RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes. 2008

Kira Glover-Cutter, and Soojin Kim, and Joaquin Espinosa, and David L Bentley
Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, UCHSC, MS8101, PO Box 6511, Aurora, Colorado 80045, USA.

We investigated co-transcriptional recruitment of pre-mRNA processing factors to human genes. Capping factors associate with paused RNA polymerase II (pol II) at the 5' ends of quiescent genes. They also track throughout actively transcribed genes and accumulate with paused polymerase in the 3' flanking region. The 3' processing factors cleavage stimulation factor and cleavage polyadenylation specificity factor are maximally recruited 0.5-1.5 kilobases downstream of poly(A) sites where they coincide with capping factors, Spt5, and Ser2-hyperphosphorylated, paused pol II. 3' end processing factors also localize at transcription start sites, and this early recruitment is enhanced after polymerase arrest with the elongation factor DRB. These results suggest that promoters may help specify recruitment of 3' end processing factors. We propose a dual-pausing model wherein elongation arrests near the transcription start site and in the 3' flank to allow co-transcriptional processing by factors recruited to the pol II ternary complex.

UI MeSH Term Description Entries
D007700 Kinetics The rate dynamics in chemical or physical systems.
D011061 Poly A A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties. Adenine Polynucleotides,Polyadenylic Acids,Poly(rA),Polynucleotides, Adenine
D011485 Protein Binding The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments. Plasma Protein Binding Capacity,Binding, Protein
D002460 Cell Line Established cell cultures that have the potential to propagate indefinitely. Cell Lines,Line, Cell,Lines, Cell
D005987 Glyceraldehyde-3-Phosphate Dehydrogenases Enzymes that catalyze the dehydrogenation of GLYCERALDEHYDE 3-PHOSPHATE. Several types of glyceraldehyde-3-phosphate-dehydrogenase exist including phosphorylating and non-phosphorylating varieties and ones that transfer hydrogen to NADP and ones that transfer hydrogen to NAD. GAPD,Glyceraldehyde-3-Phosphate Dehydrogenase,Glyceraldehydephosphate Dehydrogenase,Phosphoglyceraldehyde Dehydrogenase,Triosephosphate Dehydrogenase,Dehydrogenase, Glyceraldehyde-3-Phosphate,Dehydrogenase, Glyceraldehydephosphate,Dehydrogenase, Phosphoglyceraldehyde,Dehydrogenase, Triosephosphate,Dehydrogenases, Glyceraldehyde-3-Phosphate,Glyceraldehyde 3 Phosphate Dehydrogenase
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D001665 Binding Sites The parts of a macromolecule that directly participate in its specific combination with another molecule. Combining Site,Binding Site,Combining Sites,Site, Binding,Site, Combining,Sites, Binding,Sites, Combining
D012315 RNA Caps Nucleic acid structures found on the 5' end of eukaryotic cellular and viral messenger RNA and some heterogeneous nuclear RNAs. These structures, which are positively charged, protect the above specified RNAs at their termini against attack by phosphatases and other nucleases and promote mRNA function at the level of initiation of translation. Analogs of the RNA caps (RNA CAP ANALOGS), which lack the positive charge, inhibit the initiation of protein synthesis. RNA Cap,5' Capped RNA,5' mRNA Cap Structure,Cap, RNA,Caps, RNA,RNA, 5' Capped
D012319 RNA Polymerase II A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC 2.7.7.6. DNA-Dependent RNA Polymerase II,RNA Pol II,RNA Polymerase B,DNA Dependent RNA Polymerase II
D012322 RNA Precursors RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production. Precursor RNA,Primary RNA Transcript,RNA, Messenger, Precursors,RNA, Ribosomal, Precursors,RNA, Small Nuclear, Precursors,RNA, Transfer, Precursors,Pre-mRNA,Pre-rRNA,Pre-snRNA,Pre-tRNA,Primary Transcript, RNA,RNA Precursor,mRNA Precursor,rRNA Precursor,snRNA Precursor,tRNA Precursor,Pre mRNA,Pre rRNA,Pre snRNA,Pre tRNA,Precursor, RNA,Precursor, mRNA,Precursor, rRNA,Precursor, snRNA,Precursor, tRNA,Precursors, RNA,RNA Primary Transcript,RNA Transcript, Primary,RNA, Precursor,Transcript, Primary RNA,Transcript, RNA Primary

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