Shape of promoter antisense RNAs regulates ligand-induced transcription activation.


Journal

Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462

Informations de publication

Date de publication:
07 2021
Historique:
received: 19 11 2019
accepted: 28 04 2021
pubmed: 2 7 2021
medline: 18 1 2022
entrez: 1 7 2021
Statut: ppublish

Résumé

The size of the transcriptional program of long non-coding RNAs in the mammalian genome has engendered discussions about their biological roles

Identifiants

pubmed: 34194047
doi: 10.1038/s41586-021-03589-x
pii: 10.1038/s41586-021-03589-x
pmc: PMC8439151
mid: NIHMS1725588
doi:

Substances chimiques

Bcar1 protein, mouse 0
Crk-Associated Substrate Protein 0
Estrogen Receptor alpha 0
HP1-alpha protein, human 0
Histones 0
KDM4C protein, human 0
Ligands 0
RNA, Antisense 0
Chromobox Protein Homolog 5 107283-02-3
Jumonji Domain-Containing Histone Demethylases EC 1.14.11.-
KDM4B protein, human EC 1.14.11.-
TRIM28 protein, human EC 2.3.2.27
Tripartite Motif-Containing Protein 28 EC 2.3.2.27
Positive Transcriptional Elongation Factor B EC 2.7.11.-
RNA Polymerase II EC 2.7.7.-

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Pagination

444-449

Subventions

Organisme : NEI NIH HHS
ID : P30 EY026877
Pays : United States
Organisme : NIDDK NIH HHS
ID : R37 DK039949
Pays : United States
Organisme : Howard Hughes Medical Institute
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL150521
Pays : United States
Organisme : NIDDK NIH HHS
ID : R01 DK018477
Pays : United States
Organisme : NIDDK NIH HHS
ID : R01 DK039949
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM131780
Pays : United States
Organisme : NINDS NIH HHS
ID : R01 NS093066
Pays : United States

Informations de copyright

© 2021. The Author(s), under exclusive licence to Springer Nature Limited.

Références

Engreitz, J. M. et al. Local regulation of gene expression by lncRNA promoters, transcription and splicing. Nature 539, 452–455 (2016).
pubmed: 27783602 pmcid: 6853796 doi: 10.1038/nature20149
Sigova, A. A. et al. Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc. Natl Acad. Sci. USA 110, 2876–2881 (2013).
pubmed: 23382218 pmcid: 3581948 doi: 10.1073/pnas.1221904110
Flynn, R. A., Almada, A. E., Zamudio, J. R. & Sharp, P. A. Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome. Proc. Natl Acad. Sci. USA 108, 10460–10465 (2011).
pubmed: 21670248 pmcid: 3127934 doi: 10.1073/pnas.1106630108
Gupta, R. A. et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464, 1071–1076 (2010).
pubmed: 20393566 pmcid: 3049919 doi: 10.1038/nature08975
Chu, H. P. et al. TERRA RNA antagonizes ATRX and protects telomeres. Cell 170, 86–101 (2017).
pubmed: 28666128 pmcid: 5552367 doi: 10.1016/j.cell.2017.06.017
McHugh, C. A. et al. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature 521, 232–236 (2015).
pubmed: 25915022 pmcid: 4516396 doi: 10.1038/nature14443
Sarma, K. et al. ATRX directs binding of PRC2 to Xist RNA and Polycomb targets. Cell 159, 869–883 (2014).
pubmed: 25417162 pmcid: 4379047 doi: 10.1016/j.cell.2014.10.019
Silva, A. M. et al. Long noncoding RNAs: a missing link in osteoporosis. Bone Res. 7, 10 (2019).
pubmed: 30937214 pmcid: 6437190 doi: 10.1038/s41413-019-0048-9
Ulitsky, I. & Bartel, D. P. lincRNAs: genomics, evolution, and mechanisms. Cell 154, 26–46 (2013).
pubmed: 23827673 pmcid: 3924787 doi: 10.1016/j.cell.2013.06.020
Gebert, L. F. R. & MacRae, I. J. Regulation of microRNA function in animals. Nat. Rev. Mol. Cell Biol. 20, 21–37 (2019).
pubmed: 30108335 pmcid: 6546304 doi: 10.1038/s41580-018-0045-7
Aravin, A. et al. A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442, 203–207 (2006).
pubmed: 16751777 doi: 10.1038/nature04916
Girard, A., Sachidanandam, R., Hannon, G. J. & Carmell, M. A. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442, 199–202 (2006).
pubmed: 16751776 doi: 10.1038/nature04917
Vagin, V. V. et al. A distinct small RNA pathway silences selfish genetic elements in the germline. Science 313, 320–324 (2006).
pubmed: 16809489 doi: 10.1126/science.1129333
Treiber, T., Treiber, N. & Meister, G. Regulation of microRNA biogenesis and its crosstalk with other cellular pathways. Nat. Rev. Mol. Cell Biol. 20, 5–20 (2019).
pubmed: 30228348 doi: 10.1038/s41580-018-0059-1
Sesto, N., Wurtzel, O., Archambaud, C., Sorek, R. & Cossart, P. The excludon: a new concept in bacterial antisense RNA-mediated gene regulation. Nat. Rev. Microbiol. 11, 75–82 (2013).
pubmed: 23268228 doi: 10.1038/nrmicro2934
Arab, K. et al. Long noncoding RNA TARID directs demethylation and activation of the tumor suppressor TCF21 via GADD45A. Mol. Cell 55, 604–614 (2014).
pubmed: 25087872 doi: 10.1016/j.molcel.2014.06.031
Bester, A. C. et al. An integrated genome-wide CRISPRa approach to functionalize lncRNAs in drug resistance. Cell 173, 649–664 (2018).
pubmed: 29677511 pmcid: 6061940 doi: 10.1016/j.cell.2018.03.052
Canzio, D. et al. Antisense lncRNA transcription mediates DNA demethylation to drive stochastic protocadherin α promoter choice. Cell 177, 639–653 (2019).
pubmed: 30955885 pmcid: 6823843 doi: 10.1016/j.cell.2019.03.008
Ross-Innes, C. S. et al. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature 481, 389–393 (2012).
pubmed: 22217937 pmcid: 3272464 doi: 10.1038/nature10730
He, H. H. et al. Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics. Genome Res. 22, 1015–1025 (2012).
pubmed: 22508765 pmcid: 3371710 doi: 10.1101/gr.133280.111
Wardell, S. E., Kazmin, D. & McDonnell, D. P. Research resource: transcriptional profiling in a cellular model of breast cancer reveals functional and mechanistic differences between clinically relevant SERM and between SERM/estrogen complexes. Mol. Endocrinol. 26, 1235–1248 (2012).
pubmed: 22570330 pmcid: 3385791 doi: 10.1210/me.2012-1031
Liu, Z. et al. Enhancer activation requires trans-recruitment of a mega transcription factor complex. Cell 159, 358–373 (2014).
pubmed: 25303530 pmcid: 4465761 doi: 10.1016/j.cell.2014.08.027
Nair, S. J. et al. Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly. Nat. Struct. Mol. Biol. 26, 193–203 (2019).
pubmed: 30833784 pmcid: 6709854 doi: 10.1038/s41594-019-0190-5
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
Hah, N. et al. A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell 145, 622–634 (2011).
pubmed: 21549415 pmcid: 3099127 doi: 10.1016/j.cell.2011.03.042
Danko, C. G. et al. Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol. Cell 50, 212–222 (2013).
pubmed: 23523369 pmcid: 3640649 doi: 10.1016/j.molcel.2013.02.015
Lis, J. T. A. A 50 year history of technologies that drove discovery in eukaryotic transcription regulation. Nat. Struct. Mol. Biol. 26, 777–782 (2019).
pubmed: 31439942 pmcid: 7106917 doi: 10.1038/s41594-019-0288-9
Peterlin, B. M. & Price, D. H. Controlling the elongation phase of transcription with P-TEFb. Mol. Cell 23, 297–305 (2006).
pubmed: 16885020 doi: 10.1016/j.molcel.2006.06.014
Chu, C., Qu, K., Zhong, F. L., Artandi, S. E. & Chang, H. Y. Genomic maps of long noncoding RNA occupancy reveal principles of RNA–chromatin interactions. Mol. Cell 44, 667–678 (2011).
pubmed: 21963238 pmcid: 3249421 doi: 10.1016/j.molcel.2011.08.027
Engreitz, J. M. et al. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 341, 1237973 (2013).
pubmed: 23828888 pmcid: 3778663 doi: 10.1126/science.1237973
Simon, M. D. et al. The genomic binding sites of a noncoding RNA. Proc. Natl Acad. Sci. USA 108, 20497–20502 (2011).
pubmed: 22143764 pmcid: 3251105 doi: 10.1073/pnas.1113536108
Abudayyeh, O. O. et al. RNA targeting with CRISPR–Cas13. Nature 550, 280–284 (2017).
pubmed: 28976959 pmcid: 5706658 doi: 10.1038/nature24049
Cox, D. B. T. et al. RNA editing with CRISPR–Cas13. Science 358, 1019–1027 (2017).
pubmed: 29070703 pmcid: 5793859 doi: 10.1126/science.aaq0180
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
Larson, A. G. et al. Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature 547, 236–240 (2017).
pubmed: 28636604 pmcid: 5606208 doi: 10.1038/nature22822
McNamara, R. P. et al. KAP1 recruitment of the 7SK snRNP complex to promoters enables transcription elongation by RNA polymerase II. Mol. Cell 61, 39–53 (2016).
pubmed: 26725010 doi: 10.1016/j.molcel.2015.11.004
Bunch, H. et al. TRIM28 regulates RNA polymerase II promoter-proximal pausing and pause release. Nat. Struct. Mol. Biol. 21, 876–883 (2014).
pubmed: 25173174 pmcid: 4189995 doi: 10.1038/nsmb.2878
Liu, X. et al. In situ capture of chromatin interactions by biotinylated dCas9. Cell 170, 1028–1043 (2017).
pubmed: 28841410 pmcid: 6857456 doi: 10.1016/j.cell.2017.08.003
Mahat, D. B. et al. Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nat. Protoc. 11, 1455–1476 (2016).
pubmed: 27442863 pmcid: 5502525 doi: 10.1038/nprot.2016.086
Yang, F., Zhang, H., Mei, Y. & Wu, M. Reciprocal regulation of HIF-1α and lincRNA-p21 modulates the Warburg effect. Mol. Cell 53, 88–100 (2014).
pubmed: 24316222 doi: 10.1016/j.molcel.2013.11.004
Shechner, D. M., Hacisuleyman, E., Younger, S. T. & Rinn, J. L. Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display. Nat. Methods 12, 664–670 (2015).
pubmed: 26030444 pmcid: 4821475 doi: 10.1038/nmeth.3433
Konermann, S. et al. Genome-scale transcriptional activation by an engineered CRISPR–Cas9 complex. Nature 517, 583–588 (2015).
pubmed: 25494202 doi: 10.1038/nature14136
Smola, M. J., Rice, G. M., Busan, S., Siegfried, N. A. & Weeks, K. M. Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis. Nat. Protoc. 10, 1643–1669 (2015).
pubmed: 26426499 pmcid: 4900152 doi: 10.1038/nprot.2015.103
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
pubmed: 22388286 pmcid: 3322381 doi: 10.1038/nmeth.1923
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).
pubmed: 20513432 pmcid: 2898526 doi: 10.1016/j.molcel.2010.05.004
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).
pubmed: 19910308 doi: 10.1093/bioinformatics/btp616
Busan, S. & Weeks, K. M. Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2. RNA 24, 143–148 (2018).
pubmed: 29114018 pmcid: 5769742 doi: 10.1261/rna.061945.117
Andrews, R. J., Baber, L. & Moss, W. N. Mapping the RNA structural landscape of viral genomes. Methods 183, 57–67 (2020).
pubmed: 31711930 doi: 10.1016/j.ymeth.2019.11.001

Auteurs

Fan Yang (F)

Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA. fay009@health.ucsd.edu.

Bogdan Tanasa (B)

Department of Ophthalmology, Stanford University School of Medicine, Palo Alto, CA, USA.

Rudi Micheletti (R)

Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA.

Kenneth A Ohgi (KA)

Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA.

Aneel K Aggarwal (AK)

Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

Michael G Rosenfeld (MG)

Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA. mrosenfeld@health.ucsd.edu.

Articles similaires

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female
Humans United States Aged Cross-Sectional Studies Medicare Part C
1.00
Humans Yoga Low Back Pain Female Male

Classifications MeSH