Nucleosome destabilization by nuclear non-coding RNAs.
Journal
Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179
Informations de publication
Date de publication:
11 02 2020
11 02 2020
Historique:
received:
03
06
2019
accepted:
16
01
2020
entrez:
13
2
2020
pubmed:
13
2
2020
medline:
11
5
2021
Statut:
epublish
Résumé
In the nucleus, genomic DNA is wrapped around histone octamers to form nucleosomes. In principle, nucleosomes are substantial barriers to transcriptional activities. Nuclear non-coding RNAs (ncRNAs) are proposed to function in chromatin conformation modulation and transcriptional regulation. However, it remains unclear how ncRNAs affect the nucleosome structure. Eleanors are clusters of ncRNAs that accumulate around the estrogen receptor-α (ESR1) gene locus in long-term estrogen deprivation (LTED) breast cancer cells, and markedly enhance the transcription of the ESR1 gene. Here we detected nucleosome depletion around the transcription site of Eleanor2, the most highly expressed Eleanor in the LTED cells. We found that the purified Eleanor2 RNA fragment drastically destabilized the nucleosome in vitro. This activity was also exerted by other ncRNAs, but not by poly(U) RNA or DNA. The RNA-mediated nucleosome destabilization may be a common feature among natural nuclear RNAs, and may function in transcription regulation in chromatin.
Identifiants
pubmed: 32047236
doi: 10.1038/s42003-020-0784-9
pii: 10.1038/s42003-020-0784-9
pmc: PMC7012929
doi:
Substances chimiques
Chromatin
0
Histones
0
Nucleosomes
0
RNA, Untranslated
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
60Références
Wolffe, A. P. Chromatin: Structure & Function (Academic Press, London, UK, 1998).
Luger, K., Mäder, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389, 251–260 (1997).
doi: 10.1038/38444
pubmed: 9305837
Bondarenko, V. A. et al. Nucleosomes can form a polar barrier to transcript elongation by RNA polymerase II. Mol. Cell 24, 469–479 (2006).
pubmed: 17081995
doi: 10.1016/j.molcel.2006.09.009
pmcid: 17081995
Luger, K., Dechassa, M. L. & Tremethick, D. J. New insights into nucleosome and chromatin structure: an ordered state or a disordered affair? Nat. Rev. Mol. Cell Biol. 13, 436–447 (2012).
pubmed: 22722606
pmcid: 3408961
doi: 10.1038/nrm3382
Petesch, S. J. & Lis, J. T. Overcoming the nucleosome barrier during transcript elongation. Trends Genet. 28, 285–294 (2012).
pubmed: 22465610
pmcid: 3466053
doi: 10.1016/j.tig.2012.02.005
Wilusz, J. E., Sunwoo, H. & Spector, D. L. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev. 23, 1494–1504 (2009).
pubmed: 19571179
pmcid: 3152381
doi: 10.1101/gad.1800909
Rinn, J. L. & Chang, H. Y. Genome regulation by long noncoding RNAs. Annu. Rev. Biochem. 81, 145–166 (2012).
pubmed: 22663078
doi: 10.1146/annurev-biochem-051410-092902
pmcid: 22663078
Ding, D. Q. et al. Meiosis-specific noncoding RNA mediates robust pairing of homologous chromosomes in meiosis. Science 11, 732–736 (2012).
doi: 10.1126/science.1219518
Batista, P. J. & Chang, H. Y. Long noncoding RNAs: cellular address codes in development and disease. Cell 152, 1298–1307 (2013).
pubmed: 3651923
pmcid: 3651923
doi: 10.1016/j.cell.2013.02.012
Ulitsky, I. & Bartel, D. P. lincRNAs: genomics, evolution, and mechanisms. Cell 154, 26–46 (2013).
pubmed: 3924787
pmcid: 3924787
doi: 10.1016/j.cell.2013.06.020
Cech, T. R. & Steitz, J. A. The noncoding RNA revolution-trashing old rules to forge new ones. Cell 157, 77–94 (2014).
pubmed: 24679528
doi: 10.1016/j.cell.2014.03.008
Krawczyk, M. & Emerson, B. M. p50-associated COX-2 extragenic RNA (PACER) activates COX-2 gene expression by occluding repressive NF-kappaB complexes. eLife 3, e01776 (2014).
pubmed: 24843008
pmcid: 4017649
doi: 10.7554/eLife.01776
Kopp, F. & Mendell, J. T. Functional classification and experimental dissection of long noncoding RNAs. Cell 172, 393–407 (2018).
pubmed: 29373828
pmcid: 5978744
doi: 10.1016/j.cell.2018.01.011
The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
pmcid: 3439153
doi: 10.1038/nature11247
pubmed: 3439153
Djebali, S. et al. Landscape of transcription in human cells. Nature 489, 101–108 (2012).
pubmed: 3684276
pmcid: 3684276
doi: 10.1038/nature11233
Bánfai, B. et al. Long noncoding RNAs are rarely translated in two human cell lines. Genome Res. 22, 1646–1657 (2012).
pubmed: 22955977
pmcid: 3431482
doi: 10.1101/gr.134767.111
Carninci, P. et al. The transcriptional landscape of the mammalian genome. Science 309, 1559–1563 (2005).
pubmed: 16141072
doi: 10.1126/science.1112014
pmcid: 16141072
Derrien, T. et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22, 1775–1789 (2012).
pubmed: 22955988
pmcid: 3431493
doi: 10.1101/gr.132159.111
Jeng, M. H. et al. Estrogen receptor expression and function in long-term estrogen-deprived human breast cancer cells. Endocrinology 139, 4164–4174 (1998).
pubmed: 9751496
doi: 10.1210/endo.139.10.6229
pmcid: 9751496
Chan, C. M., Martin, L. A., Johnston, S. R., Ali, S. & Dowsett, M. Molecular changes associated with the acquisition of oestrogen hypersensitivity in MCF-7 breast cancer cells on long-term oestrogen deprivation. J. Steroid Biochem. Mol. Biol. 81, 333–341 (2002).
pubmed: 12361723
doi: 10.1016/S0960-0760(02)00074-2
Martin, L. A. et al. Enhanced estrogen receptor (ER) alpha, ERBB2, and MAPK signal transduction pathways operate during the adaptation of MCF-7 cells to long term estrogen deprivation. J. Biol. Chem. 278, 30458–30468 (2003).
pubmed: 12775708
doi: 10.1074/jbc.M305226200
Martin, L. A., Farmer, I., Johnston, S. R., Ali, S. & Dowsett, M. Elevated ERK1/ERK2/estrogen receptor cross-talk enhances estrogen-mediated signaling during long-term estrogen deprivation. Endocr. Relat. Cancer 12, S75–S84 (2005).
pubmed: 16113101
doi: 10.1677/erc.1.01023
Aguilar, H. et al. Biological reprogramming in acquired resistance to endocrine therapy of breast cancer. Oncogene 29, 6071–6083 (2010).
pubmed: 20711236
doi: 10.1038/onc.2010.333
Magnani, L. et al. Genome-wide reprogramming of the chromatin landscape underlies endocrine therapy resistance in breast cancer. Proc. Natl Acad. Sci. USA 110, E1490–E1499 (2013).
pubmed: 23576735
doi: 10.1073/pnas.1219992110
Tomita, S. et al. A cluster of noncoding RNAs activates the ESR1 locus during breast cancer adaptation. Nat. Commun. 6, 6966 (2015).
pubmed: 25923108
pmcid: 4421845
doi: 10.1038/ncomms7966
West, J. A. et al. The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites. Mol. Cell 55, 791–802 (2014).
pubmed: 25155612
pmcid: 4428586
doi: 10.1016/j.molcel.2014.07.012
Miyagawa, R. et al. Identification of cis- and trans-acting factors involved in the localization of MALAT-1 noncoding RNA to nuclear speckles. RNA 18, 738–751 (2012).
pubmed: 22355166
pmcid: 3312561
doi: 10.1261/rna.028639.111
Rhie, S. K. et al. Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits. Epigenetics Chromatin 9, 50 (2016).
pubmed: 27833659
pmcid: 5103450
doi: 10.1186/s13072-016-0102-4
Niknafs, Y. S. et al. The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression. Nat. Commun. 7, 12791 (2016).
pubmed: 27666543
pmcid: 5052669
doi: 10.1038/ncomms12791
Iyer, M. K. et al. The landscape of long noncoding RNAs in the human transcriptome. Nat. Genet. 47, 199–208 (2015).
pubmed: 25599403
pmcid: 4417758
doi: 10.1038/ng.3192
Dyer, P. N. et al. Reconstitution of nucleosome core particles from recombinant histones and DNA. Methods Enzymol. 375, 23–44 (2004).
pubmed: 14870657
doi: 10.1016/S0076-6879(03)75002-2
pmcid: 14870657
Taguchi, H., Horikoshi, N., Arimura, Y. & Kurumizaka, H. A method for evaluating nucleosome stability with a protein-binding fluorescent dye. Methods 70, 119–126 (2014).
pubmed: 25220913
doi: 10.1016/j.ymeth.2014.08.019
pmcid: 25220913
Frouws, T. D., Duda, S. C. & Richmond, T. J. X-ray structure of the MMTV-A nucleosome core. Proc. Natl Acad. Sci. USA 113, 1214–1219 (2016).
pubmed: 26787910
doi: 10.1073/pnas.1524607113
pmcid: 26787910
Ji, P. et al. MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene 22, 8031–8041 (2003).
pubmed: 12970751
doi: 10.1038/sj.onc.1206928
pmcid: 12970751
Yoshimoto, R., Mayeda, A., Yoshida, M. & Nakagawa, S. MALAT1 long non-coding RNA in cancer. Biochim. Biophys. Acta 1859, 192–199 (2016).
pubmed: 26434412
doi: 10.1016/j.bbagrm.2015.09.012
pmcid: 26434412
Sun, Q., Hao, Q. & Prasanth, K. V. Nuclear long noncoding RNAs: key regulators of gene expression. Trends Genet. 34, 142–157 (2017).
doi: 10.1016/j.tig.2017.11.005
Misteli, T. et al. The dynamics of a pre-mRNA splicing factor in living cells. Nature 387, 523–527 (1997).
pubmed: 9168118
doi: 10.1038/387523a0
pmcid: 9168118
Shopland, L. S. et al. Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains: evidence for local euchromatic neighborhoods. J. Cell Biol. 162, 981–990 (2003).
pubmed: 12975345
pmcid: 2172856
doi: 10.1083/jcb.200303131
Wutz, A. Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation. Nat. Rev. Genet. 12, 542–553 (2011).
pubmed: 21765457
doi: 10.1038/nrg3035
pmcid: 21765457
Zhang, B. et al. PHGDH defines a metabolic subtype in lung adenocarcinomas with poor prognosis. Cell Rep. 19, 2289–2303 (2017).
pubmed: 28614715
doi: 10.1016/j.celrep.2017.05.067
pmcid: 28614715
Richards, E. G., Flessel, C. P. & Fresco, J. R. Polynucleotides. VI. Molecular properties and conformation of polyribouridylic acid. Biopolymers 1, 431–446 (1963).
doi: 10.1002/bip.360010504
Esteller, M. Non-coding RNAs in human disease. Nat. Rev. Genet. 12, 861–874 (2011).
pubmed: 22094949
doi: 10.1038/nrg3074
pmcid: 22094949
Abdalla, M. O. A. et al. The Eleanor ncRNAs activate the topological domain of the ESR1 locus to balance against apoptosis. Nat. Commun. 10, 3778 (2019).
pubmed: 31439835
pmcid: 6706407
doi: 10.1038/s41467-019-11378-4
Yamamoto, T. et al. Endocrine therapy-resistant breast cancer model cells are inhibited by soybean glyceollin I through Eleanor non-coding RNA. Sci. Rep. 8, 15202 (2018).
pubmed: 30315184
pmcid: 6185934
doi: 10.1038/s41598-018-33227-y
Li, X. et al. GRID-seq reveals the global RNA-chromatin interactome. Nat. Biotechnol. 35, 940–950 (2017).
pubmed: 28922346
pmcid: 5953555
doi: 10.1038/nbt.3968
Wang, K. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472, 120–124 (2011).
pubmed: 21423168
pmcid: 3670758
doi: 10.1038/nature09819
Li, W. et al. Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 498, 516–520 (2013).
pubmed: 23728302
pmcid: 3718886
doi: 10.1038/nature12210
Davidovich, C., Zheng, L., Goodrich, K. J. & Cech, T. R. Promiscuous RNA binding by Polycomb repressive complex 2. Nat. Struct. Mol. Biol. 20, 1250–1257 (2013).
pubmed: 24077223
pmcid: 3823624
doi: 10.1038/nsmb.2679
Cifuentes-Rojas, C., Hernandez, A. J., Sarma, K. & Lee, J. T. Regulatory interactions between RNA and polycomb repressive complex 2. Mol. Cell 55, 171–185 (2014).
pubmed: 24882207
pmcid: 4107928
doi: 10.1016/j.molcel.2014.05.009
Holoch, D. & Margueron, R. Mechanisms regulating PRC2 recruitment and enzymatic activity. Trends Biochem. Sci. 42, 531–542 (2017).
pubmed: 28483375
pmcid: 28483375
doi: 10.1016/j.tibs.2017.04.003
Zhao, J., Sun, B. K., Erwin, J. A., Song, J. J. & Lee, J. T. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 322, 750–756 (2008).
pubmed: 18974356
pmcid: 2748911
doi: 10.1126/science.1163045
Pandey, R. R. et al. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol. Cell 32, 232–246 (2008).
pubmed: 18951091
doi: 10.1016/j.molcel.2008.08.022
Yap, K. L. et al. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol. Cell 38, 662–674 (2010).
pubmed: 20541999
pmcid: 2886305
doi: 10.1016/j.molcel.2010.03.021
O’Leary, V. B. et al. PARTICLE, a triplex-forming long ncRNA, regulates locus-specific methylation in response to low-dose irradiation. Cell Rep. 11, 474–485 (2015).
pubmed: 25900080
doi: 10.1016/j.celrep.2015.03.043
Beltran, M. et al. The interaction of PRC2 with RNA or chromatin is mutually antagonistic. Genome Res. 26, 896–907 (2016).
pubmed: 27197219
pmcid: 4937559
doi: 10.1101/gr.197632.115
Han, P. & Chang, C. P. Long non-coding RNA and chromatin remodelling. RNA Biol. 12, 1094–1098 (2015).
pubmed: 26177256
pmcid: 4829272
doi: 10.1080/15476286.2015.1063770
Audia, J. E. & Campbell, R. M. Histone modifications and cancer. Cold Spring Harb. Perspect. Biol. 8, a019521 (2016).
pubmed: 27037415
pmcid: 4817802
doi: 10.1101/cshperspect.a019521
Simon, M. et al. Histone fold modifications control nucleosome unwrapping and disassembly. Proc. Natl Acad. Sci. USA 108, 12711–12716 (2011).
pubmed: 21768347
doi: 10.1073/pnas.1106264108
Krajewski, W. A., Li, J. & Dou, Y. Effects of histone H2B ubiquitylation on the nucleosome structure and dynamics. Nucleic Acids Res. 46, 7631–7642 (2018).
pubmed: 29931239
pmcid: 6125632
doi: 10.1093/nar/gky526
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
pubmed: 19451168
pmcid: 19451168
Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).
pubmed: 21221095
pmcid: 3346182
doi: 10.1038/nbt.1754
Thorvaldsdóttir, H., Robinson, J. T. & Mesirov, J. P. Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14, 178–192 (2013).
pubmed: 22517427
doi: 10.1093/bib/bbs017
Tanaka, Y. et al. Expression and purification of recombinant human histones. Methods 33, 3–11 (2004).
pubmed: 15039081
doi: 10.1016/j.ymeth.2003.10.024
Machida, S. et al. Structural basis of heterochromatin formation by human HP1. Mol. Cell 69, 385–397 (2018).
pubmed: 29336876
doi: 10.1016/j.molcel.2017.12.011
Tachiwana, H. et al. Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T. Proc. Natl Acad. Sci. USA 107, 10454–10459 (2010).
pubmed: 20498094
doi: 10.1073/pnas.1003064107
Hamada, M., Kiryu, H., Sato, K., Mituyama, T. & Asai, K. Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics 25, 465–473 (2009).
pubmed: 19095700
doi: 10.1093/bioinformatics/btn601
McCaskill, J. S. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29, 1105–1119 (1990).
pubmed: 1695107
doi: 10.1002/bip.360290621
Corces, M. R. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat. Methods 14, 959–962 (2017).
pubmed: 28846090
pmcid: 5623106
doi: 10.1038/nmeth.4396
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
pubmed: 3322381
pmcid: 3322381
doi: 10.1038/nmeth.1923
Ramírez, F., Dündar, F., Diehl, S., Grüning, B. A. & Manke, T. deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 42, W187–191 (2014).
pubmed: 24799436
pmcid: 4086134
doi: 10.1093/nar/gku365