Chromatin density and splicing destiny: on the cross‐talk between chromatin structure and splicing

How are short exonic sequences recognized within the vast intronic oceans in which they reside? Despite decades of research, this remains one of the most fundamental, yet enigmatic, questions in the field of pre‐mRNA splicing research. For many years, studies aiming to shed light on this process were focused at the RNA level, characterizing the manner by which splicing factors and auxiliary proteins interact with splicing signals, thereby enabling, facilitating and regulating splicing. However, we increasingly understand that splicing is not an isolated process; rather it occurs co‐transcriptionally and is presumably also regulated by transcription‐related processes. In fact, studies by our group and others over the past year suggest that DNA structure in terms of nucleosome positioning and specific histone modifications, which have a well established role in transcription, may also have a role in splicing. In this review we discuss evidence for the coupling between transcription and splicing, focusing on recent findings suggesting a link between chromatin structure and splicing, and highlighting challenges this emerging field is facing.

[1]  M. Carmo-Fonseca,et al.  The CTD role in cotranscriptional RNA processing and surveillance , 2008, FEBS letters.

[2]  M. Alló,et al.  Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing , 2009, Proceedings of the National Academy of Sciences.

[3]  Tracy L. Johnson,et al.  Acetylation by the Transcriptional Coactivator Gcn5 Plays a Novel Role in Co-Transcriptional Spliceosome Assembly , 2009, PLoS genetics.

[4]  Michael R. Green,et al.  Human β-globin pre-mRNA synthesized in vitro is accurately spliced in xenopus oocyte nuclei , 1983, Cell.

[5]  U. Schibler,et al.  Physical isolation of nascent RNA chains transcribed by RNA polymerase II: evidence for cotranscriptional splicing , 1994, Molecular and cellular biology.

[6]  D. Bentley,et al.  RNA Polymerase II Carboxy-Terminal Domain Phosphorylation Is Required for Cotranscriptional Pre-mRNA Splicing and 3′-End Formation , 2004, Molecular and Cellular Biology.

[7]  R. Padgett,et al.  Rates of in situ transcription and splicing in large human genes , 2009, Nature Structural &Molecular Biology.

[8]  Steven Chu,et al.  DNA methylation increases nucleosome compaction and rigidity. , 2010, Journal of the American Chemical Society.

[9]  G. Ast,et al.  SR proteins: a foot on the exon before the transition from intron to exon definition. , 2007, Trends in genetics : TIG.

[10]  H. Rye,et al.  GroEL stimulates protein folding through forced unfolding , 2008, Nature Structural &Molecular Biology.

[11]  T. Hashimshony,et al.  The role of DNA methylation in setting up chromatin structure during development , 2003, Nature Genetics.

[12]  M. Hild,et al.  Localized H3K36 methylation states define histone H4K16 acetylation during transcriptional elongation in Drosophila , 2007, The EMBO journal.

[13]  T. Hashimshony,et al.  DNA methylation models histone acetylation , 1998, Nature.

[14]  Chromatin Organization , 2011, Cell.

[15]  Jerry L. Workman,et al.  ATP-Dependent Chromatin-Remodeling Complexes , 2000, Molecular and Cellular Biology.

[16]  Irene K. Moore,et al.  A genomic code for nucleosome positioning , 2006, Nature.

[17]  A. Kornblihtt.  Chromatin, transcript elongation and alternative splicing , 2006, Nature Structural &Molecular Biology.

[18]  K. J. Howe.  RNA polymerase II conducts a symphony of pre-mRNA processing activities. , 2002, Biochimica et biophysica acta.

[19]  N. Proudfoot,et al.  Exon tethering in transcription by RNA polymerase II. , 2006, Molecular cell.

[20]  Lee E. Edsall,et al.  Human DNA methylomes at base resolution show widespread epigenomic differences , 2009, Nature.

[21]  B. Graveley.  Alternative splicing: increasing diversity in the proteomic world. , 2001, Trends in genetics : TIG.

[22]  J. Ahringer,et al.  Differential chromatin marking of introns and expressed exons by H3K36me3 , 2008, Nature Genetics.

[23]  Timothy R. Hughes,et al.  G+C content dominates intrinsic nucleosome occupancy , 2009, BMC Bioinformatics.

[24]  B. Sarg,et al.  Histone H4-Lysine 20 Monomethylation Is Increased in Promoter and Coding Regions of Active Genes and Correlates with Hyperacetylation* , 2005, Journal of Biological Chemistry.

[25]  Irene K. Moore,et al.  A genomic code for nucleosome , 2006 .

[26]  M. Vigneron,et al.  A 10 residue motif at the C‐terminus of the RNA pol II CTD is required for transcription, splicing and 3′ end processing , 2003, The EMBO journal.

[27]  A. Yuryev,et al.  The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[28]  K. J. Hertel,et al.  Linking Splicing to Pol II Transcription Stabilizes Pre-mRNAs and Influences Splicing Patterns , 2006, PLoS biology.

[29]  A. Kornblihtt,et al.  A slow RNA polymerase II affects alternative splicing in vivo. , 2003, Molecular cell.

[30]  C. Allis,et al.  DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA , 2007, Nature.

[31]  J. Valcárcel,et al.  Alternative pre-mRNA splicing: the logic of combinatorial control. , 2000, Trends in biochemical sciences.

[32]  L. Mahadevan,et al.  Dynamic histone H3 methylation during gene induction: HYPB/Setd2 mediates all H3K36 trimethylation , 2007, The EMBO journal.

[33]  A. Furger,et al.  Integrating mRNA Processing with Transcription , 2002, Cell.

[34]  R. Loomis,et al.  Chromatin binding of SRp20 and ASF/SF2 and dissociation from mitotic chromosomes is modulated by histone H3 serine 10 phosphorylation. , 2009, Molecular cell.

[35]  Dustin E. Schones,et al.  Dynamic Regulation of Nucleosome Positioning in the Human Genome , 2008, Cell.

[36]  Loni Pickle,et al.  A human splicing factor, SKIP, associates with P-TEFb and enhances transcription elongation by HIV-1 Tat. , 2005, Genes & development.

[37]  En Li,et al.  Suv 39 h-Mediated Histone H 3 Lysine 9 Methylation Directs DNA Methylation to Major Satellite Repeats at Pericentric Heterochromatin , 2003 .

[38]  Michael Q. Zhang,et al.  High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing , 2009 .

[39]  G. Ast,et al.  Chromatin organization marks exon-intron structure , 2009, Nature Structural &Molecular Biology.

[40]  Y. Osheim,et al.  Splice site selection, rate of splicing, and alternative splicing on nascent transcripts. , 1988, Genes & development.

[41]  J M Gale,et al.  UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[42]  A. Krainer,et al.  SR proteins function in coupling RNAP II transcription to pre-mRNA splicing. , 2007, Molecular cell.

[43]  Stefano Piccolo,et al.  MicroRNA control of signal transduction , 2010, Nature Reviews Molecular Cell Biology.

[44]  M. Wickens,et al.  The C-terminal domain of RNA polymerase II couples mRNA processing to transcription , 1997, Nature.

[45]  Xiang-Dong Fu,et al.  The splicing factor SC35 has an active role in transcriptional elongation , 2008, Nature Structural &Molecular Biology.

[46]  Gil Ast,et al.  How did alternative splicing evolve? , 2004, Nature Reviews Genetics.

[47]  J. Mattick,et al.  Nucleosomes are preferentially positioned at exons in somatic and sperm cells , 2009, Cell cycle.

[48]  A. Kornblihtt,et al.  Multiple links between transcription and splicing. , 2004, RNA.

[49]  S. Berget.  Exon Recognition in Vertebrate Splicing (*) , 1995, The Journal of Biological Chemistry.

[50]  Steven Henikoff,et al.  Histone variants — ancient wrap artists of the epigenome , 2010, Nature Reviews Molecular Cell Biology.

[51]  Kristi L Fox-Walsh,et al.  Splice-site pairing is an intrinsically high fidelity process , 2009, Proceedings of the National Academy of Sciences.

[52]  Ian M. Fingerman,et al.  Histone H3 K36 methylation is mediated by a trans-histone methylation pathway involving an interaction between Set2 and histone H4. , 2008, Genes & development.

[53]  J. Cáceres,et al.  The SR protein family of splicing factors: master regulators of gene expression. , 2009, The Biochemical journal.

[54]  C. Muchardt,et al.  Splicing, transcription, and chromatin: a ménage à trois. , 2008, Current opinion in genetics & development.

[55]  A. Kornblihtt,et al.  Transcriptional Activators Differ in Their Abilities to Control Alternative Splicing* , 2002, The Journal of Biological Chemistry.

[56]  Christopher R. Vakoc,et al.  Profile of Histone Lysine Methylation across Transcribed Mammalian Chromatin , 2006, Molecular and Cellular Biology.

[57]  Bert W O'Malley,et al.  Coordinate Regulation of Transcription and Splicing by Steroid Receptor Coregulators , 2002, Science.

[58]  Peter A. Jones,et al.  The Epigenomics of Cancer , 2007, Cell.

[59]  H. Cedar,et al.  Linking DNA methylation and histone modification: patterns and paradigms , 2009, Nature Reviews Genetics.

[60]  E. Segal,et al.  What controls nucleosome positions? , 2009, Trends in genetics : TIG.

[61]  Nevan J Krogan,et al.  A single SR-like protein, Npl3, promotes pre-mRNA splicing in budding yeast. , 2008, Molecular cell.

[62]  D. Bentley,et al.  "Cotranscriptionality": the transcription elongation complex as a nexus for nuclear transactions. , 2009, Molecular cell.

[63]  Christoforos Nikolaou,et al.  Nucleosome positioning as a determinant of exon recognition , 2009, Nature Structural &Molecular Biology.

[64]  Carlos Bustamante,et al.  Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II , 2009, Science.

[65]  M. Garcia-Blanco,et al.  The Transcription Elongation Factor CA150 Interacts with RNA Polymerase II and the Pre-mRNA Splicing Factor SF1 , 2001, Molecular and Cellular Biology.

[66]  Guey-Shin Wang,et al.  Splicing in disease: disruption of the splicing code and the decoding machinery , 2007, Nature Reviews Genetics.

[67]  R. Kornberg,et al.  Twenty-Five Years of the Nucleosome, Fundamental Particle of the Eukaryote Chromosome , 1999, Cell.

[68]  Wei Chen,et al.  The organization of nucleosomes around splice sites , 2010, Nucleic acids research.

[69]  Paul Tempst,et al.  Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing. , 2007, Molecular cell.

[70]  I. Albert,et al.  Nucleosome positions predicted through comparative genomics , 2006, Nature Genetics.

[71]  Jan Komorowski,et al.  Nucleosomes are well positioned in exons and carry characteristic histone modifications. , 2009, Genome research.

[72]  D. Crothers,et al.  Bending and flexibility of methylated and unmethylated EcoRI DNA. , 2002, Journal of molecular biology.

[73]  K. Neugebauer,et al.  On the importance of being co-transcriptional , 2002, Journal of Cell Science.

[74]  M. Yaniv,et al.  The human SWI/SNF subunit Brm is a regulator of alternative splicing , 2006, Nature Structural &Molecular Biology.

[75]  G. C. Roberts,et al.  Co-transcriptional commitment to alternative splice site selection. , 1998, Nucleic acids research.

[76]  Dustin E. Schones,et al.  High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.

[77]  D. Komura,et al.  A wave of nascent transcription on activated human genes , 2009, Proceedings of the National Academy of Sciences.

[78]  T. Nilsen,et al.  Expansion of the eukaryotic proteome by alternative splicing , 2010, Nature.

[79]  C. Thummel,et al.  Splicing precedes polyadenylation during Drosophila E74A transcription , 1990, Molecular and cellular biology.

[80]  Bing Ren,et al.  Discovery and Annotation of Functional Chromatin Signatures in the Human Genome , 2009, PLoS Comput. Biol..

[81]  E. Lander,et al.  The Mammalian Epigenome , 2007, Cell.

[82]  Sumio Sugano,et al.  Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites , 2009, Science.

[83]  T. Kouzarides.  Chromatin Modifications and Their Function , 2007, Cell.

[84]  A. Kornblihtt,et al.  RNA polymerase II C-terminal domain mediates regulation of alternative splicing by SRp20 , 2006, Nature Structural &Molecular Biology.

[85]  L. Wieslander,et al.  The intranuclear site of excision of each intron in Balbiani ring 3 pre-mRNA is influenced by the time remaining to transcription termination and different excision efficiencies for the various introns. , 1996, RNA.

[86]  D. Black.  Mechanisms of alternative pre-messenger RNA splicing. , 2003, Annual review of biochemistry.

[87]  Noah Spies,et al.  Biased chromatin signatures around polyadenylation sites and exons. , 2009, Molecular cell.

[88]  K. Neugebauer,et al.  Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells , 2006, Nature Structural &Molecular Biology.

[89]  Schraga Schwartz,et al.  Alu Exonization Events Reveal Features Required for Precise Recognition of Exons by the Splicing Machinery , 2009, PLoS Comput. Biol..

[90]  Maho Takahashi,et al.  Coactivator-associated Arginine Methyltransferase 1, CARM1, Affects Pre-mRNA Splicing in an Isoform-specific Manner*♦ , 2005, Journal of Biological Chemistry.

[91]  C. Burge,et al.  A computational analysis of sequence features involved in recognition of short introns , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[92]  D. Black,et al.  Co-transcriptional splicing of constitutive and alternative exons. , 2009, RNA.

[93]  R. Reed,et al.  Functional coupling of RNAP II transcription to spliceosome assembly. , 2006, Genes & development.

[94]  J. Kjems,et al.  A 5' splice site enhances the recruitment of basal transcription initiation factors in vivo. , 2008, Molecules and Cells.

[95]  B. Cairns.  The logic of chromatin architecture and remodelling at promoters , 2009, Nature.

[96]  Rainer Machné,et al.  Evolutionary footprints of nucleosome positions in yeast. , 2008, Trends in genetics : TIG.

[97]  B. Blencowe,et al.  Regulation of Alternative Splicing by Histone Modifications , 2010, Science.

[98]  B. Thrall,et al.  Nucleosome structure modulates benzo[a]pyrenediol epoxide adduct formation. , 1994, Biochemistry.

[99]  Edward N Trifonov,et al.  Gene splice sites correlate with nucleosome positions. , 2004, Gene.

[100]  Daniel F Tardiff,et al.  A genome-wide analysis indicates that yeast pre-mRNA splicing is predominantly posttranscriptional. , 2006, Molecular cell.

[101]  M. Sundaralingam,et al.  Nine polymorphic crystal structures of d(CCGGGCCCGG), d(CCGGGCCm5CGG), d(Cm5CGGGCCm5CGG) and d(CCGGGCC(Br)5CGG) in three different conformations: effects of spermine binding and methylation on the bending and condensation of A-DNA. , 1997, Journal of molecular biology.

[102]  H. Klamut,et al.  The human dystrophin gene requires 16 hours to be transcribed and is cotranscriptionally spliced , 1995, Nature Genetics.

[103]  Irene K. Moore,et al.  The DNA-encoded nucleosome organization of a eukaryotic genome , 2009, Nature.

[104]  Manuel de la Mata,et al.  Control of alternative splicing through siRNA-mediated transcriptional gene silencing , 2009, Nature Structural &Molecular Biology.