RBM9 explained

RNA binding motif protein 9 (RBM9), also known as Rbfox2, is a protein which in humans is encoded by the RBM9 gene.^[1]

Function

Rbfox2 is one of several human genes similar to the C. elegans gene Fox-1. This gene encodes an RNA binding protein that is thought to be a key regulator of alternative splicing in the nervous system and other cell types. Rbfox2 and the related protein Rbfox1 bind to conserved (U)GCAUG RNA motifs in the introns adjacent to many alternatively spliced exons and promotes inclusion or exclusion of the alternative exon in mature transcripts.^{[2] [3]} The protein also interacts with the estrogen receptor 1 transcription factor and regulates estrogen receptor 1 transcriptional activity. Multiple transcript variants encoding different isoforms have been found for this gene.

Rbfox2, as determined by CLIP-seq, binds near alternatively spliced exons and regulates the inclusion or exclusion of exons during alternative splicing by binding in introns either downstream (inclusion) or upstream (exon skipping) of exons. Its presence is important for stem cell survival and knockdowns of Rbfox2 activate markers for apoptosis.^[4]

See also

• Alternative splicing
• RNA-binding protein

Further reading

• Dunham I . The DNA sequence of human chromosome 22 . Nature . 402 . 6761 . 489–495 . 1999 . 10591208 . 10.1038/990031 . vanc. Shimizu N . Roe BA . 3 . Bruskiewich . R. . Beare . D. M. . Clamp . M. . Smink . L. J. . Ainscough . R. . Almeida . J. P. . 1999Natur.402..489D . free .
• Lieberman AP . Androgens regulate the mammalian homologues of invertebrate sex determination genes tra-2 and fox-1 . Biochem. Biophys. Res. Commun. . 282 . 2 . 499–506 . 2001 . 11401487 . 10.1006/bbrc.2001.4617 . vanc. Friedlich DL . Harmison G . 3 . Howell . BW . Jordan . CL . Breedlove . SM . Fischbeck . KH . 16858834 .
• Norris JD, Fan D, Sherk A, McDonnell DP . A negative coregulator for the human ER . Mol. Endocrinol. . 16 . 3 . 459–468 . 2002 . 11875103 . 10.1210/me.16.3.459 . free .
• Strausberg RL . Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences . Proc. Natl. Acad. Sci. U.S.A. . 99 . 26 . 16899–16903 . 2003 . 12477932 . 10.1073/pnas.242603899 . 139241 . vanc. Feingold EA . Grouse LH . 3 . Derge . JG . Klausner . RD . Collins . FS . Wagner . L . Shenmen . CM . Schuler . GD . 2002PNAS...9916899M . free .
• Collins JE . Reevaluating human gene annotation: a second-generation analysis of chromosome 22 . Genome Res. . 13 . 1 . 27–36 . 2003 . 12529303 . 10.1101/gr.695703 . 430954 . vanc. Goward ME . Cole CG . 3 . Smink . LJ . Huckle . EJ . Knowles . S . Bye . JM . Beare . DM . Dunham . I .
• Ota T . Complete sequencing and characterization of 21,243 full-length human cDNAs . Nat. Genet. . 36 . 1 . 40–45 . 2004 . 14702039 . 10.1038/ng1285 . vanc. Suzuki Y . Nishikawa T . 3 . Otsuki . Tetsuji . Sugiyama . Tomoyasu . Irie . Ryotaro . Wakamatsu . Ai . Hayashi . Koji . Sato . Hiroyuki . free .
• Collins JE . A genome annotation-driven approach to cloning the human ORFeome . Genome Biol. . 5 . 10 . R84 . 2005 . 15461802 . 10.1186/gb-2004-5-10-r84 . 545604 . vanc. Wright CL . Edwards CA . 3 . Davis . Matthew P . Grinham . James A . Cole . Charlotte G . Goward . Melanie E . Aguado . Begoña . Mallya . Meera . free .
• Gerhard DS . The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC) . Genome Res. . 14 . 10B . 2121–2127 . 2004 . 15489334 . 10.1101/gr.2596504 . 528928 . vanc. Wagner L . Feingold EA . 3 . Shenmen . CM . Grouse . LH . Schuler . G . Klein . SL . Old . S . Rasooly . R .
• Rual JF . Towards a proteome-scale map of the human protein-protein interaction network . Nature . 437 . 7062 . 1173–1178 . 2005 . 16189514 . 10.1038/nature04209 . vanc. Venkatesan K . Hao T . 3 . Hirozane-Kishikawa . Tomoko . Dricot . Amélie . Li . Ning . Berriz . Gabriel F. . Gibbons . Francis D. . Dreze . Matija . 2005Natur.437.1173R . 4427026 .
• Underwood JG . Homologues of the Caenorhabditis elegans Fox-1 protein are neuronal splicing regulators in mammals . Mol. Cell. Biol. . 25 . 22 . 10005–10016 . 2005 . 16260614 . 10.1128/MCB.25.22.10005-10016.2005 . 1280273 . vanc. Boutz PL . Dougherty JD . 3 . Stoilov . P. . Black . D. L. .
• Kimura K . Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes . Genome Res. . 16 . 1 . 55–65 . 2006 . 16344560 . 10.1101/gr.4039406 . 1356129 . vanc. Wakamatsu A . Suzuki Y . 3 . Ota . T . Nishikawa . T . Yamashita . R . Yamamoto . J . Sekine . M . Tsuritani . K .
• Ponthier JL . Fox-2 splicing factor binds to a conserved intron motif to promote inclusion of protein 4.1R alternative exon 16 . J. Biol. Chem. . 281 . 18 . 12468–12474 . 2006 . 16537540 . 10.1074/jbc.M511556200 . vanc. Schluepen C . Chen W . 3 . Lersch . RA . Gee . SL . Hou . VC . Lo . AJ . Short . SA . Chasis . JA . free .
• Lim J . A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration . Cell . 125 . 4 . 801–814 . 2006 . 16713569 . 10.1016/j.cell.2006.03.032 . vanc. Hao T . Shaw C . 3 . Patel . Akash J. . Szabó . Gábor . Rual . Jean-François . Fisk . C. Joseph . Li . Ning . Smolyar . Alex . free .

Notes and References

1. Web site: Entrez Gene: RBM9 RNA binding motif protein 9.
2. Jin . Y. . A vertebrate RNA-binding protein Fox-1 regulates tissue-specific splicing via the pentanucleotide GCAUG . The EMBO Journal . 22 . 4 . 2003-02-17 . 1460-2075 . 10.1093/emboj/cdg089 . 12574126 . 905–912. 145449 .
3. Ponthier . Julie L. . Schluepen . Christina . Chen . Weiguo . Lersch . Robert A. . Gee . Sherry L. . Hou . Victor C. . Lo . Annie J. . Short . Sarah A. . Chasis . Joel A. . Winkelmann . John C. . Conboy . John G. . Fox-2 Splicing Factor Binds to a Conserved Intron Motif to Promote Inclusion of Protein 4.1R Alternative Exon 16 . Journal of Biological Chemistry . 281 . 18 . 2006-03-14 . 0021-9258 . 10.1074/jbc.m511556200 . 16537540 . 12468–12474. free .
4. Yeo GW, Coufal NG, Liang TY, Peng GE, Fu XD, Gage FH . An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells . Nature Structural & Molecular Biology . 16 . 2 . 130–137 . February 2009 . 19136955 . 10.1038/nsmb.1545 . 2735254 .