title: Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition.
abstract: Biogenesis of eukaryotic messenger ribonucleoprotein complexes (mRNPs) involves the synthesis, splicing, and 3' processing of pre-mRNA, and the assembly of mature mRNPs for nuclear export. We mapped 23 mRNP biogenesis factors onto the yeast transcriptome, providing 10(4)-10(6) high-confidence RNA interaction sites per factor. The data reveal how mRNP biogenesis factors recognize pre-mRNA elements in vivo. They define conserved interactions between splicing factors and pre-mRNA introns, including the recognition of intron-exon junctions and the branchpoint. They also identify a unified arrangement of 3' processing factors at pre-mRNA polyadenylation (pA) sites in yeast and human, which results from an A-U sequence bias at pA sites. Global data analysis indicates that 3' processing factors have roles in splicing and RNA surveillance, and that they couple mRNP biogenesis events to restrict nuclear export to mature mRNPs.
authors.affiliation: Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany.
authors.forename: Carlo
authors.initials: C
authors.lastname: Baejen
authors.affiliation: Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany.
authors.forename: Phillipp
authors.initials: P
authors.lastname: Torkler
authors.affiliation: Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany.
authors.forename: Saskia
authors.initials: S
authors.lastname: Gressel
authors.affiliation: Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany.
authors.forename: Katharina
authors.initials: K
authors.lastname: Essig
authors.affiliation: Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany. Electronic address: johannes.soeding@mpibpc.mpg.de.
authors.forename: Johannes
authors.initials: J
authors.lastname: Söding
authors.affiliation: Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany; Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany. Electronic address: patrick.cramer@mpibpc.mpg.de.
authors.forename: Patrick
authors.initials: P
authors.lastname: Cramer
mesh_terms: D021581:Active Transport, Cell Nucleus; D020869:Gene Expression Profiling; D006801:Humans; D007438:Introns; D008957:Models, Genetic; D012322:RNA Precursors / Q000737:chemistry / Q000378:metabolism*; D012326:RNA Splicing; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism*; D012261:Ribonucleoproteins / Q000096:biosynthesis*; D012441:Saccharomyces cerevisiae / Q000235:genetics
chemical_list: D012322:RNA Precursors; D012333:RNA, Messenger; D012261:Ribonucleoproteins; C026452:messenger ribonucleoprotein