Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery - PubMed (original) (raw)

doi: 10.1038/ng1080. Epub 2003 Jan 13.

Affiliations

PMID: 12524544
DOI: 10.1038/ng1080

Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery

Haley Hieronymus et al. Nat Genet. 2003 Feb.

Abstract

Nuclear export of mRNA is mediated by a complex machinery of RNA-binding proteins that recognizes and routes mRNAs through a messenger ribonucleoprotein (mRNP) network. The full spectrum of mRNA cargoes for any dedicated mRNA export factor is unknown. We identified the mRNAs that bind two conserved yeast mRNA export factors, Yra1 (refs. 1-5) and Mex67 (refs. 6,7), on a genome-wide scale and determined their level of binding. Yra1 and Mex67 bind approximately 1,000 and 1,150 mRNAs, respectively, corresponding to almost 20% of the yeast genome and roughly 36% of all transcriptional events each. The binding level of Yra1 targets is related to their transcriptional frequency, but that of Mex67 targets is not. Yra1-bound transcripts are enriched in mRNAs that are regulated by a number of transcription factors. Yra1- and Mex67-bound populations also show enrichment of mRNAs encoding distinct functional classes of proteins, some of which are regulated by these transcription factors. We determined that one such transcription factor, Abf1 (refs. 8-10), associates with Yra1. These results indicate a previously unidentified specificity of mRNA export factors, which coordinates the export of transcriptionally co-regulated, functional classes of transcripts, perhaps through interactions with the transcriptional machinery.

PubMed Disclaimer

Comment in

Organizing mRNA export.
Keene JD. Keene JD. Nat Genet. 2003 Feb;33(2):111-2. doi: 10.1038/ng0203-111. Nat Genet. 2003. PMID: 12560814 No abstract available.

Cited by

Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast.
Gerber AP, Herschlag D, Brown PO. Gerber AP, et al. PLoS Biol. 2004 Mar;2(3):E79. doi: 10.1371/journal.pbio.0020079. Epub 2004 Mar 16. PLoS Biol. 2004. PMID: 15024427 Free PMC article.
Actin-related protein Arp6 influences H2A.Z-dependent and -independent gene expression and links ribosomal protein genes to nuclear pores.
Yoshida T, Shimada K, Oma Y, Kalck V, Akimura K, Taddei A, Iwahashi H, Kugou K, Ohta K, Gasser SM, Harata M. Yoshida T, et al. PLoS Genet. 2010 Apr 15;6(4):e1000910. doi: 10.1371/journal.pgen.1000910. PLoS Genet. 2010. PMID: 20419146 Free PMC article.
Role for the Ran binding protein, Mog1p, in Saccharomyces cerevisiae SLN1-SKN7 signal transduction.
Lu JM, Deschenes RJ, Fassler JS. Lu JM, et al. Eukaryot Cell. 2004 Dec;3(6):1544-56. doi: 10.1128/EC.3.6.1544-1556.2004. Eukaryot Cell. 2004. PMID: 15590828 Free PMC article.
The Trypanosoma cruzi RNA-binding protein RBP42 is expressed in the cytoplasm throughout the life cycle of the parasite.
Tyler Weisbarth R, Das A, Castellano P, Fisher MA, Wu H, Bellofatto V. Tyler Weisbarth R, et al. Parasitol Res. 2018 Apr;117(4):1095-1104. doi: 10.1007/s00436-018-5787-9. Epub 2018 Feb 23. Parasitol Res. 2018. PMID: 29473141 Free PMC article.
The export factor Yra1 modulates mRNA 3' end processing.
Johnson SA, Kim H, Erickson B, Bentley DL. Johnson SA, et al. Nat Struct Mol Biol. 2011 Sep 25;18(10):1164-71. doi: 10.1038/nsmb.2126. Nat Struct Mol Biol. 2011. PMID: 21947206 Free PMC article.

Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery - PubMed (original) (raw)