RNA-mediated regulation of chromatin structures

다국어 초록 (Multilingual Abstract)

It is now evident that transcriptional gene regulation usually requires the re-organization of chromatin architecture. Increasing evidence suggested various kinds of RNAs are involved in this process. Especially the nascent RNAs retained at their site of transcription can serve as a scaffold for organizing transcriptionally either favorable or unfavorable chromatin structures. An emerging concept of phase separation explains how these chromatin structures can be maintained as physically discrete subcompartments within membrane-less nucleoplasm. Evidences that support the crucial role of nascent RNAs in the formation of phase-separated condensates are now rapidly growing.

참고문헌 (Reference)

1 Pintacuda G, "hnRNPK recruits PCGF3/5-PRC1 to the Xist RNA B-repeat to establish polycomb-mediated chromosomal silencing" 68 : 955-969e910, 2017

2 Colognori D, "Xist deletional analysis reveals an interdependency between Xist RNA and polycomb complexes for spreading along the inactive X" 74 : 101-117 e110, 2019

3 Loda A, "Xist RNA in action : Past, present, and future" 15 : e1008333-, 2019

4 Galupa R, "X-chromosome inactivation : new insights into cis and trans regulation" 31 : 57-66, 2015

5 Kim TK, "Widespread transcription at neuronal activity-regulated enhancers" 465 : 182-187, 2010

6 Harris H, "Turnover of nuclear and cytoplasmic ribonucleic acid in two types of animal cell, with some further observations on the nucleolus" 73 : 362-369, 1959

7 Sienski G, "Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression" 151 : 964-980, 2012

8 Ferrari F, "Transcriptional control of a whole chromosome : emerging models for dosage compensation" 21 : 118-125, 2014

9 Tuan D, "Transcription of the hypersensitive site HS2 enhancer in erythroid cells" 89 : 11219-11223, 1992

10 신하연, "The structural and functional roles of CTCF in the regulation of cell type-specific and human disease-associated super-enhancers" 한국유전학회 41 (41): 257-265, 2019

11 Batki J, "The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation" 26 : 720-731, 2019

12 Zylicz JJ, "The implication of early chromatin changes in X chromosome inactivation" 176 : 182-197e123, 2019

13 Brown CJ, "The human XIST gene : analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus" 71 : 527-542, 1992

14 McHugh CA, "The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3" 521 : 232-236, 2015

15 Cajigas I, "The Evf2 ultraconserved enhancer lncRNA functionally and spatially organizes megabase distant genes in the developing forebrain" 71 : 956-972e959, 2018

16 Chu C, "Systematic discovery of Xist RNA binding proteins" 161 : 404-416, 2015

17 Mikami S, "Structural insights into the recruitment of SMRT by the corepressor SHARP under phosphorylative regulation" 22 : 35-46, 2014

18 Sienski G, "Silencio/CG9754 connects the Piwi-piRNA complex to the cellular heterochromatin machinery" 29 : 2258-2271, 2015

19 Dossin F, "SPEN integrates transcriptional and epigenetic control of X-inactivation" 578 : 455-460, 2020

20 Verdel A, "RNAi-mediated targeting of heterochromatin by the RITS complex" 303 : 672-676, 2004

21 Johnson WL, "RNA-mediated regulation of heterochromatin" 46 : 102-109, 2017

22 Johnson WL, "RNA-dependent stabilization of SUV39H1 at constitutive heterochromatin" 6 : e25299-, 2017

23 Zhao J, "Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome" 322 : 750-756, 2008

24 Le Thomas A, "Piwi induces piRNAguided transcriptional silencing and establishment of a repressive chromatin state" 27 : 390-399, 2013

25 Nair SJ, "Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly" 26 : 193-203, 2019

26 Yu Y, "Panoramix enforces piRNA-dependent cotranscriptional silencing" 350 : 339-342, 2015

27 Almeida M, "PCGF3/5-PRC1 initiates polycomb recruitment in X chromosome inactivation" 356 : 1081-1084, 2017

28 Murano K, "Nuclear RNA export factor variant initiates piRNA-guided co-transcriptional silencing" 38 : e102870-, 2019

29 Velazquez Camacho O, "Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNAnucleosome association and RNA : DNA hybrid formation" 6 : e25293-, 2017

30 Lee JT, "Lessons from X-chromosome inactivation : long ncRNA as guides and tethers to the epigenome" 23 : 1831-1842, 2009

31 Djebali S, "Landscape of transcription in human cells" 489 : 101-108, 2012

32 Shirai A, "Impact of nucleic acid and methylated H3K9 binding activities of Suv39h1 on its heterochromatin assembly" 6 : e25317-, 2017

33 Ling J, "HS2enhancer function is blocked by a transcriptional terminator inserted between the enhancer and the promoter" 279 : 51704-51713, 2004

34 Maison C, "HP1 and the dynamics of heterochromatin maintenance" 5 : 296-304, 2004

35 Li X, "GRID-seq reveals the global RNA-chromatin interactome" 35 : 940-950, 2017

36 Li W, "Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation" 498 : 516-520, 2013

37 Li W, "Enhancers as non-coding RNA transcription units : recent insights and future perspectives" 17 : 207-223, 2016

38 Lam MT, "Enhancer RNAs and regulated transcriptional programs" 39 : 170-182, 2014

39 Arnold PR, "Diversity and emerging roles of enhancer RNA in regulation of gene expression and cell fate" 7 : 377-, 2019

40 Collis P, "Definition of the minimal requirements within the human beta-globin gene and the dominant control region for high level expression" 9 : 233-240, 1990

41 Sabari BR, "Coactivator condensation at super-enhancers links phase separation and gene control" 361 : eaar958-, 2018

42 Minajigi A, "Chromosomes. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation" 349 : aab2276-, 2015

43 Wutz A, "Chromosomal silencing and localization are mediated by different domains of Xist RNA" 30 : 167-174, 2002

44 Li X, "Chromatin-associated RNAs as facilitators of functional genomic interactions" 20 : 503-519, 2019

45 Borsani G, "Characterization of a murine gene expressed from the inactive X chromosome" 351 : 325-329, 1991

46 Yamazaki T, "Architectural RNAs for membraneless nuclear body formation" 2020

47 Tsai PF, "A muscle-specific enhancer RNA mediates cohesin recruitment and regulates transcription in trans" 71 : 129-141e128, 2018

48 De Santa F, "A large fraction of extragenic RNA pol II transcription sites overlap enhancers" 8 : e1000384-, 2010