SF3B1

SF3B1
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 2F9D, 2F9J, 2PEH, 3LQV, 4OZ1, 2FHO
Identifiers
Aliases	SF3B1 , Hsh155, MDS, PRP10, PRPF10, SAP155, SF3b155, splicing factor 3b subunit 1
External IDs	OMIM: 605590; MGI: 1932339; HomoloGene: 6696; GeneCards: SF3B1; OMA:SF3B1 - orthologs
Gene location (Human) Chr. Chromosome 2 (human) [1] Band 2q33.1 Start 197,388,515 bp [1] End 197,435,079 bp [1]
Gene location (Mouse) Chr. Chromosome 1 (mouse) [2] Band 1 C1.2|1 27.98 cM Start 54,985,169 bp [2] End 55,027,481 bp [2]
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in tibia ventricular zone epithelium of nasopharynx right uterine tube skin of thigh skin of hip left ovary superficial temporal artery granulocyte body of uterus Top expressed in Gonadal ridge hand Rostral migratory stream maxillary prominence aortic valve ascending aorta human fetus mandibular prominence primitive streak genital tubercle More reference expression data BioGPS More reference expression data
Gene ontology Molecular function protein binding mRNA binding RNA binding Cellular component U11/U12 snRNP catalytic step 2 spliceosome spliceosomal complex U12-type spliceosomal complex U2-type prespliceosome nucleus U2 snRNP nucleoplasm nuclear speck U2-type precatalytic spliceosome Biological process RNA splicing, via transesterification reactions epigenetic maintenance of chromatin in transcription-competent conformation mRNA splicing, via spliceosome spliceosomal complex assembly mRNA processing RNA splicing Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 23451 81898 Ensembl ENSG00000115524 ENSMUSG00000025982 UniProt O75533 Q99NB9 RefSeq (mRNA) NM_001005526 NM_001308824 NM_012433 NM_031179 RefSeq (protein) NP_001005526 NP_001295753 NP_036565 n/a Location (UCSC) Chr 2: 197.39 – 197.44 Mb Chr 1: 54.99 – 55.03 Mb PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Splicing factor 3B subunit 1 is a protein that in humans is encoded by the SF3B1 gene. ^{[5] [6]}

Function

This gene encodes subunit 1 of the splicing factor 3b protein complex. Splicing factor 3b, together with splicing factor 3a and U2 spliceosomal RNA, forms the U2 small nuclear ribonucleoproteins complex (U2 snRNP). The splicing factor 3b/3a complex binds pre-mRNA upstream of the intron's branch site in a sequence independent manner and may anchor the U2 snRNP to the pre-mRNA. Splicing factor 3b is also a component of the minor U12-type spliceosome. The carboxy-terminal two-thirds of subunit 1 have 22 non-identical, tandem HEAT repeats that form rod-like, helical structures. Alternative splicing results in multiple transcript variants encoding different isoforms. ^[6]

Interactions

SF3B1 has been shown to interact with:

• CDC5L, ^[7]
• DDX42, ^[8]
• PPP1R8, ^[9]
• SF3B2, ^{[8] [10]}
• SF3B3, ^{[8] [10]}
• SF3B6, ^{[8] [11]}

Clinical relevance

Mutations in this gene have been recurrently seen in cases of advanced chronic lymphocytic leukemia, ^[12] myelodysplastic syndromes ^[13] and breast cancer. ^[14] SF3B1 mutations are found in the vast majority of myelodysplastic syndrome with ring sideroblasts (MDS-RS) and MDS with ring sideroblasts and thrombocytosis (MDS-RS-T), so much so that mutated SF3B1 has become a diagnostic criterion for these per the 5th edition of the WHO Classification and the International Consensus Classification (ICC).

There is also an emerging body of evidence to suggest implications of SF3B1 mutations being involved in orbital melanoma^{[ citation needed ]}.

Inhibitors

• H3B-8800

References

1. GRCh38: Ensembl release 89: ENSG00000115524 – Ensembl, May 2017
2. GRCm38: Ensembl release 89: ENSMUSG00000025982 – Ensembl, May 2017
3. "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
4. "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
5. Wang C, Chua K, Seghezzi W, Lees E, Gozani O, Reed R (May 1998). "Phosphorylation of spliceosomal protein SAP 155 coupled with splicing catalysis". Genes & Development. 12 (10): 1409–1414. doi:10.1101/gad.12.10.1409. PMC   316838 . PMID   9585501.
6. "Entrez Gene: SF3B1 splicing factor 3b, subunit 1, 155kDa".
7. Ajuh P, Kuster B, Panov K, Zomerdijk JC, Mann M, Lamond AI (December 2000). "Functional analysis of the human CDC5L complex and identification of its components by mass spectrometry". The EMBO Journal. 19 (23): 6569–6581. doi:10.1093/emboj/19.23.6569. PMC   305846 . PMID   11101529.
8. Will CL, Urlaub H, Achsel T, Gentzel M, Wilm M, Lührmann R (September 2002). "Characterization of novel SF3b and 17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein". The EMBO Journal. 21 (18): 4978–4988. doi:10.1093/emboj/cdf480. PMC   126279 . PMID   12234937.
9. Boudrez A, Beullens M, Waelkens E, Stalmans W, Bollen M (August 2002). "Phosphorylation-dependent interaction between the splicing factors SAP155 and NIPP1". The Journal of Biological Chemistry. 277 (35): 31834–31841. doi: 10.1074/jbc.M204427200 . PMID   12105215.
10. Das BK, Xia L, Palandjian L, Gozani O, Chyung Y, Reed R (October 1999). "Characterization of a protein complex containing spliceosomal proteins SAPs 49, 130, 145, and 155". Molecular and Cellular Biology. 19 (10): 6796–6802. doi:10.1128/mcb.19.10.6796. PMC   84676 . PMID   10490618.
11. Will CL, Schneider C, MacMillan AM, Katopodis NF, Neubauer G, Wilm M, et al. (August 2001). "A novel U2 and U11/U12 snRNP protein that associates with the pre-mRNA branch site". The EMBO Journal. 20 (16): 4536–4546. doi:10.1093/emboj/20.16.4536. PMC   125580 . PMID   11500380.
12. Quesada V, Conde L, Villamor N, Ordóñez GR, Jares P, Bassaganyas L, et al. (December 2011). "Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia". Nature Genetics. 44 (1): 47–52. doi:10.1038/ng.1032. hdl: 10651/8189 . PMID   22158541. S2CID   205343043.
13. Malcovati L, Papaemmanuil E, Bowen DT, Boultwood J, Della Porta MG, Pascutto C, et al. (December 2011). "Clinical significance of SF3B1 mutations in myelodysplastic syndromes and myelodysplastic/myeloproliferative neoplasms". Blood. 118 (24): 6239–6246. doi:10.1182/blood-2011-09-377275. PMC   3236114 . PMID   21998214.
14. Koboldt DC, Fulton RS, McLellan MD, Schmidt H, Kalicki-Veizer J, McMichael JF, et al. (October 2012). "Comprehensive molecular portraits of human breast tumours". Nature. 490 (7418): 61–70. Bibcode:2012Natur.490...61T. doi:10.1038/nature11412. PMC   3465532 . PMID   23000897.

Further reading

• Andersson B, Wentland MA, Ricafrente JY, Liu W, Gibbs RA (April 1996). "A "double adaptor" method for improved shotgun library construction". Analytical Biochemistry. 236 (1): 107–113. doi:10.1006/abio.1996.0138. PMID   8619474.
• Yu W, Andersson B, Worley KC, Muzny DM, Ding Y, Liu W, et al. (April 1997). "Large-scale concatenation cDNA sequencing". Genome Research. 7 (4): 353–358. doi:10.1101/gr.7.4.353. PMC   139146 . PMID   9110174.
• Gozani O, Potashkin J, Reed R (August 1998). "A potential role for U2AF-SAP 155 interactions in recruiting U2 snRNP to the branch site". Molecular and Cellular Biology. 18 (8): 4752–4760. doi:10.1128/mcb.18.8.4752. PMC   109061 . PMID   9671485.
• Das BK, Xia L, Palandjian L, Gozani O, Chyung Y, Reed R (October 1999). "Characterization of a protein complex containing spliceosomal proteins SAPs 49, 130, 145, and 155". Molecular and Cellular Biology. 19 (10): 6796–6802. doi:10.1128/mcb.19.10.6796. PMC   84676 . PMID   10490618.
• Pauling MH, McPheeters DS, Ares M (March 2000). "Functional Cus1p is found with Hsh155p in a multiprotein splicing factor associated with U2 snRNA". Molecular and Cellular Biology. 20 (6): 2176–2185. doi:10.1128/MCB.20.6.2176-2185.2000. PMC   110834 . PMID   10688664.
• Dias Neto E, Correa RG, Verjovski-Almeida S, Briones MR, Nagai MA, da Silva W, et al. (March 2000). "Shotgun sequencing of the human transcriptome with ORF expressed sequence tags". Proceedings of the National Academy of Sciences of the United States of America. 97 (7): 3491–3496. Bibcode:2000PNAS...97.3491D. doi: 10.1073/pnas.97.7.3491 . PMC   16267 . PMID   10737800.
• Das R, Zhou Z, Reed R (May 2000). "Functional association of U2 snRNP with the ATP-independent spliceosomal complex E". Molecular Cell. 5 (5): 779–787. doi: 10.1016/S1097-2765(00)80318-4 . PMID   10882114.
• Brand M, Moggs JG, Oulad-Abdelghani M, Lejeune F, Dilworth FJ, Stevenin J, et al. (June 2001). "UV-damaged DNA-binding protein in the TFTC complex links DNA damage recognition to nucleosome acetylation". The EMBO Journal. 20 (12): 3187–3196. doi:10.1093/emboj/20.12.3187. PMC   150203 . PMID   11406595.
• Will CL, Schneider C, MacMillan AM, Katopodis NF, Neubauer G, Wilm M, et al. (August 2001). "A novel U2 and U11/U12 snRNP protein that associates with the pre-mRNA branch site". The EMBO Journal. 20 (16): 4536–4546. doi:10.1093/emboj/20.16.4536. PMC   125580 . PMID   11500380.
• Jurica MS, Licklider LJ, Gygi SR, Grigorieff N, Moore MJ (April 2002). "Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis". RNA. 8 (4) S1355838202021088: 426–439. doi:10.1017/S1355838202021088. PMC   1370266 . PMID   11991638.
• Boudrez A, Beullens M, Waelkens E, Stalmans W, Bollen M (August 2002). "Phosphorylation-dependent interaction between the splicing factors SAP155 and NIPP1". The Journal of Biological Chemistry. 277 (35): 31834–31841. doi: 10.1074/jbc.M204427200 . PMID   12105215.
• Will CL, Urlaub H, Achsel T, Gentzel M, Wilm M, Lührmann R (September 2002). "Characterization of novel SF3b and 17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein". The EMBO Journal. 21 (18): 4978–4988. doi:10.1093/emboj/cdf480. PMC   126279 . PMID   12234937.
• Golas MM, Sander B, Will CL, Lührmann R, Stark H (May 2003). "Molecular architecture of the multiprotein splicing factor SF3b". Science. 300 (5621): 980–984. Bibcode:2003Sci...300..980G. doi:10.1126/science.1084155. PMID   12738865. S2CID   31046270.
• Banerjee H, Rahn A, Gawande B, Guth S, Valcarcel J, Singh R (February 2004). "The conserved RNA recognition motif 3 of U2 snRNA auxiliary factor (U2AF 65) is essential in vivo but dispensable for activity in vitro". RNA. 10 (2): 240–253. doi:10.1261/rna.5153204. PMC   1370536 . PMID   14730023.
• Will CL, Schneider C, Hossbach M, Urlaub H, Rauhut R, Elbashir S, et al. (June 2004). "The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome". RNA. 10 (6): 929–941. doi:10.1261/rna.7320604. PMC   1370585 . PMID   15146077.
• Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villén J, Li J, et al. (August 2004). "Large-scale characterization of HeLa cell nuclear phosphoproteins". Proceedings of the National Academy of Sciences of the United States of America. 101 (33): 12130–12135. Bibcode:2004PNAS..10112130B. doi: 10.1073/pnas.0404720101 . PMC   514446 . PMID   15302935.
• Lin KT, Lu RM, Tarn WY (October 2004). "The WW domain-containing proteins interact with the early spliceosome and participate in pre-mRNA splicing in vivo". Molecular and Cellular Biology. 24 (20): 9176–9185. doi:10.1128/MCB.24.20.9176-9185.2004. PMC   517884 . PMID   15456888.