SLX4

SLX4 (also known as BTBD12 and FANCP) is a protein involved in DNA repair, where it has important roles in the final steps of homologous recombination.[5] Mutations in the gene are associated with the disease Fanconi anemia.[6][7]

SLX4
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 4M7C, 4UYI, 4ZOU
Identifiers
Aliases	SLX4, BTBD12, FANCP, MUS312, SLX4 structure-specific endonuclease subunit
External IDs	OMIM: 613278 MGI: 106299 HomoloGene: 23770 GeneCards: SLX4
Gene location (Human) Chr. Chromosome 16 (human)[1] Band 16p13.3 Start 3,581,181 bp[1] End 3,611,606 bp[1]
Gene location (Mouse) Chr. Chromosome 16 (mouse)[2] Band 16 A1|16 2.34 cM Start 3,979,105 bp[2] End 4,003,770 bp[2]
Gene ontology Molecular function • GO:0001948 protein binding • GO:0010577 enzyme activator activity • endodeoxyribonuclease activity • crossover junction endodeoxyribonuclease activity • 5'-flap endonuclease activity • 3'-flap endonuclease activity Cellular component • ERCC4-ERCC1 complex • nucleoplasm • cell junction • nuclear chromatin • Holliday junction resolvase complex • nuclear chromosome, telomeric region • cell nucleus • chromosome, telomeric region • cytosol • Slx1-Slx4 complex Biological process • nucleotide-excision repair • DNA recombination • positive regulation of t-circle formation • cellular response to DNA damage stimulus • DNA double-strand break processing involved in repair via single-strand annealing • DNA replication • response to intra-S DNA damage checkpoint signaling • GO:0048554 positive regulation of catalytic activity • DNA repair • interstrand cross-link repair • resolution of meiotic recombination intermediates • double-strand break repair via homologous recombination • meiotic DNA double-strand break processing • telomeric D-loop disassembly • t-circle formation • negative regulation of telomere maintenance via telomere lengthening Sources:Amigo / QuickGO
Orthologs
Species	Human	Mouse
Entrez	84464	52864
Ensembl	ENSG00000188827	ENSMUSG00000039738
UniProt	Q8IY92	Q6P1D7
RefSeq (mRNA)	NM_032444	NM_177472
RefSeq (protein)	NP_115820	NP_803423
Location (UCSC)	Chr 16: 3.58 – 3.61 Mb	Chr 16: 3.98 – 4 Mb
PubMed search	[3]	[4]
Wikidata
View/Edit Human View/Edit Mouse

The version of SLX4 present in humans and other mammals acts as a sort of scaffold upon which other proteins form several different multiprotein complexes. The SLX1-SLX4 complex acts as a Holliday junction resolvase. As such, the complex cleaves the links between two homologous chromosomes that form during homologous recombination. This allows the two linked chromosomes to resolve into two unconnected double-strand DNA molecules.[8] The SLX4 interacting protein interacts with SLX4 in the DNA repair process, specifically in interstrand crosslink repair.[9] SLX4 also associates with RAD1, RAD10 and SAW1 in the single-strand annealing pathway of homologous recombination.[10] The DNA repair function of SLX4 is involved in sensitivity to proton beam radiation.[11]

Model organisms

Model organisms have been prominent in the study of SLX4 function. It was identified in 2001 during a screen for lethal mutations in yeast cells lacking a functional copy of the Sgs1 protein. Based on that, SLX4 was grouped with several other proteins produced by SLX (synthetic lethal of unknown function) genes.[12]

Slx4 knockout mouse phenotype

Characteristic	Phenotype
Homozygote viability	Abnormal
Fertility	Abnormal
Body weight	Abnormal[13]
Anxiety	Normal
Neurological assessment	Normal
Grip strength	Normal
Hot plate	Normal
Dysmorphology	Abnormal[14]
Indirect calorimetry	Normal
Glucose tolerance test	Normal
Auditory brainstem response	Normal
DEXA	Abnormal[15]
Radiography	Abnormal[16]
Body temperature	Normal
Eye morphology	Abnormal[17]
Clinical chemistry	Normal
Haematology	Abnormal[18]
Peripheral blood lymphocytes	Normal
Micronucleus test	Abnormal
Heart weight	Abnormal[19]
Skin Histopathology	Normal
Brain histopathology	Normal
Salmonella infection	Normal[20]
Citrobacter infection	Normal[21]
All tests and analysis from[22][23]

A conditional knockout mouse line, called Slx4^{tm1a(EUCOMM)Wtsi}[24] was generated as part of the International Knockout Mouse Consortium program, a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists.[25][26][27]

Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion.[7][22] Twenty four tests were carried out on mutant mice and ten significant abnormalities were observed.[22] A viability at weaning study found less homozygous mutant animals were present than predicted by Mendelian ratio. Homozygous mutant animals of both sexes were sub-fertile and homozygous females had a reduced body weight, body length, heart weight, platelet count and lean mass.[28] Homozygotes of both sex had abnormal eye sizes, narrow eye openings, skeletal defects (including scoliosis and fusion of vertebrae), and displayed an increase in DNA instability as shown by a micronucleus test.[22] This and further analysis revealed the mouse phenotype to model the human genetic illness, Fanconi anemia.[7][28] The association was confirmed when patients with the disease were found to have mutations in their SLX4 gene.[6]

References

1. GRCh38: Ensembl release 89: ENSG00000188827 - Ensembl, May 2017
2. GRCm38: Ensembl release 89: ENSMUSG00000039738 - 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. Klein, HL; Symington, LS (10 July 2009). "Breaking up just got easier to do". Cell. 138 (1): 20–22. doi:10.1016/j.cell.2009.06.039. PMID 19596231.
6. Kim Y; Lach FP; Desetty R; Hanenberg H; Auerbach AD; Smogorzewska A (February 2011). "Mutations of the SLX4 gene in Fanconi anemia". Nat. Genet. 43 (2): 142–6. doi:10.1038/ng.750. PMC 3345287. PMID 21240275.
7. van der Weyden L; White JK; Adams DJ; Logan DW (2011). "The mouse genetics toolkit: revealing function and mechanism". Genome Biol. 12 (6): 224. doi:10.1186/gb-2011-12-6-224. PMC 3218837. PMID 21722353.
8. Svendsen, JM; et al. (10 July 2009). "Mammalian BTBD12/SLX4 assembles a Holliday junction resolvase and is required for DNA repair". Cell. 138 (1): 63–77. doi:10.1016/j.cell.2009.06.030. PMC 2720686. PMID 19596235.
9. Zhang, Huimin; Chen, Zhen; Ye, Yin; Ye, Zu; Cao, Dan; Xiong, Yun; Srivastava, Mrinal; Feng, Xu; Tang, Mengfan; Wang, Chao; Tainer, John A. (2019-11-04). "SLX4IP acts with SLX4 and XPF-ERCC1 to promote interstrand crosslink repair". Nucleic Acids Research. 47 (19): 10181–10201. doi:10.1093/nar/gkz769. ISSN 1362-4962. PMC 6821277. PMID 31495888.
10. Mimitou, EP; Symington, LS (2 September 2009). "DNA end resection: Many nucleases make light work". DNA Repair. 8 (9): 983–995. doi:10.1016/j.dnarep.2009.04.017. PMC 2760233. PMID 19473888.
11. Liu, Q; Underwood, TA (1 May 2016). "Disruption of SLX4-MUS81 Function Increases the Relative Biological Effectiveness of Proton Radiation". Int J Radiation Oncol Biol Phys. 95 (1): 78–85. doi:10.1016/j.ijrobp.2016.01.046. PMC 4889010. PMID 27084631.
12. Mullen, JR; et al. (January 2001). "Requirement for three novel protein complexes in the absence of the Sgs1 DNA helicase in Saccharomyces cerevisiae". Genetics. 157 (1): 103–118. PMC 1461486. PMID 11139495.
13. "Body weight data for Slx4". Wellcome Trust Sanger Institute.
14. "Dysmorphology data for Slx4". Wellcome Trust Sanger Institute.
15. "DEXA data for Slx4". Wellcome Trust Sanger Institute.
16. "Radiography data for Slx4". Wellcome Trust Sanger Institute.
17. "Eye morphology data for Slx4". Wellcome Trust Sanger Institute.
18. "Haematology data for Slx4". Wellcome Trust Sanger Institute.
19. "Heart weight data for Slx4". Wellcome Trust Sanger Institute.
20. "Salmonella infection data for Slx4". Wellcome Trust Sanger Institute.
21. "Citrobacter infection data for Slx4". Wellcome Trust Sanger Institute.
22. Gerdin AK (2010). "The Sanger Mouse Genetics Programme: High throughput characterisation of knockout mice". Acta Ophthalmologica. 88 (S248). doi:10.1111/j.1755-3768.2010.4142.x.
23. Mouse Resources Portal, Wellcome Trust Sanger Institute.
24. "International Knockout Mouse Consortium".
25. Skarnes, W. C.; Rosen, B.; West, A. P.; Koutsourakis, M.; Bushell, W.; Iyer, V.; Mujica, A. O.; Thomas, M.; Harrow, J.; Cox, T.; Jackson, D.; Severin, J.; Biggs, P.; Fu, J.; Nefedov, M.; De Jong, P. J.; Stewart, A. F.; Bradley, A. (2011). "A conditional knockout resource for the genome-wide study of mouse gene function". Nature. 474 (7351): 337–342. doi:10.1038/nature10163. PMC 3572410. PMID 21677750.
26. Dolgin E (June 2011). "Mouse library set to be knockout". Nature. 474 (7351): 262–3. doi:10.1038/474262a. PMID 21677718.
27. Collins FS; Rossant J; Wurst W (January 2007). "A mouse for all reasons". Cell. 128 (1): 9–13. doi:10.1016/j.cell.2006.12.018. PMID 17218247.
28. Crossan GP, van der Weyden L, Rosado IV, et al. (February 2011). "Disruption of mouse Slx4, a regulator of structure-specific nucleases, phenocopies Fanconi anemia". Nat. Genet. 43 (2): 147–52. doi:10.1038/ng.752. PMC 3624090. PMID 21240276.