Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse.

Spliceosome assembly and/or splicing of a nascent transcript may be crucial for proper isoform expression and gene regulation in higher eukaryotes. We recently showed that cotranscriptional splicing occurs efficiently in Drosophila, but there are not comparable genome-wide nascent splicing data from mammals. To provide this comparison, we analyze a recently generated, high-throughput sequencing data set of mouse liver nascent RNA, originally studied for circadian transcriptional regulation. Cotranscriptional splicing is approximately twofold less efficient in mouse liver than in Drosophila, i.e., nascent intron levels relative to exon levels are ∼0.55 in mouse versus 0.25 in the fly. An additional difference between species is that only mouse cotranscriptional splicing is optimal when 5'-exon length is between 50 and 500 bp, and intron length does not correlate with splicing efficiency, consistent with exon definition. A similar analysis of intron and exon length dependence in the fly is more consistent with intron definition. Contrasted with these differences are many similarities between the two systems: Alternatively annotated introns are less efficiently spliced cotranscriptionally than constitutive introns, and introns of single-intron genes are less efficiently spliced than introns from multi-intron genes. The most striking common feature is intron position: Cotranscriptional splicing is much more efficient when introns are far from the 3' ends of their genes. Additionally, absolute gene length correlates positively with cotranscriptional splicing efficiency independently of intron location and position, in flies as well as in mice. The gene length and distance effects indicate that more "nascent time" gives rise to greater cotranscriptional splicing efficiency in both systems.

[1]  M. Rosbash,et al.  Nascent-Seq reveals novel features of mouse circadian transcriptional regulation , 2012, eLife.

[2]  Gautier Koscielny,et al.  Ensembl 2012 , 2011, Nucleic Acids Res..

[3]  C. Schlötterer,et al.  The Genomic Signature of Splicing-Coupled Selection Differs between Long and Short Introns , 2011, Molecular biology and evolution.

[4]  D. Burstein,et al.  Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons. , 2012, Genome research.

[5]  M. Rosbash,et al.  Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila. , 2011, Genes & development.

[6]  Sanjay Tyagi,et al.  Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing , 2011, Cell.

[7]  Hyunmin Kim,et al.  Pre-mRNA splicing is a determinant of histone H3K36 methylation , 2011, Proceedings of the National Academy of Sciences.

[8]  Nicole I Bieberstein,et al.  Pause locally, splice globally. , 2011, Trends in cell biology.

[9]  Arun K. Ramani,et al.  Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation. , 2011, Genome research.

[10]  J. Weissman,et al.  Nascent transcript sequencing visualizes transcription at nucleotide resolution , 2011, Nature.

[11]  X. Darzacq,et al.  The In Vivo Kinetics of RNA Polymerase II Elongation during Co-Transcriptional Splicing , 2011, PLoS biology.

[12]  S. Preibisch,et al.  Global analysis of nascent RNA reveals transcriptional pausing in terminal exons. , 2010, Molecular cell.

[13]  Ross D. Alexander,et al.  Splicing-Dependent RNA Polymerase Pausing in Yeast , 2010, Molecular cell.

[14]  A. Kornblihtt,et al.  First come, first served revisited: factors affecting the same alternative splicing event have different effects on the relative rates of intron removal. , 2010, RNA.

[15]  B. Harr,et al.  Genome‐wide analysis of alternative splicing evolution among Mus subspecies , 2010, Molecular ecology.

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

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

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

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

[20]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

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

[22]  Tatiana A. Tatusova,et al.  NCBI Reference Sequences: current status, policy and new initiatives , 2008, Nucleic Acids Res..

[23]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[24]  Eric T. Wang,et al.  Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.

[25]  S. Véronneau,et al.  Deletion of Many Yeast Introns Reveals a Minority of Genes That Require Splicing for Function Strains and Plasmids Direct Introns Displacement Strategy Growth Assays Fitness Test , 2022 .

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

[27]  Ed Hurt,et al.  Exporting RNA from the nucleus to the cytoplasm , 2007, Nature Reviews Molecular Cell Biology.

[28]  G. Ast,et al.  Different levels of alternative splicing among eukaryotes , 2006, Nucleic acids research.

[29]  R. Reed,et al.  Human mRNA Export Machinery Recruited to the 5′ End of mRNA , 2006, Cell.

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

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

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

[33]  Daniel F Tardiff,et al.  In vivo commitment to yeast cotranscriptional splicing is sensitive to transcription elongation mutants. , 2006, Genes & development.

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

[35]  F. Rigo,et al.  The RNA tether from the poly(A) signal to the polymerase mediates coupling of transcription to cleavage and polyadenylation. , 2005, Molecular cell.

[36]  P. Baldi,et al.  The architecture of pre-mRNAs affects mechanisms of splice-site pairing. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[37]  K. Neugebauer,et al.  Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex. , 2005, Molecular cell.

[38]  S. Lacadie,et al.  Cotranscriptional spliceosome assembly dynamics and the role of U1 snRNA:5'ss base pairing in yeast. , 2005, Molecular cell.

[39]  Marc A. Schaub,et al.  Subdivision of Large Introns in Drosophila by Recursive Splicing at Nonexonic Elements , 2005, Genetics.

[40]  Dawood B. Dudekula,et al.  Genome-wide assembly and analysis of alternative transcripts in mouse. , 2005, Genome research.

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

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

[43]  Hiroshi Kimura,et al.  U1 snRNA associates with TFIIH and regulates transcriptional initiation , 2002, Nature Structural Biology.

[44]  C. Guthrie,et al.  Expression of the essential mRNA export factor Yra1p is autoregulated by a splicing-dependent mechanism. , 2002, RNA.

[45]  F. Robert,et al.  A Human RNA Polymerase II-containing Complex Associated with Factors Necessary for Spliceosome Assembly* , 2002, The Journal of Biological Chemistry.

[46]  Mouse Genome Sequencing Consortium.  Initial sequencing and comparative analysis of the mouse genome , 2002, Nature.

[47]  A. Kornblihtt,et al.  Antagonistic effects of T‐Ag and VP16 reveal a role for RNA pol II elongation on alternative splicing , 2001, The EMBO journal.

[48]  J. Alwine,et al.  Utilization of Splicing Elements and Polyadenylation Signal Elements in the Coupling of Polyadenylation and Last-Intron Removal , 1999, Molecular and Cellular Biology.

[49]  F. Grosveld,et al.  Inefficient processing impairs release of RNA from the site of transcription , 1999, The EMBO journal.

[50]  J. Manley,et al.  Phosphorylated RNA polymerase II stimulates pre-mRNA splicing. , 1999, Genes & development.

[51]  N. Proudfoot,et al.  Terminal exon definition occurs cotranscriptionally and promotes termination of RNA polymerase II. , 1999, Molecular cell.

[52]  I. Stagljar,et al.  A Novel SR-Related Protein Specifically Interacts with the Carboxy-Terminal Domain (CTD) of RNA Polymerase through a Conserved Interaction Domain , 1997, Biological chemistry.

[53]  I. Stagljar,et al.  A serine/arginine-rich nuclear matrix cyclophilin interacts with the C-terminal domain of RNA polymerase II. , 1997, Nucleic acids research.

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

[55]  D. Bregman,et al.  Splicing Factors Associate with Hyperphosphorylated RNA Polymerase II in the Absence of Pre-mRNA , 1997, The Journal of cell biology.

[56]  S. Berget,et al.  Architectural limits on split genes. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[57]  C. McGuigan,et al.  A nuclear cap-binding complex facilitates association of U1 snRNP with the cap-proximal 5' splice site. , 1996, Genes & development.

[58]  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.

[59]  R. Iggo,et al.  Autoregulation of expression of the yeast Dbp2p ‘DEAD‐box’ protein is mediated by sequences in the conserved DBP2 intron. , 1995, The EMBO journal.

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

[61]  E. Kiseleva,et al.  Assembly and disassembly of spliceosomes along a specific pre‐messenger RNP fiber. , 1994, The EMBO journal.

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

[63]  S. Berget,et al.  Intron definition in splicing of small Drosophila introns , 1994, Molecular and cellular biology.

[64]  L. Wieslander,et al.  Splicing of Balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription , 1994, Cell.

[65]  Michael R. Green,et al.  Localization of pre-mRNA splicing in mammalian nuclei , 1994, Nature.

[66]  L. Chasin,et al.  Order of intron removal during splicing of endogenous adenine phosphoribosyltransferase and dihydrofolate reductase pre-mRNA , 1993, Molecular and cellular biology.

[67]  Stephen M. Mount,et al.  Splicing signals in Drosophila: intron size, information content, and consensus sequences. , 1992, Nucleic acids research.

[68]  S. Berget,et al.  Mutation of the AAUAAA polyadenylation signal depresses in vitro splicing of proximal but not distal introns. , 1991, Genes & development.

[69]  P. Grabowski,et al.  Control of alternative splicing by the differential binding of U1 small nuclear ribonucleoprotein particle. , 1991, Science.

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

[71]  S. Berget,et al.  Exon definition may facilitate splice site selection in RNAs with multiple exons. , 1990, Molecular and cellular biology.

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

[73]  M. Dabeva,et al.  Autogenous regulation of splicing of the transcript of a yeast ribosomal protein gene. , 1986, Proceedings of the National Academy of Sciences of the United States of America.