Artículo

Estamos trabajando para incorporar este artículo al repositorio
Consulte el artículo en la página del editor
Consulte la política de Acceso Abierto del editor

Abstract:

Splicing is a predominantly co-transcriptional process that has been shown to be tightly coupled to transcription. Chromatin structure is a key factor that mediates this functional coupling. In light of recent evidence that shows the importance of higher order chromatin organization in the coordination and regulation of gene expression, we discuss here the possible roles of long-range chromatin organization in splicing and alternative splicing regulation. © 2014 Landes Bioscience.

Registro:

Documento: Artículo
Título:Long range chromatin organization: A new layer in splicing regulation?
Autor:Gómez Acuña, L.I.; Kornblihtt, A.R.
Filiación:Laboratorio de Fisiología y Biología Molecular, Departamento de Fisiología, Biología Molecular y Celular, IFIBYNE-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
Palabras clave:Alternative splicing; Chromatin; Coupling between transcription and splicing; Long-range chromatin interactions; cohesin; estradiol receptor; heterogeneous nuclear ribonucleoprotein L; histone; polycomb group protein; RNA polymerase II; transcription factor CTCF; chromatin; alternative RNA splicing; article; chromatin structure; DNA methylation; DNA template; embryonic stem cell; enhancer region; fibroblast; gene activation; genetic association; globin gene; human; promoter region; regulator gene; transcription initiation; animal; chromatin; genetic transcription; metabolism; RNA splicing; Animals; Chromatin; Humans; RNA Splicing; Transcription, Genetic
Año:2014
Volumen:5
Número:APR
Página de inicio:e28726
Página de fin:1-e28726-5
DOI: http://dx.doi.org/10.4161/trns.28726
Título revista:Transcription
Título revista abreviado:Transcription
ISSN:21541264
CAS:histone, 9062-68-4; Chromatin
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_21541264_v5_nAPR_pe28726_GomezAcuna

Referencias:

  • Listerman, I., Sapra, A.K., Neugebauer, K.M., Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells (2006) Nat Struct Mol Biol, 13, pp. 815-822. , http://dx.doi.org/10.1038/nsmb1135, PMID:16921380
  • Tilgner, H., Knowles, D.G., Johnson, R., Davis, C.A., Chakrabortty, S., Djebali, S., Curado, J., Guigó, R., Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs (2012) Genome Res, 22, pp. 1616-1625. , http://dx.doi.org/10.1101/gr.134445.111, PMID:22955974
  • Kotovic, K.M., Lockshon, D., Boric, L., Neugebauer, K.M., Cotranscriptional recruitment of the U1 snRNP to intron-containing genes in yeast (2003) Mol Cell Biol, 23, pp. 5768-5779. , http://dx.doi.org/10.1128/MCB.23.16.5768-5779.2003, PMID:12897147
  • Kornblihtt, A.R., Schor, I.E., Alló, M., Dujardin, G., Petrillo, E., Muñoz, M.J., Alternative splicing: A pivotal step between eukaryotic transcription and translation (2013) Nat Rev Mol Cell Biol, 14, pp. 153-165. , http://dx.doi.org/10.1038/nrm3525, PMID:23385723
  • Barash, Y., Calarco, J.A., Gao, W., Pan, Q., Wang, X., Shai, O., Blencowe, B.J., Frey, B.J., Deciphering the splicing code (2010) Nature, 465, pp. 53-59. , http://dx.doi.org/10.1038/nature09000, PMID:20445623
  • Risso, G., Pelisch, F., Quaglino, A., Pozzi, B., Srebrow, A., Regulating the regulators: Serine/arginine-rich proteins under scrutiny (2012) IUBMB Life, 64, pp. 809-816. , http://dx.doi.org/10.1002/iub.1075, PMID:22941908
  • Das, R., Yu, J., Zhang, Z., Gygi, M.P., Krainer, A.R., Gygi, S.P., Reed, R., SR proteins function in coupling RNAP II transcription to pre-mRNA splicing (2007) Mol Cell, 26, pp. 867-881. , http://dx.doi.org/10.1016/j.molcel.2007.05.036, PMID:17588520
  • Muñoz, M.J., de la Mata, M., Kornblihtt, A.R., The carboxy terminal domain of RNA polymerase II and alternative splicing (2010) Trends Biochem Sci, 35, pp. 497-504. , http://dx.doi.org/10.1016/j.tibs.2010.03.010, PMID:20418102
  • de la Mata, M., Muñoz, M.J., Alló, M., Fededa, J.P., Schor, I.E., Kornblihtt, A.R., RNA polymerase II elongation at the crossroads of transcription and alternative aplicing (2011) Genet Res Int, 2011, p. 309865. , http://dx.doi.org/10.4061/2011/309865, PMID:22567350
  • Huang, Y., Li, W., Yao, X., Lin, Q.J., Yin, J.W., Liang, Y., Heiner, M., Wang, G., Mediator complex regulates alternative mRNA processing via the MED23 subunit (2012) Mol Cell, 45, pp. 459-469. , http://dx.doi.org/10.1016/j.molcel.2011.12.022, PMID:22264826
  • Auboeuf, D., Dowhan, D.H., Kang, Y.K., Larkin, K., Lee, J.W., Berget, S.M., O'Malley, B.W., Differential recruitment of nuclear receptor coactivators may determine alternative RNA splice site choice in target genes (2004) Proc Natl Acad Sci U S A, 101, pp. 2270-2274. , http://dx.doi.org/10.1073/pnas.0308133100, PMID:14982999
  • de la Mata, M., Alonso, C.R., Kadener, S., Fededa, J.P., Blaustein, M., Pelisch, F., Cramer, P., Kornblihtt, A.R., A slow RNA polymerase II affects alternative splicing in vivo (2003) Mol Cell, 12, pp. 525-532. , http://dx.doi.org/10.1016/j.molcel.2003.08.001, PMID:14536091
  • Ip, J.Y., Schmidt, D., Pan, Q., Ramani, A.K., Fraser, A.G., Odom, D.T., Blencowe, B.J., Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation (2011) Genome Res, 21, pp. 390-401. , http://dx.doi.org/10.1101/gr.111070.110, PMID:21163941
  • Luco, R.F., Allo, M., Schor, I.E., Kornblihtt, A.R., Misteli, T., Epigenetics in alternative pre-mRNA splicing (2011) Cell, 144, pp. 16-26. , http://dx.doi.org/10.1016/j.cell.2010.11.056, PMID:21215366
  • Luco, R.F., Pan, Q., Tominaga, K., Blencowe, B.J., Pereira-Smith, O.M., Misteli, T., Regulation of alternative splicing by histone modifications (2010) Science, 327, pp. 996-1000. , http://dx.doi.org/10.1126/science.1184208, PMID:20133523
  • Sims III, R.J., Millhouse, S., Chen, C.F., Lewis, B.A., Erdjument-Bromage, H., Tempst, P., Manley, J.L., Reinberg, D., Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing (2007) Mol Cell, 28, pp. 665-676. , http://dx.doi.org/10.1016/j.molcel.2007.11.010, PMID:18042460
  • Hodges, C., Bintu, L., Lubkowska, L., Kashlev, M., Bustamante, C., Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II (2009) Science, 325, pp. 626-628. , http://dx.doi.org/10.1126/science.1172926, PMID:19644123
  • Petesch, S.J., Lis, J.T., Overcoming the nucleosome barrier during transcript elongation (2012) Trends Genet, 28, pp. 285-294. , http://dx.doi.org/10.1016/j.tig.2012.02.005, PMID:22465610
  • Kouzarides, T., Chromatin modifications and their function (2007) Cell, 128, pp. 693-705. , http://dx.doi.org/10.1016/j.cell.2007.02.005, PMID:17320507
  • Schwartz, S., Meshorer, E., Ast, G., Chromatin organization marks exon-intron structure (2009) Nat Struct Mol Biol, 16, pp. 990-995. , http://dx.doi.org/10.1038/nsmb.1659, PMID:19684600
  • Tilgner, H., Nikolaou, C., Althammer, S., Sammeth, M., Beato, M., Valcárcel, J., Guigó, R., Nucleosome positioning as a determinant of exon recognition (2009) Nat Struct Mol Biol, 16, pp. 996-1001. , http://dx.doi.org/10.1038/nsmb.1658, PMID:19684599
  • Alló, M., Buggiano, V., Fededa, J.P., Petrillo, E., Schor, I., de la Mata, M., Agirre, E., Elela, S.A., Control of alternative splicing through siRNA-mediated transcriptional gene silencing (2009) Nat Struct Mol Biol, 16, pp. 717-724. , http://dx.doi.org/10.1038/nsmb.1620, PMID:19543290
  • Ameyar-Zazoua, M., Rachez, C., Souidi, M., Robin, P., Fritsch, L., Young, R., Morozova, N., Andrau, J.C., Argonaute proteins couple chromatin silencing to alternative splicing (2012) Nat Struct Mol Biol, 19, pp. 998-1004. , http://dx.doi.org/10.1038/nsmb.2373, PMID:22961379
  • Saint-André, V., Batsché, E., Rachez, C., Muchardt, C., Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons (2011) Nat Struct Mol Biol, 18, pp. 337-344. , http://dx.doi.org/10.1038/nsmb.1995, PMID:21358630
  • Schor, I.E., Fiszbein, A., Petrillo, E., Kornblihtt, A.R., Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation (2013) EMBO J, 32, pp. 2264-2274. , http://dx.doi.org/10.1038/emboj.2013.167, PMID:23892457
  • Schor, I.E., Rascovan, N., Pelisch, F., Alló, M., Kornblihtt, A.R., Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing (2009) Proc Natl Acad Sci U S A, 106, pp. 4325-4330. , http://dx.doi.org/10.1073/pnas.0810666106, PMID:19251664
  • Shukla, S., Kavak, E., Gregory, M., Imashimizu, M., Shutinoski, B., Kashlev, M., Oberdoerffer, P., Oberdoerffer, S., CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing (2011) Nature, 479, pp. 74-79. , http://dx.doi.org/10.1038/nature10442, PMID:21964334
  • Dixon, J.R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Ren, B., Topological domains in mammalian genomes identified by analysis of chromatin interactions (2012) Nature, 485, pp. 376-380. , http://dx.doi.org/10.1038/nature11082, PMID:22495300
  • Bickmore, W.A., The spatial organization of the human genome (2013) Annu Rev Genomics Hum Genet, 14, pp. 67-84. , http://dx.doi.org/10.1146/annurev-genom-091212-153515, PMID:23875797
  • Fullwood, M.J., Liu, M.H., Pan, Y.F., Liu, J., Xu, H., Mohamed, Y.B., Orlov, Y.L., Mei, P.H., An oestrogen-receptor-alpha-bound human chromatin interactome (2009) Nature, 462, pp. 58-64. , http://dx.doi.org/10.1038/nature08497, PMID:19890323
  • Hakim, O., Sung, M.H., Voss, T.C., Splinter, E., John, S., Sabo, P.J., Thurman, R.E., Hager, G.L., Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements (2011) Genome Res, 21, pp. 697-706. , http://dx.doi.org/10.1101/gr.111153.110, PMID:21471403
  • Jin, F., Li, Y., Dixon, J.R., Selvaraj, S., Ye, Z., Lee, A.Y., Yen, C.A., Ren, B., A high-resolution map of the three-dimensional chromatin interactome in human cells (2013) Nature, 503, pp. 290-294. , PMID:24141950
  • Lee, B.K., Iyer, V.R., Genome-wide studies of CCCTC-binding factor (CTCF) and cohesin provide insight into chromatin structure and regulation (2012) J Biol Chem, 287, pp. 30906-30913. , http://dx.doi.org/10.1074/jbc.R111.324962, PMID:22952237
  • Li, G., Ruan, X., Auerbach, R.K., Sandhu, K.S., Zheng, M., Wang, P., Poh, H.M., Zhang, J., Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation (2012) Cell, 148, pp. 84-98. , http://dx.doi.org/10.1016/j.cell.2011.12.014, PMID:22265404
  • Sanyal, A., Lajoie, B.R., Jain, G., Dekker, J., The long-range interaction landscape of gene promoters (2012) Nature, 489, pp. 109-113. , http://dx.doi.org/10.1038/nature11279, PMID:22955621
  • Li, W., Notani, D., Ma, Q., Tanasa, B., Nunez, E., Chen, A.Y., Merkurjev, D., Song, X., Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation (2013) Nature, 498, pp. 516-520. , http://dx.doi.org/10.1038/nature12210, PMID:23728302
  • Stadhouders, R., van den Heuvel, A., Kolovos, P., Jorna, R., Leslie, K., Grosveld, F., Soler, E., Transcription regulation by distal enhancers: Who's in the loop? (2012) Transcription, 3, pp. 181-186. , http://dx.doi.org/10.4161/trns.20720, PMID:22771987
  • Tolhuis, B., Palstra, R.J., Splinter, E., Grosveld, F., de Laat, W., Looping and interaction between hypersensitive sites in the active beta-globin locus (2002) Mol Cell, 10, pp. 1453-1465. , http://dx.doi.org/10.1016/S1097-2765(02)00781-5, PMID:12504019
  • Vakoc, C.R., Letting, D.L., Gheldof, N., Sawado, T., Bender, M.A., Groudine, M., Weiss, M.J., Blobel, G.A., Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1 (2005) Mol Cell, 17, pp. 453-462. , http://dx.doi.org/10.1016/j.molcel.2004.12.028, PMID:15694345
  • Vernimmen, D., De Gobbi, M., Sloane-Stanley, J.A., Wood, W.G., Higgs, D.R., Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression (2007) EMBO J, 26, pp. 2041-2051. , http://dx.doi.org/10.1038/sj.emboj.7601654, PMID:17380126
  • Deng, W., Lee, J., Wang, H., Miller, J., Reik, A., Gregory, P.D., Dean, A., Blobel, G.A., Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor (2012) Cell, 149, pp. 1233-1244. , http://dx.doi.org/10.1016/j.cell.2012.03.051, PMID:22682246
  • Kowalczyk, M.S., Hughes, J.R., Garrick, D., Lynch, M.D., Sharpe, J.A., Sloane-Stanley, J.A., McGowan, S.J., Vernimmen, D., Intragenic enhancers act as alternative promoters (2012) Mol Cell, 45, pp. 447-458. , http://dx.doi.org/10.1016/j.molcel.2011.12.021, PMID:22264824
  • Heintzman, N.D., Hon, G.C., Hawkins, R.D., Kheradpour, P., Stark, A., Harp, L.F., Ye, Z., Ching, C.W., Histone modifications at human enhancers reflect global cell-type-specific gene expression (2009) Nature, 459, pp. 108-112. , http://dx.doi.org/10.1038/nature07829, PMID:19295514
  • Tan-Wong, S.M., Zaugg, J.B., Camblong, J., Xu, Z., Zhang, D.W., Mischo, H.E., Ansari, A.Z., Proudfoot, N.J., Gene loops enhance transcriptional directionality (2012) Science, 338, pp. 671-675. , http://dx.doi.org/10.1126/science.1224350, PMID:23019609
  • Cheutin, T., Cavalli, G., Polycomb silencing: From linear chromatin domains to 3D chromosome folding (2014) Curr Opin Genet Dev, 25 C, pp. 30-37. , http://dx.doi.org/10.1016/j.gde.2013.11.016, PMID:24434548
  • Mercer, T.R., Edwards, S.L., Clark, M.B., Neph, S.J., Wang, H., Stergachis, A.B., John, S., Sandhu, K.S., DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements (2013) Nat Genet, 45, pp. 852-859. , http://dx.doi.org/10.1038/ng.2677, PMID:23793028
  • Merkenschlager, M., Odom, D.T., CTCF and cohesin: Linking gene regulatory elements with their targets (2013) Cell, 152, pp. 1285-1297. , http://dx.doi.org/10.1016/j.cell.2013.02.029, PMID:23498937
  • Nogues, G., Kadener, S., Cramer, P., Bentley, D., Kornblihtt, A.R., Transcriptional activators differ in their abilities to control alternative splicing (2002) J Biol Chem, 277, pp. 43110-43114. , http://dx.doi.org/10.1074/jbc.M208418200, PMID:12221105
  • Kagey, M.H., Newman, J.J., Bilodeau, S., Zhan, Y., Orlando, D.A., van Berkum, N.L., Ebmeier, C.C., Levine, S.S., Mediator and cohesin connect gene expression and chromatin architecture (2010) Nature, 467, pp. 430-435. , http://dx.doi.org/10.1038/nature09380, PMID:20720539
  • Ernst, J., Kheradpour, P., Mikkelsen, T.S., Shoresh, N., Ward, L.D., Epstein, C.B., Zhang, X., Coyne, M., Mapping and analysis of chromatin state dynamics in nine human cell types (2011) Nature, 473, pp. 43-49. , http://dx.doi.org/10.1038/nature09906, PMID:21441907
  • Phillips-Cremins, J.E., Sauria, M.E., Sanyal, A., Gerasimova, T.I., Lajoie, B.R., Bell, J.S., Ong, C.T., Sun, Y., Architectural protein subclasses shape 3D organization of genomes during lineage commitment (2013) Cell, 153, pp. 1281-1295. , http://dx.doi.org/10.1016/j.cell.2013.04.053, PMID:23706625

Citas:

---------- APA ----------
Gómez Acuña, L.I. & Kornblihtt, A.R. (2014) . Long range chromatin organization: A new layer in splicing regulation?. Transcription, 5(APR), e28726-1-e28726-5.
http://dx.doi.org/10.4161/trns.28726
---------- CHICAGO ----------
Gómez Acuña, L.I., Kornblihtt, A.R. "Long range chromatin organization: A new layer in splicing regulation?" . Transcription 5, no. APR (2014) : e28726-1-e28726-5.
http://dx.doi.org/10.4161/trns.28726
---------- MLA ----------
Gómez Acuña, L.I., Kornblihtt, A.R. "Long range chromatin organization: A new layer in splicing regulation?" . Transcription, vol. 5, no. APR, 2014, pp. e28726-1-e28726-5.
http://dx.doi.org/10.4161/trns.28726
---------- VANCOUVER ----------
Gómez Acuña, L.I., Kornblihtt, A.R. Long range chromatin organization: A new layer in splicing regulation?. Transcription. 2014;5(APR):e28726-1-e28726-5.
http://dx.doi.org/10.4161/trns.28726