SMARCAL1

SMARCAL1
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 4MQV
Identifiers
Aliases	SMARCAL1 , HARP, HHARP, SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1
External IDs	OMIM: 606622; MGI: 1859183; HomoloGene: 8558; GeneCards: SMARCAL1; OMA:SMARCAL1 - orthologs
Gene location (Human) Chr. Chromosome 2 (human) [1] Band 2q35 Start 216,412,414 bp [1] End 216,483,053 bp [1]
Gene location (Mouse) Chr. Chromosome 1 (mouse) [2] Band 1 C3|1 36.72 cM Start 72,622,410 bp [2] End 72,672,293 bp [2]
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in gonad stromal cell of endometrium sural nerve ventricular zone granulocyte ganglionic eminence testicle right adrenal cortex apex of heart islet of Langerhans Top expressed in primary oocyte zygote genital tubercle secondary oocyte tail of embryo neural layer of retina superior frontal gyrus otic vesicle dentate gyrus of hippocampal formation granule cell ventricular zone More reference expression data BioGPS More reference expression data
Gene ontology Molecular function nucleotide binding ATP-dependent activity, acting on DNA protein binding hydrolase activity ATP binding helicase activity ATP-dependent DNA/DNA annealing activity Cellular component site of double-strand break DNA replication factor A complex nucleus nucleoplasm nuclear replication fork Biological process regulation of transcription by RNA polymerase II DNA metabolic process cellular response to DNA damage stimulus t-circle formation DNA repair replication fork processing DNA rewinding replication fork protection Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 50485 54380 Ensembl ENSG00000138375 ENSMUSG00000039354 UniProt Q9NZC9 Q8BJL0 RefSeq (mRNA) NM_001127207 NM_014140 NM_018817 RefSeq (protein) NP_001120679 NP_054859 NP_061287 Location (UCSC) Chr 2: 216.41 – 216.48 Mb Chr 1: 72.62 – 72.67 Mb PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 is a protein that in humans is encoded by the SMARCAL1 gene. ^{[5] [6] [7]}

Function

The protein encoded by this gene is a member of the SWI/SNF family of proteins. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The SMARCAL1 protein convert RPA-bound, single stranded DNA into double-stranded DNA, an enzyme activity termed "annealing helicase". ^[8] This activity is important for two cellular functions: replication fork reversal, ^[9] and R-loop unwinding. ^[10]

The encoded protein shows sequence similarity to the E. coli RNA polymerase-binding protein HepA. Mutations in this gene are a cause of Schimke immunoosseous dysplasia (SIOD), an autosomal recessive disorder with the diagnostic features of spondyloepiphyseal dysplasia, renal dysfunction, and T-cell immunodeficiency. ^[7]

References

1. GRCh38: Ensembl release 89: ENSG00000138375 – Ensembl, May 2017
2. GRCm38: Ensembl release 89: ENSMUSG00000039354 – 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. Muthuswami R, Truman PA, Mesner LD, Hockensmith JW (Mar 2000). "A eukaryotic SWI2/SNF2 domain, an exquisite detector of double-stranded to single-stranded DNA transition elements". The Journal of Biological Chemistry. 275 (11): 7648–55. doi: 10.1074/jbc.275.11.7648 . PMID   10713074.
6. Coleman MA, Eisen JA, Mohrenweiser HW (May 2000). "Cloning and characterization of HARP/SMARCAL1: a prokaryotic HepA-related SNF2 helicase protein from human and mouse". Genomics. 65 (3): 274–82. CiteSeerX   10.1.1.186.4879 . doi:10.1006/geno.2000.6174. PMID   10857751.
7. "Entrez Gene: SMARCAL1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1".
8. Yusufzai T, Kadonaga JT (Oct 2008). "HARP is an ATP-driven annealing helicase". Science. 322 (5902): 748–50. Bibcode:2008Sci...322..748Y. doi:10.1126/science.1161233. PMC   2587503 . PMID   18974355.
   • Lay summary in: "Biologists Discover Motor Protein That Rewinds DNA". ScienceDaily (Press release). November 2, 2008.
9. Bétous, Rémy; Mason, Aaron C.; Rambo, Robert P.; Bansbach, Carol E.; Badu-Nkansah, Akosua; Sirbu, Bianca M.; Eichman, Brandt F.; Cortez, David (2012-01-15). "SMARCAL1 catalyzes fork regression and Holliday junction migration to maintain genome stability during DNA replication". Genes & Development. 26 (2): 151–162. doi:10.1101/gad.178459.111. ISSN   0890-9369. PMC   3273839 . PMID   22279047.
10. Hodson, Charlotte; van Twest, Sylvie; Dylewska, Malgorzata; O’Rourke, Julienne J.; Tan, Winnie; Murphy, Vincent J.; Walia, Mannu; Abbouche, Lara; Nieminuszczy, Jadwiga; Dunn, Elyse; Bythell-Douglas, Rohan; Heierhorst, Jörg; Niedzwiedz, Wojciech; Deans, Andrew J. (2022). "Branchpoint translocation by fork remodelers as a general mechanism of R-loop removal". Cell Reports. 41 (10): 111749. doi: 10.1016/j.celrep.2022.111749 . PMID   36476850.

Further reading

• Boerkoel CF, Takashima H, John J, Yan J, Stankiewicz P, Rosenbarker L, André JL, Bogdanovic R, Burguet A, Cockfield S, Cordeiro I, Fründ S, Illies F, Joseph M, Kaitila I, Lama G, Loirat C, McLeod DR, Milford DV, Petty EM, Rodrigo F, Saraiva JM, Schmidt B, Smith GC, Spranger J, Stein A, Thiele H, Tizard J, Weksberg R, Lupski JR, Stockton DW (Feb 2002). "Mutant chromatin remodeling protein SMARCAL1 causes Schimke immuno-osseous dysplasia". Nature Genetics. 30 (2): 215–20. doi:10.1038/ng821. PMID   11799392. S2CID   8954897.
• Lou S, Lamfers P, McGuire N, Boerkoel CF (Dec 2002). "Longevity in Schimke immuno-osseous dysplasia". Journal of Medical Genetics. 39 (12): 922–5. doi:10.1136/jmg.39.12.922. PMC   1757210 . PMID   12471207.
• Bökenkamp A, deJong M, van Wijk JA, Block D, van Hagen JM, Ludwig M (Dec 2005). "R561C missense mutation in the SMARCAL1 gene associated with mild Schimke immuno-osseous dysplasia". Pediatric Nephrology. 20 (12): 1724–8. doi:10.1007/s00467-005-2047-x. PMID   16237566. S2CID   35371382.
• Clewing JM, Antalfy BC, Lücke T, Najafian B, Marwedel KM, Hori A, Powel RM, Do AF, Najera L, SantaCruz K, Hicks MJ, Armstrong DL, Boerkoel CF (Feb 2007). "Schimke immuno-osseous dysplasia: a clinicopathological correlation". Journal of Medical Genetics. 44 (2): 122–30. doi:10.1136/jmg.2006.044313. PMC   2598061 . PMID   16840568.

External links

• GeneReviews/NCBI/NIH/UW entry on Schimke Immunoosseous Dysplasia