A Broad Set of Chromatin Factors Influences Splicing.
Several studies propose an influence of chromatin on pre-mRNA splicing, but it is still unclear how widespread and how direct this phenomenon is. We find here that when assembled in vivo, the U2 snRNP co-purifies with a subset of chromatin-proteins, including histones and remodeling complexes like SWI/SNF. Yet, an unbiased RNAi screen revealed that the outcome of splicing is influenced by a much larger variety of chromatin factors not all associating with the spliceosome. The availability of this broad range of chromatin factors impacting splicing further unveiled their very context specific effect, resulting in either inclusion or skipping, depending on the exon under scrutiny. Finally, a direct assessment of the impact of chromatin on splicing using an in vitro co-transcriptional splicing assay with pre-mRNAs transcribed from a nucleosomal template, demonstrated that chromatin impacts nascent pre-mRNP in their competence for splicing. Altogether, our data show that numerous chromatin factors associated or not with the spliceosome can affect the outcome of splicing, possibly as a function of the local chromatin environment that by default interferes with the efficiency of splicing.
Institut Pasteur, Unit of Epigenetic regulation, Paris, France.|CNRS, UMR3738, Paris, France.
Eric
E
Allemand
ICGEB Trieste, Protein Networks unit, Trieste, Italy.
Michael P
MP
Myers
Institute for Integrative Biology of the Cell (I2BC), IBiTecs, CEA, CNRS, Gif-sur-Yvette, France.|Université Paris Saclay, Gif-sur-Yvette, France.
Jose
J
Garcia-Bernardo
Institute for Integrative Biology of the Cell (I2BC), IBiTecs, CEA, CNRS, Gif-sur-Yvette, France.|Université Paris Saclay, Gif-sur-Yvette, France.
Annick
A
Harel-Bellan
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America.
Adrian R
AR
Krainer
Institut Pasteur, Unit of Epigenetic regulation, Paris, France.|CNRS, UMR3738, Paris, France.
Christian
C
Muchardt
Genes Dev. 2011 Feb 15;25(4):373-84
21325135
J Biol Chem. 1992 Mar 5;267(7):4322-6
1531649
Genes Dev. 2005 Mar 1;19(5):536-41
15741318
PLoS Genet. 2012;8(5):e1002717
22615581
Mol Cell. 2007 Nov 30;28(4):665-76
18042460
Cold Spring Harb Perspect Biol. 2011 Jul 01;3(7):null
21441581
Mol Cell. 2014 Oct 23;56(2):298-310
25263594
Science. 2002 Oct 11;298(5592):416-9
12376702
Nucleic Acids Res. 2014 Dec 16;42(22):13662-73
25414343
PLoS One. 2011 Feb 02;6(2):e16727
21311748
Proc Natl Acad Sci U S A. 2011 Feb 1;108(5):2004-9
21245291
Mol Cell. 2012 Mar 9;45(5):656-68
22325991
Nat Struct Mol Biol. 2006 Jan;13(1):22-9
16341228
Cell. 2009 Feb 20;136(4):701-18
19239890
EMBO J. 1995 Jul 17;14(14):3540-51
7543047
Nature. 2002 Dec 12;420(6916):691-5
12478298
Cell. 1997 Jul 11;90(1):145-55
9230310
Nucleic Acids Res. 2013 Mar 1;41(5):3010-21
23361464
EMBO J. 2010 May 19;29(10):1629-36
20407423
BMC Mol Biol. 2011 Nov 02;12:46
22047075
Proc Natl Acad Sci U S A. 1997 Oct 14;94(21):11456-60
9326631
Proc Natl Acad Sci U S A. 2014 Nov 4;111(44):15622-9
25313066
Cell Rep. 2015 Apr 28;11(4):618-29
25892229
EMBO J. 2002 Sep 16;21(18):4978-88
12234937
Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4325-30
19251664
Nat Struct Mol Biol. 2011 Mar;18(3):337-44
21358630
Nat Struct Mol Biol. 2015 May;22(5):370-6
25849144
Nat Genet. 2013 Aug;45(8):852-9
23793028
J Biol Chem. 2006 Jun 16;281(24):16264-71
16603771
Cell Rep. 2015 Feb 24;10 (7):1122-34
25704815
Nat Protoc. 2006;1(2):581-5
17406285
Proc Natl Acad Sci U S A. 2007 Jul 10;104(28):11574-9
17606899
Mol Cell Biol. 2006 Jan;26(1):362-70
16354706
J Biol Chem. 2014 Oct 17;289(42):28956-70
25190814
Nat Rev Mol Cell Biol. 2009 Nov;10(11):741-54
19773805
Mol Cell. 2007 Jun 22;26(6):867-81
17588520
Nature. 2002 Sep 12;419(6903):182-5
12226669
Genes Dev. 2006 May 1;20(9):1100-9
16651655
PLoS Genet. 2015 Mar 31;11(3):e1005074
25825871
Nat Struct Mol Biol. 2007 Jul;14 (7):630-8
17572683
Nucleic Acids Res. 2012 Mar;40(6):2639-52
22110043
Science. 2010 Feb 19;327(5968):996-1000
20133523
Nature. 2011 Nov 3;479(7371):74-9
21964334
Methods Enzymol. 2003;371:499-515
14712724
Nucleic Acids Res. 1999 Jun 1;27(11):2377-86
10325428
PLoS One. 2007 Jun 20;2(6):e538
17579712