Home LiteratureArticle Details
PMID: 15192704 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, P.H.S.

Biochemical analysis of TREX complex recruitment to intronless and intron-containing yeast genes.

The EMBO journal ·Vol. 23 ·No. 13 ·2004-07-07 ·Pages 2620-31

Abruzzi KC, Lacadie S, Rosbash M

Abstract

The TREX complex is involved in both transcription elongation and mRNA export and is recruited to nascent transcription complexes. We have examined Yra1p, Sub2p and Hpr1p recruitment to nine genes of varying lengths and transcription frequencies. All three proteins increase from the 5' to the 3' ends of the four intronless genes examined. A modified chromatin immunoprecipitation assay that includes an RNase step indicates that Sub2p is bound to nascent RNA, Yra1p is associated with both RNA and DNA, and Hpr1p is associated with DNA. Although Hpr1p is recruited similarly to both intronless and intron-containing genes, low Yra1p and Sub2p levels are present on a subset of intron-containing genes. The residual Yra1p and Sub2p recruitment is less RNA-associated, and this correlates with high levels of U1 SnRNP on these genes. These experiments support a model in which TREX is recruited via the transcription machinery and then Yra1p and Sub2p are transferred to the nascent RNA. On some intron-containing genes, retention and/or transfer of Yra1p and Sub2p to nascent RNA are inhibited.

MeSH Terms
Adenosine Triphosphatases/metabolism Chromatin Immunoprecipitation DNA-Binding Proteins/metabolism Fungal Proteins/metabolism Gene Expression Regulation, Fungal Genes, Fungal Introns Models, Biological Nuclear Proteins/metabolism RNA Helicases/metabolism RNA Splicing RNA, Fungal/metabolism RNA, Messenger/metabolism RNA-Binding Proteins/metabolism Saccharomyces cerevisiae/physiology Saccharomyces cerevisiae Proteins/metabolism Transcription, Genetic
Chemicals
DNA-Binding Proteins Fungal Proteins HPR1 protein, S cerevisiae Nuclear Proteins RNA, Fungal RNA, Messenger RNA-Binding Proteins Saccharomyces cerevisiae Proteins YRA1 protein, S cerevisiae Adenosine Triphosphatases RNA-dependent ATPase RNA Helicases
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Abruzzi Katharine Compton
Department of Biology, Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02454, USA.
Lacadie Scott
Rosbash Michael
References (50)
50 references, click to expand
  1. Interruption of coding sequences by heterologous introns can enhance the functional expression of recombinant genes.
    Gene Ther. 2001 Apr;8(8):649-53 PMID: 11320412
  2. The yeast hnRNP-Like proteins Yra1p and Yra2p participate in mRNA export through interaction with Mex67p.
    Mol Cell Biol. 2001 Jul;21(13):4219-32 PMID: 11390651
  3. Messenger RNAs are recruited for nuclear export during transcription.
    Genes Dev. 2001 Jul 15;15(14):1771-82 PMID: 11459827
  4. High-copy-number expression of Sub2p, a member of the RNA helicase superfamily, suppresses hpr1-mediated genomic instability.
    Mol Cell Biol. 2001 Aug;21(16):5459-70 PMID: 11463828
  5. Primer3 on the WWW for general users and for biologist programmers.
    Methods Mol Biol. 2000;132:365-86 PMID: 10547847
  6. Yra1p, a conserved nuclear RNA-binding protein, interacts directly with Mex67p and is required for mRNA export.
    EMBO J. 2000 Feb 1;19(3):410-20 PMID: 10722314
  7. A dual role for BBP/ScSF1 in nuclear pre-mRNA retention and splicing.
    EMBO J. 2000 Apr 17;19(8):1873-86 PMID: 10775271
  8. REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export.
    RNA. 2000 Apr;6(4):638-50 PMID: 10786854
  9. Binding of the Mex67p/Mtr2p heterodimer to FXFG, GLFG, and FG repeat nucleoporins is essential for nuclear mRNA export.
    J Cell Biol. 2000 Aug 21;150(4):695-706 PMID: 10952996
  10. The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans.
    Nature. 2000 Sep 21;407(6802):401-5 PMID: 11014198
  11. Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription.
    Genes Dev. 2000 Oct 1;14(19):2452-60 PMID: 11018013
  12. A protein complex containing Tho2, Hpr1, Mft1 and a novel protein, Thp2, connects transcription elongation with mitotic recombination in Saccharomyces cerevisiae.
    EMBO J. 2000 Nov 1;19(21):5824-34 PMID: 11060033
  13. The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions.
    EMBO J. 2000 Dec 15;19(24):6860-9 PMID: 11118221
  14. Identification and characterization of yUAP/Sub2p, a yeast homolog of the essential human pre-mRNA splicing factor hUAP56.
    Genes Dev. 2001 Jan 1;15(1):30-5 PMID: 11156602
  15. Multiple roles for the yeast SUB2/yUAP56 gene in splicing.
    Genes Dev. 2001 Jan 1;15(1):36-41 PMID: 11156603
  16. Deletion of MUD2, the yeast homolog of U2AF65, can bypass the requirement for sub2, an essential spliceosomal ATPase.
    Genes Dev. 2001 Jan 1;15(1):42-9 PMID: 11156604
  17. REF proteins mediate the export of spliced and unspliced mRNAs from the nucleus.
    Proc Natl Acad Sci U S A. 2001 Jan 30;98(3):1030-5 PMID: 11158589
  18. Intron status and 3'-end formation control cotranscriptional export of mRNA.
    Genes Dev. 2002 Nov 1;16(21):2761-6 PMID: 12414728
  19. 5' exon interactions within the human spliceosome establish a framework for exon junction complex structure and assembly.
    Genes Dev. 2002 Nov 1;16(21):2778-91 PMID: 12414731
  20. Promoter proximal splice sites enhance transcription.
    Genes Dev. 2002 Nov 1;16(21):2792-9 PMID: 12414732
  21. Stable mRNP formation and export require cotranscriptional recruitment of the mRNA export factors Yra1p and Sub2p by Hpr1p.
    Mol Cell Biol. 2002 Dec;22(23):8241-53 PMID: 12417727
  22. Interactions between mRNA export commitment, 3'-end quality control, and nuclear degradation.
    Mol Cell Biol. 2002 Dec;22(23):8254-66 PMID: 12417728
  23. Protein composition of human prespliceosomes isolated by a tobramycin affinity-selection method.
    Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16719-24 PMID: 12477934
  24. Chromatin immunoprecipitation: a tool for studying histone acetylation and transcription factor binding.
    Methods. 2003 Sep;31(1):67-75 PMID: 12893175
  25. Cotranscriptional recruitment of the U1 snRNP to intron-containing genes in yeast.
    Mol Cell Biol. 2003 Aug;23(16):5768-79 PMID: 12897147
  26. Rds3p is required for stable U2 snRNP recruitment to the splicing apparatus.
    Mol Cell Biol. 2003 Oct;23(20):7339-49 PMID: 14517302
  27. Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination.
    Mol Cell. 2003 Sep;12(3):711-21 PMID: 14527416
  28. Nuclear retention of unspliced mRNAs in yeast is mediated by perinuclear Mlp1.
    Cell. 2004 Jan 9;116(1):63-73 PMID: 14718167
  29. Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3' end processing.
    Mol Cell. 2004 Jan 16;13(1):67-76 PMID: 14731395
  30. Transitions in RNA polymerase II elongation complexes at the 3' ends of genes.
    EMBO J. 2004 Jan 28;23(2):354-64 PMID: 14739930
  31. Introns increase transcriptional efficiency in transgenic mice.
    Proc Natl Acad Sci U S A. 1988 Feb;85(3):836-40 PMID: 3422466
  32. Some cis- and trans-acting mutants for splicing target pre-mRNA to the cytoplasm.
    Cell. 1989 May 19;57(4):573-83 PMID: 2655924
  33. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae.
    Genetics. 1989 May;122(1):19-27 PMID: 2659436
  34. Inhibition of in vivo and in vitro transcription by monoclonal antibodies prepared against wheat germ RNA polymerase II that react with the heptapeptide repeat of eukaryotic RNA polymerase II.
    J Biol Chem. 1989 Jul 5;264(19):11511-20 PMID: 2472398
  35. In vitro polyadenylation is stimulated by the presence of an upstream intron.
    Genes Dev. 1990 Sep;4(9):1552-9 PMID: 1701407
  36. Heterologous introns can enhance expression of transgenes in mice.
    Proc Natl Acad Sci U S A. 1991 Jan 15;88(2):478-82 PMID: 1988947
  37. Proteins binding to 5' untranslated region sites: a general mechanism for translational regulation of mRNAs in human and yeast cells.
    Mol Cell Biol. 1994 Sep;14(9):5898-909 PMID: 8065323
  38. Mex67p, a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores.
    EMBO J. 1997 Jun 2;16(11):3256-71 PMID: 9214641
  39. Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex.
    Nat Genet. 1998 Sep;20(1):46-50 PMID: 9731529
  40. Dissecting the regulatory circuitry of a eukaryotic genome.
    Cell. 1998 Nov 25;95(5):717-28 PMID: 9845373
  41. Terminal exon definition occurs cotranscriptionally and promotes termination of RNA polymerase II.
    Mol Cell. 1999 Mar;3(3):371-8 PMID: 10198639
  42. The Saccharomyces cerevisiae hyperrecombination mutant hpr1Delta is synthetically lethal with two conditional alleles of the acetyl coenzyme A carboxylase gene and causes a defect in nuclear export of polyadenylated RNA.
    Mol Cell Biol. 1999 May;19(5):3415-22 PMID: 10207065
  43. Pre-mRNA splicing and mRNA export linked by direct interactions between UAP56 and Aly.
    Nature. 2001 Oct 11;413(6856):644-7 PMID: 11675789
  44. Splicing factor Sub2p is required for nuclear mRNA export through its interaction with Yra1p.
    Nature. 2001 Oct 11;413(6856):648-52 PMID: 11675790
  45. Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis.
    RNA. 2002 Apr;8(4):426-39 PMID: 11991638
  46. HEL/UAP56 binds cotranscriptionally to the Balbiani ring pre-mRNA in an intron-independent manner and accompanies the BR mRNP to the nuclear pore.
    Curr Biol. 2002 May 14;12(10):859-62 PMID: 12015125
  47. TREX is a conserved complex coupling transcription with messenger RNA export.
    Nature. 2002 May 16;417(6886):304-8 PMID: 11979277
  48. Functional interaction of yeast pre-mRNA 3' end processing factors with RNA polymerase II.
    Mol Cell. 2002 May;9(5):1101-11 PMID: 12049745
  49. The yeast THO complex and mRNA export factors link RNA metabolism with transcription and genome instability.
    EMBO J. 2002 Jul 1;21(13):3526-35 PMID: 12093753
  50. Large-scale proteomic analysis of the human spliceosome.
    Genome Res. 2002 Aug;12(8):1231-45 PMID: 12176931
Article Info
Journal
The EMBO journal
Abbr.
EMBO J
ISSN
0261-4189
DOI
10.1038/sj.emboj.7600261
Published
2004-07-07
Epub
2004-00-10
Pages
2620-31
Language
English
Region
England
NLM ID
8208664
PMCID
PMC449771
Subset
IM
Grants
NIGMS NIH HHS · R01 GM023549 · United States
NIGMS NIH HHS · GM23549 · United States
External Links
PubMed source DOI: 10.1038/sj.emboj.7600261 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2