubmed: 31029541
pmcid: 6561741
doi: 10.1016/j.molcel.2019.03.024
Taherbhoy, A. M., Huang, O. W. & Cochran, A. G. BMI1-RING1B is an autoinhibited RING E3 ubiquitin ligase. Nat. Commun. 6, 7621 (2015).
pubmed: 26151332
doi: 10.1038/ncomms8621
Zhu, Y. et al. Functional redundancy among polycomb complexes in maintaining the pluripotent state of embryonic stem cells. Stem. Cell Rep. 17, 1198–1214 (2022).
doi: 10.1016/j.stemcr.2022.02.020
Aldera, A. P. & Govender, D. Gene of the month: BCOR. J. Clin. Pathol. 73, 314–317 (2020).
pubmed: 32161069
doi: 10.1136/jclinpath-2020-206513
He, J. et al. Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of developmental genes. Nat. Cell Biol. 15, 373–384 (2013).
pubmed: 23502314
pmcid: 4078788
doi: 10.1038/ncb2702
Isshiki, Y. et al. KDM2B in polycomb repressive complex 1.1 functions as a tumor suppressor in the initiation of T-cell leukemogenesis. Blood Adv. 3, 2537–2549 (2019).
pubmed: 31471323
pmcid: 6737409
doi: 10.1182/bloodadvances.2018028522
Wang, Z. et al. A non-canonical BCOR-PRC1.1 complex represses differentiation programs in human ESCs. Cell Stem. Cell 22, 235–251 e9 (2018).
pubmed: 29337181
pmcid: 5797497
doi: 10.1016/j.stem.2017.12.002
Tiacci, E. et al. The corepressors BCOR and BCORL1: two novel players in acute myeloid leukemia. Haematologica 97, 3–5 (2012).
pubmed: 22210327
pmcid: 3248923
doi: 10.3324/haematol.2011.057901
van den Boom, V. et al. Non-canonical PRC1.1 targets active genes independent of H3K27me3 and is essential for leukemogenesis. Cell Rep 14, 332–346 (2016).
pubmed: 26748712
doi: 10.1016/j.celrep.2015.12.034
Lempiainen, J. K. et al. BCOR-coupled H2A monoubiquitination represses a subset of androgen receptor target genes regulating prostate cancer proliferation. Oncogene 39, 2391–2407 (2020).
pubmed: 31925334
doi: 10.1038/s41388-020-1153-3
Deaton, A. M. & Bird, A. CpG islands and the regulation of transcription. Genes Dev. 25, 1010–1022 (2011).
pubmed: 21576262
pmcid: 3093116
doi: 10.1101/gad.2037511
Farcas, A. M. et al. KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands. Elife 1, e00205 (2012).
pubmed: 23256043
pmcid: 3524939
doi: 10.7554/eLife.00205
Wu, X., Johansen, J. V. & Helin, K. Fbxl10/Kdm2b recruits polycomb repressive complex 1 to CpG islands and regulates H2A ubiquitylation. Mol. Cell 49, 1134–1146 (2013).
pubmed: 23395003
doi: 10.1016/j.molcel.2013.01.016
Xie, W. et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153, 1134–1148 (2013).
pubmed: 23664764
pmcid: 3786220
doi: 10.1016/j.cell.2013.04.022
Saxonov, S., Berg, P. & Brutlag, D. L. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc. Natl Acad. Sci. USA 103, 1412–1417 (2006).
pubmed: 16432200
pmcid: 1345710
doi: 10.1073/pnas.0510310103
Schaefer, E. J. et al. BCOR and BCORL1 mutations drive epigenetic reprogramming and oncogenic signaling by unlinking PRC1.1 from target genes. Blood Cancer Discov. 3, 116–135 (2022).
pubmed: 35015684
pmcid: 9414116
doi: 10.1158/2643-3230.BCD-21-0115
Wong, S. J. et al. KDM2B recruitment of the polycomb group complex, PRC1.1, requires cooperation between PCGF1 and BCORL1. Structure 24, 1795–1801 (2016).
pubmed: 27568929
pmcid: 5088048
doi: 10.1016/j.str.2016.07.011
Wong, S. J. et al. Structure and role of BCOR PUFD in noncanonical PRC1 assembly and disease. Biochemistry 59, 2718–2728 (2020).
pubmed: 32628469
doi: 10.1021/acs.biochem.0c00285
Boulard, M., Edwards, J. R. & Bestor, T. H. FBXL10 protects polycomb-bound genes from hypermethylation. Nat. Genet. 47, 479–485 (2015).
pubmed: 25848754
doi: 10.1038/ng.3272
Sportoletti, P., Sorcini, D. & Falini, B. BCOR gene alterations in hematologic diseases. Blood 138, 2455–2468 (2021).
pubmed: 33945606
pmcid: 8887995
doi: 10.1182/blood.2021010958
de Miranda, M. C. et al. Epidermal growth factor (EGF) triggers nuclear calcium signaling through the intranuclear phospholipase Cdelta-4 (PLCdelta4). J. Biol. Chem. 294, 16650–16662 (2019).
pubmed: 31537645
pmcid: 6851314
doi: 10.1074/jbc.RA118.006961
Alonso, M. T. & Garcia-Sancho, J. Nuclear Ca(2+) signalling. Cell Calcium 49, 280–289 (2011).
pubmed: 21146212
doi: 10.1016/j.ceca.2010.11.004
Kunrath-Lima, M. et al. Phospholipase C delta 4 (PLCdelta4) is a nuclear protein involved in cell proliferation and senescence in mesenchymal stromal stem cells. Cell Signal 49, 59–67 (2018).
pubmed: 29859928
pmcid: 6095203
doi: 10.1016/j.cellsig.2018.05.011
Chun, J.T., Santella, L. & Miller, J.J. Calcium | intracellular calcium waves. In Encyclopedia of Biological Chemistry III (ed. Jez, J.) 669–677 (Elsevier, 2021).
Vernon, R.M. et al. Pi-Pi contacts are an overlooked protein feature relevant to phase separation. Elife 7, e31486 (2018).
Nakajima-Takagi, Y. et al. Polycomb repressive complex 1.1 coordinates homeostatic and emergency myelopoiesis. eLife 12, e83004 (2023).
Sato, K., Fukami, Y. & Stith, B. J. Signal transduction pathways leading to Ca2+ release in a vertebrate model system: lessons from Xenopus eggs. Semin Cell Dev. Biol. 17, 285–292 (2006).
pubmed: 16584903
doi: 10.1016/j.semcdb.2006.02.008
Monteith, G. R., Prevarskaya, N. & Roberts-Thomson, S. J. The calcium-cancer signalling nexus. Nat. Rev. Cancer 17, 367–380 (2017).
pubmed: 28386091
doi: 10.1038/nrc.2017.18
So, C. L., Saunus, J. M., Roberts-Thomson, S. J. & Monteith, G. R. Calcium signalling and breast cancer. Semin. Cell Dev. Biol. 94, 74–83 (2019).
pubmed: 30439562
doi: 10.1016/j.semcdb.2018.11.001
Izquierdo-Torres, E., Hernandez-Oliveras, A., Fuentes-Garcia, G. & Zarain-Herzberg, A. Calcium signaling and epigenetics: a key point to understand carcinogenesis. Cell Calcium 91, 102285 (2020).
pubmed: 32942140
doi: 10.1016/j.ceca.2020.102285
Shi, X. et al. Ca2+ regulates T-cell receptor activation by modulating the charge property of lipids. Nature 493, 111–115 (2013).
pubmed: 23201688
doi: 10.1038/nature11699
Berridge, M. J., Bootman, M. D. & Roderick, H. L. Calcium signalling: dynamics, homeostasis and remodelling. Nat. Rev. Mol. Cell Biol. 4, 517–529 (2003).
pubmed: 12838335
doi: 10.1038/nrm1155
Snoeck, H. W. Calcium regulation of stem cells. EMBO Rep. 21, e50028 (2020).
pubmed: 32419314
pmcid: 7271657
doi: 10.15252/embr.202050028
Clapham, D. E. Calcium signaling. Cell 131, 1047–1058 (2007).
pubmed: 18083096
doi: 10.1016/j.cell.2007.11.028
Wang, L. et al. Histone modifications regulate chromatin compartmentalization by contributing to a phase separation mechanism. Mol. Cell 76, 646–659 e6 (2019).
pubmed: 31543422
doi: 10.1016/j.molcel.2019.08.019
Sanulli, S. et al. HP1 reshapes nucleosome core to promote phase separation of heterochromatin. Nature 575, 390–394 (2019).
pubmed: 31618757
pmcid: 7039410
doi: 10.1038/s41586-019-1669-2
Zhang, H. et al. Liquid-liquid phase separation in biology: mechanisms, physiological functions and human diseases. Sci. China Life Sci. 63, 953–985 (2020).
pubmed: 32548680
doi: 10.1007/s11427-020-1702-x
Pirrotta, V. & Li, H. B. A view of nuclear polycomb bodies. Curr. Opin. Genet. Dev. 22, 101–109 (2012).
pubmed: 22178420
doi: 10.1016/j.gde.2011.11.004
Eeftens, J. M., Kapoor, M. & Brangwynne, C. P. Epigenetic memory as a time integral over prior history of polycomb phase separation. bioRvix https://doi.org/10.1101/2020.08.19.254706 (2020).
Guo, Y., Zhao, S. & Wang, G. G. Polycomb gene silencing mechanisms: PRC2 chromatin targeting, H3K27me3 ‘readout’, and phase separation-based compaction. Trends Genet. 37, 547–565 (2021).
pubmed: 33494958
pmcid: 8119337
doi: 10.1016/j.tig.2020.12.006
Plys, A. J. et al. Phase separation of polycomb-repressive complex 1 is governed by a charged disordered region of CBX2. Genes Dev. 33, 799–813 (2019).
pubmed: 31171700
pmcid: 6601514
doi: 10.1101/gad.326488.119
Fox, C. H. et al. A method for measuring intracellular free magnesium concentration in platelets using flow cytometry. Magnes Res. 20, 200–207 (2007).
pubmed: 17972463
Maat, H. et al. The USP7-TRIM27 axis mediates non-canonical PRC1.1 function and is a druggable target in leukemia. iScience 24, 102435 (2021).
pubmed: 34113809
pmcid: 8169803
doi: 10.1016/j.isci.2021.102435
Zhang, W.-Z. et al. The protein complex crystallography beamline (BL19U1) at the shanghai synchrotron radiation facility. Nuclear Sci. Tech. 30, 170 (2019).
doi: 10.1007/s41365-019-0683-2
Evans, P. R. An introduction to data reduction: space-group determination, scaling and intensity statistics. Acta. Crystallogr. D Biol. Crystallogr. 67, 282–292 (2011).
pubmed: 21460446
pmcid: 3069743
doi: 10.1107/S090744491003982X
Lebedev, A. A., Vagin, A. A. & Murshudov, G. N. Model preparation in MOLREP and examples of model improvement using X-ray data. Acta. Crystallogr. D Biol. Crystallogr. 64, 33–39 (2008).
pubmed: 18094465
doi: 10.1107/S0907444907049839
Kovalevskiy, O., Nicholls, R. A., Long, F., Carlon, A. & Murshudov, G. N. Overview of refinement procedures within REFMAC5: utilizing data from different sources. Acta. Crystallogr. D Struct. Biol. 74, 215–227 (2018).
pubmed: 29533229
pmcid: 5947762
doi: 10.1107/S2059798318000979
Yang, B. et al. Identification of cross-linked peptides from complex samples. Nat. Methods 9, 904–906 (2012).
pubmed: 22772728
doi: 10.1038/nmeth.2099
Lu, S. et al. Mapping native disulfide bonds at a proteome scale. Nat. Methods 12, 329–331 (2015).
pubmed: 25664544
doi: 10.1038/nmeth.3283
Schneidman-Duhovny, D., Hammel, M. & Sali, A. Macromolecular docking restrained by a small angle X-ray scattering profile. J. Struct. Biol. 173, 461–471 (2011).
pubmed: 20920583
doi: 10.1016/j.jsb.2010.09.023
Schneidman-Duhovny, D., Hammel, M., Tainer, J. A. & Sali, A. FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles. Nucleic Acids Res. 44, W424–W429 (2016).
pubmed: 27151198
pmcid: 4987932
doi: 10.1093/nar/gkw389
Fiser, A., Do, R. K. & Sali, A. Modeling of loops in protein structures. Protein Sci. 9, 1753–1773 (2000).
pubmed: 11045621
pmcid: 2144714
doi: 10.1110/ps.9.9.1753