title: Splicing of many human genes involves sites embedded within introns.
abstract: The conventional model for splicing involves excision of each intron in one piece; we demonstrate this inaccurately describes splicing in many human genes. First, after switching on transcription of SAMD4A, a gene with a 134 kb-long first intron, splicing joins the 3' end of exon 1 to successive points within intron 1 well before the acceptor site at exon 2 is made. Second, genome-wide analysis shows that >60% of active genes yield products generated by such intermediate intron splicing. These products are present at ∼15% the levels of primary transcripts, are encoded by conserved sequences similar to those found at canonical acceptors, and marked by distinctive structural and epigenetic features. Finally, using targeted genome editing, we demonstrate that inhibiting the formation of these splicing intermediates affects efficient exon-exon splicing. These findings greatly expand the functional and regulatory complexity of the human transcriptome.
authors.affiliation: Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom.
authors.forename: Steven
authors.initials: S
authors.lastname: Kelly
authors.affiliation: Centre for Molecular Medicine, University of Cologne, Cologne D-50931, Germany.
authors.forename: Theodore
authors.initials: T
authors.lastname: Georgomanolis
authors.affiliation: Centre for Molecular Medicine, University of Cologne, Cologne D-50931, Germany.
authors.forename: Anne
authors.initials: A
authors.lastname: Zirkel
authors.affiliation: Institut für Biochemie III, University of Regensburg, Regensburg D-93053, Germany.
authors.forename: Sarah
authors.initials: S
authors.lastname: Diermeier
authors.affiliation: Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom.
authors.forename: Dawn
authors.initials: D
authors.lastname: O'Reilly
authors.affiliation: Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom.
authors.forename: Shona
authors.initials: S
authors.lastname: Murphy
authors.affiliation: Institut für Biochemie III, University of Regensburg, Regensburg D-93053, Germany.
authors.forename: Gernot
authors.initials: G
authors.lastname: Längst
authors.affiliation: Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom.
authors.forename: Peter R
authors.initials: PR
authors.lastname: Cook
authors.affiliation: Centre for Molecular Medicine, University of Cologne, Cologne D-50931, Germany argyris.papantonis@uni-koeln.de.
authors.forename: Argyris
authors.initials: A
authors.lastname: Papantonis
mesh_terms: D002478:Cells, Cultured; D005091:Exons; D061307:Human Umbilical Vein Endothelial Cells / Q000378:metabolism; D006801:Humans; D007438:Introns; D022821:RNA Splice Sites; D012326:RNA Splicing; D012097:Repressor Proteins / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D022821:RNA Splice Sites; D012097:Repressor Proteins; C507993:SAMD4A protein, human