SETMAR: Difference between revisions

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{{Infobox_gene}}
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'''Histone-lysine N-methyltransferase SETMAR''' is an [[enzyme]] that in humans is encoded by the ''SETMAR'' [[gene]].<ref name="pmid9461395">{{cite journal |author1=Robertson HM |author2=Zumpano KL | title = Molecular evolution of an ancient mariner transposon, Hsmar1, in the human genome | journal = Gene | volume = 205 | issue = 1-2 | pages = 203–17 |date=Feb 1998 | pmid = 9461395 | pmc =  | doi =10.1016/S0378-1119(97)00472-1 }}</ref><ref name="entrez">{{cite web | title = Entrez Gene: SETMAR SET domain and mariner transposase fusion gene| url = https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=6419| accessdate = }}</ref>
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{{GNF_Protein_box
| image = 
| image_source =
| PDB =  
| Name = SET domain and mariner transposase fusion gene
| HGNCid = 10762
| Symbol = SETMAR
| AltSymbols =; METNASE
| OMIM = 609834
| ECnumber =
| Homologene = 68519
| MGIid = 1921979
  | GeneAtlas_image1 = PBB_GE_SETMAR_206554_x_at_tn.png
| Function = {{GNF_GO|id=GO:0003677 |text = DNA binding}} {{GNF_GO|id=GO:0004803 |text = transposase activity}} {{GNF_GO|id=GO:0008168 |text = methyltransferase activity}} {{GNF_GO|id=GO:0008270 |text = zinc ion binding}} {{GNF_GO|id=GO:0016740 |text = transferase activity}} {{GNF_GO|id=GO:0018024 |text = histone-lysine N-methyltransferase activity}}
  | Component = {{GNF_GO|id=GO:0005575 |text = cellular_component}} {{GNF_GO|id=GO:0005634 |text = nucleus}}
| Process = {{GNF_GO|id=GO:0006281 |text = DNA repair}} {{GNF_GO|id=GO:0006313 |text = transposition, DNA-mediated}} {{GNF_GO|id=GO:0016568 |text = chromatin modification}}
| Orthologs = {{GNF_Ortholog_box
    | Hs_EntrezGene = 6419
    | Hs_Ensembl = ENSG00000170364
    | Hs_RefseqProtein = NP_006506
    | Hs_RefseqmRNA = NM_006515
    | Hs_GenLoc_db = 
    | Hs_GenLoc_chr = 3
    | Hs_GenLoc_start = 4319999
    | Hs_GenLoc_end = 4333949
    | Hs_Uniprot = Q53H47
    | Mm_EntrezGene = 74729
    | Mm_Ensembl = ENSMUSG00000034639
    | Mm_RefseqmRNA = XM_001001353
    | Mm_RefseqProtein = XP_001001353
    | Mm_GenLoc_db = 
    | Mm_GenLoc_chr = 6
    | Mm_GenLoc_start = 108030823
    | Mm_GenLoc_end = 108042897
    | Mm_Uniprot = Q80UJ9
  }}
}}
'''SET domain and mariner transposase fusion gene''', also known as '''SETMAR''', is a human [[gene]].<ref name="entrez">{{cite web | title = Entrez Gene: SETMAR SET domain and mariner transposase fusion gene| url = http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=6419| accessdate = }}</ref>


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==Model organisms==
{| class="wikitable sortable collapsible collapsed" border="1" cellpadding="2" style="float: right;" |
|+ ''Setmar'' knockout mouse phenotype
|-
! Characteristic!! Phenotype
|-
| [[Homozygote]] viability || bgcolor="#488ED3"|Normal
|-
| Homozygous Fertility || bgcolor="#488ED3"|Normal
|-
| Body weight || bgcolor="#488ED3"|Normal
|-
| [[Open Field (animal test)|Anxiety]] || bgcolor="#488ED3"|Normal
|-
| Neurological assessment || bgcolor="#488ED3"|Normal
|-
| Grip strength || bgcolor="#488ED3"|Normal
|-
| [[Hot plate test|Hot plate]] || bgcolor="#488ED3"|Normal
|-
| [[Dysmorphology]] || bgcolor="#488ED3"|Normal
|-
| [[Indirect calorimetry]] || bgcolor="#488ED3"|Normal
|-
| [[Glucose tolerance test]] || bgcolor="#488ED3"|Normal
|-
| [[Auditory brainstem response]] || bgcolor="#488ED3"|Normal
|-
| [[Dual-energy X-ray absorptiometry|DEXA]] || bgcolor="#488ED3"|Normal
|-
| [[Radiography]] || bgcolor="#488ED3"|Normal
|-
| Body temperature || bgcolor="#488ED3"|Normal
|-
| Eye morphology || bgcolor="#C40000"|Abnormal<ref name="Eye morphology">{{cite web |url=http://www.sanger.ac.uk/mouseportal/phenotyping/MAVM/eye-morphology/ |title=Eye morphology data for Setmar |publisher=Wellcome Trust Sanger Institute}}</ref>
|-
| [[Clinical chemistry]] || bgcolor="#488ED3"|Normal
|-
| [[Blood plasma|Plasma]] [[immunoglobulin]]s || bgcolor="#488ED3"|Normal
|-
| [[Haematology]] || bgcolor="#488ED3"|Normal
|-
| [[Peripheral blood lymphocyte]]s || bgcolor="#C40000"|Abnormal<ref name="Peripheral blood lymphocytes">{{cite web |url=http://www.sanger.ac.uk/mouseportal/phenotyping/MAVM/peripheral-blood-lymphocytes/ |title=Peripheral blood lymphocytes data for Setmar |publisher=Wellcome Trust Sanger Institute}}</ref>
|-
| [[Micronucleus test]] || bgcolor="#488ED3"|Normal
|-
| Heart weight || bgcolor="#488ED3"|Normal
|-
| Skin Histopathology || bgcolor="#488ED3"|Normal
|-
| Brain histopathology || bgcolor="#488ED3"|Normal
|-
| ''[[Salmonella]]'' infection || bgcolor="#488ED3"|Normal<ref name="''Salmonella'' infection">{{cite web |url=http://www.sanger.ac.uk/mouseportal/phenotyping/MAVM/salmonella-challenge/ |title=''Salmonella'' infection data for Setmar |publisher=Wellcome Trust Sanger Institute}}</ref>
|-
| ''[[Citrobacter]]'' infection || bgcolor="#488ED3"|Normal<ref name="''Citrobacter'' infection">{{cite web |url=http://www.sanger.ac.uk/mouseportal/phenotyping/MAVM/citrobacter-challenge/ |title=''Citrobacter'' infection data for Setmar |publisher=Wellcome Trust Sanger Institute}}</ref>
|-
| colspan=2; style="text-align: center;" | All tests and analysis from<ref name="mgp_reference">{{cite journal | doi = 10.1111/j.1755-3768.2010.4142.x | title = The Sanger Mouse Genetics Programme: High throughput characterisation of knockout mice | year = 2010 | last1 = Gerdin | first1 = AK | journal = Acta Ophthalmologica | volume = 88 | pages =  925–7 }}</ref><ref>[http://www.sanger.ac.uk/mouseportal/ Mouse Resources Portal], Wellcome Trust Sanger Institute.</ref>
|}
[[Model organism]]s have been used in the study of SETMAR function. A conditional [[knockout mouse]] line, called ''Setmar<sup>tm1a(EUCOMM)Wtsi</sup>''<ref name="allele_ref">{{cite web |url=http://www.knockoutmouse.org/martsearch/search?query=Setmar |title=International Knockout Mouse Consortium}}</ref><ref name="mgi_allele_ref">{{cite web |url=http://www.informatics.jax.org/searchtool/Search.do?query=MGI:4432061 |title=Mouse Genome Informatics}}</ref> 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.<ref name="pmid21677750">{{Cite journal
| last1 = Skarnes |first1 =W. C.
| doi = 10.1038/nature10163
| last2 = Rosen | first2 = B.
| last3 = West | first3 = A. P.
| last4 = Koutsourakis | first4 = M.
| last5 = Bushell | first5 = W.
| last6 = Iyer | first6 = V.
| last7 = Mujica | first7 = A. O.
| last8 = Thomas | first8 = M.
| last9 = Harrow | first9 = J.
| last10 = Cox | first10 = T.
| last11 = Jackson | first11 = D.
| last12 = Severin | first12 = J.
| last13 = Biggs | first13 = P.
| last14 = Fu | first14 = J.
| last15 = Nefedov | first15 = M.
| last16 = De Jong | first16 = P. J.
| last17 = Stewart | first17 = A. F.
| last18 = Bradley | first18 = A.
| title = A conditional knockout resource for the genome-wide study of mouse gene function
| journal = Nature
| volume = 474
| issue = 7351
| pages = 337–342
| year = 2011
| pmid = 21677750
| pmc =3572410
}}</ref><ref name="mouse_library">{{cite journal | doi = 10.1038/474262a | title = Mouse library set to be knockout | year = 2011 | last1 = Dolgin | first1 = Elie | journal = Nature | volume = 474 | issue = 7351 | pages = 262–3 | pmid = 21677718 }}</ref><ref name="mouse_for_all_reasons">{{cite journal | doi = 10.1016/j.cell.2006.12.018 | title = A Mouse for All Reasons | year = 2007 | journal = Cell | volume = 128 | pages = 9–13 | pmid = 17218247 | author1 = International Mouse Knockout Consortium | last2 = Collins | first2 = FS | last3 = Rossant | first3 = J | last4 = Wurst | first4 = W | issue = 1 }}</ref>
Male and female animals underwent a standardized [[phenotypic screen]] to determine the effects of deletion.<ref name="mgp_reference" /><ref name="pmid21722353">{{cite journal|author1=van der Weyden L |author2=White JK |author3=Adams DJ |author4=Logan DW | title=The mouse genetics toolkit: revealing function and mechanism. | journal=Genome Biol | year= 2011 | volume= 12 | issue= 6 | pages= 224 | pmid=21722353 | doi=10.1186/gb-2011-12-6-224  | pmc=3218837}}</ref> Twenty five tests were carried out on [[mutant]] mice and two significant abnormalities were observed.<ref name="mgp_reference" /> Homozygous mutant animals of both sex had abnormal retinal [[pigmentation]] and morphology, while males also had atypical [[peripheral blood lymphocyte]] parameters.<ref name="mgp_reference" />


==References==
==References==
{{reflist|2}}
{{reflist}}
 
==Further reading==
==Further reading==
{{refbegin | 2}}
{{refbegin | 2}}
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| citations =  
| citations =  
*{{cite journal | author=Berry R, Stevens TJ, Walter NA, ''et al.'' |title=Gene-based sequence-tagged-sites (STSs) as the basis for a human gene map. |journal=Nat. Genet. |volume=10 |issue= 4 |pages= 415-23 |year= 1995 |pmid= 7670491 |doi= 10.1038/ng0895-415 }}
*{{cite journal   |vauthors=Berry R, Stevens TJ, Walter NA, etal |title=Gene-based sequence-tagged-sites (STSs) as the basis for a human gene map. |journal=Nat. Genet. |volume=10 |issue= 4 |pages= 415–23 |year= 1995 |pmid= 7670491 |doi= 10.1038/ng0895-415 }}
*{{cite journal  | author=Maruyama K, Sugano S |title=Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. |journal=Gene |volume=138 |issue= 1-2 |pages= 171-4 |year= 1994 |pmid= 8125298 |doi=  }}
*{{cite journal  |author1=Maruyama K |author2=Sugano S |title=Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. |journal=Gene |volume=138 |issue= 1-2 |pages= 171–4 |year= 1994 |pmid= 8125298 |doi=10.1016/0378-1119(94)90802-8 }}
*{{cite journal | author=Andersson B, Wentland MA, Ricafrente JY, ''et al.'' |title=A "double adaptor" method for improved shotgun library construction. |journal=Anal. Biochem. |volume=236 |issue= 1 |pages= 107-13 |year= 1996 |pmid= 8619474 |doi= 10.1006/abio.1996.0138 }}
*{{cite journal   |vauthors=Andersson B, Wentland MA, Ricafrente JY, etal |title=A "double adaptor" method for improved shotgun library construction. |journal=Anal. Biochem. |volume=236 |issue= 1 |pages= 107–13 |year= 1996 |pmid= 8619474 |doi= 10.1006/abio.1996.0138 }}
*{{cite journal | author=Yu W, Andersson B, Worley KC, ''et al.'' |title=Large-scale concatenation cDNA sequencing. |journal=Genome Res. |volume=7 |issue= 4 |pages= 353-8 |year= 1997 |pmid= 9110174 |doi=  }}
*{{cite journal   |vauthors=Yu W, Andersson B, Worley KC, etal |title=Large-scale concatenation cDNA sequencing. |journal=Genome Res. |volume=7 |issue= 4 |pages= 353–8 |year= 1997 |pmid= 9110174 |doi= 10.1101/gr.7.4.353| pmc=139146 }}
*{{cite journal | author=Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K, ''et al.'' |title=Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library. |journal=Gene |volume=200 |issue= 1-2 |pages= 149-56 |year= 1997 |pmid= 9373149 |doi= }}
*{{cite journal   |vauthors=Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K, etal |title=Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library. |journal=Gene |volume=200 |issue= 1-2 |pages= 149–56 |year= 1997 |pmid= 9373149 |doi=10.1016/S0378-1119(97)00411-3 }}
*{{cite journal  | author=Robertson HM, Zumpano KL |title=Molecular evolution of an ancient mariner transposon, Hsmar1, in the human genome. |journal=Gene |volume=205 |issue= 1-2 |pages= 203-17 |year= 1998 |pmid= 9461395 |doi= }}
*{{cite journal   |vauthors=Strausberg RL, Feingold EA, Grouse LH, etal |title=Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=99 |issue= 26 |pages= 16899–903 |year= 2003 |pmid= 12477932 |doi= 10.1073/pnas.242603899 | pmc=139241 |bibcode = 2002PNAS...9916899M }}
*{{cite journal | author=Strausberg RL, Feingold EA, Grouse LH, ''et al.'' |title=Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=99 |issue= 26 |pages= 16899-903 |year= 2003 |pmid= 12477932 |doi= 10.1073/pnas.242603899 }}
*{{cite journal   |vauthors=Gerhard DS, Wagner L, Feingold EA, etal |title=The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). |journal=Genome Res. |volume=14 |issue= 10B |pages= 2121–7 |year= 2004 |pmid= 15489334 |doi= 10.1101/gr.2596504 | pmc=528928 }}
*{{cite journal | author=Gerhard DS, Wagner L, Feingold EA, ''et al.'' |title=The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). |journal=Genome Res. |volume=14 |issue= 10B |pages= 2121-7 |year= 2004 |pmid= 15489334 |doi= 10.1101/gr.2596504 }}
*{{cite journal   |vauthors=Lee SH, Oshige M, Durant ST, etal |title=The SET domain protein Metnase mediates foreign DNA integration and links integration to nonhomologous end-joining repair. |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=102 |issue= 50 |pages= 18075–80 |year= 2006 |pmid= 16332963 |doi= 10.1073/pnas.0503676102 | pmc=1312370 |bibcode = 2005PNAS..10218075L }}
*{{cite journal | author=Lee SH, Oshige M, Durant ST, ''et al.'' |title=The SET domain protein Metnase mediates foreign DNA integration and links integration to nonhomologous end-joining repair. |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=102 |issue= 50 |pages= 18075-80 |year= 2006 |pmid= 16332963 |doi= 10.1073/pnas.0503676102 }}
*{{cite journal  |author1=Cordaux R |author2=Udit S |author3=Batzer MA |author4=Feschotte C |title=Birth of a chimeric primate gene by capture of the transposase gene from a mobile element. |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=103 |issue= 21 |pages= 8101–6 |year= 2006 |pmid= 16672366 |doi= 10.1073/pnas.0601161103 | pmc=1472436 |bibcode=2006PNAS..103.8101C}}
*{{cite journal  | author=Cordaux R, Udit S, Batzer MA, Feschotte C |title=Birth of a chimeric primate gene by capture of the transposase gene from a mobile element. |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=103 |issue= 21 |pages= 8101-6 |year= 2006 |pmid= 16672366 |doi= 10.1073/pnas.0601161103 }}
*{{cite journal   |vauthors=Keravala A, Liu D, Lechman ER, etal |title=Hyperactive Himar1 transposase mediates transposition in cell culture and enhances gene expression in vivo. |journal=Hum. Gene Ther. |volume=17 |issue= 10 |pages= 1006–18 |year= 2007 |pmid= 16989604 |doi= 10.1089/hum.2006.17.1006 }}
*{{cite journal | author=Keravala A, Liu D, Lechman ER, ''et al.'' |title=Hyperactive Himar1 transposase mediates transposition in cell culture and enhances gene expression in vivo. |journal=Hum. Gene Ther. |volume=17 |issue= 10 |pages= 1006-18 |year= 2007 |pmid= 16989604 |doi= 10.1089/hum.2006.17.ft-245 }}
*{{cite journal   |vauthors=Liu D, Bischerour J, Siddique A, etal |title=The human SETMAR protein preserves most of the activities of the ancestral Hsmar1 transposase. |journal=Mol. Cell. Biol. |volume=27 |issue= 3 |pages= 1125–32 |year= 2007 |pmid= 17130240 |doi= 10.1128/MCB.01899-06 | pmc=1800679 }}
*{{cite journal | author=Liu D, Bischerour J, Siddique A, ''et al.'' |title=The human SETMAR protein preserves most of the activities of the ancestral Hsmar1 transposase. |journal=Mol. Cell. Biol. |volume=27 |issue= 3 |pages= 1125-32 |year= 2007 |pmid= 17130240 |doi= 10.1128/MCB.01899-06 }}
*{{cite journal   |vauthors=Miskey C, Papp B, Mátés L, etal |title=The ancient mariner sails again: transposition of the human Hsmar1 element by a reconstructed transposase and activities of the SETMAR protein on transposon ends. |journal=Mol. Cell. Biol. |volume=27 |issue= 12 |pages= 4589–600 |year= 2007 |pmid= 17403897 |doi= 10.1128/MCB.02027-06 | pmc=1900042 }}
*{{cite journal | author=Miskey C, Papp B, Mátés L, ''et al.'' |title=The ancient mariner sails again: transposition of the human Hsmar1 element by a reconstructed transposase and activities of the SETMAR protein on transposon ends. |journal=Mol. Cell. Biol. |volume=27 |issue= 12 |pages= 4589-600 |year= 2007 |pmid= 17403897 |doi= 10.1128/MCB.02027-06 }}
*{{cite journal   |vauthors=Roman Y, Oshige M, Lee YJ, etal |title=Biochemical characterization of a SET and transposase fusion protein, Metnase: its DNA binding and DNA cleavage activity. |journal=Biochemistry |volume=46 |issue= 40 |pages= 11369–76 |year= 2007 |pmid= 17877369 |doi= 10.1021/bi7005477 |pmc=3374406}}
*{{cite journal | author=Roman Y, Oshige M, Lee YJ, ''et al.'' |title=Biochemical characterization of a SET and transposase fusion protein, Metnase: its DNA binding and DNA cleavage activity. |journal=Biochemistry |volume=46 |issue= 40 |pages= 11369-76 |year= 2007 |pmid= 17877369 |doi= 10.1021/bi7005477 }}
}}
}}
{{refend}}
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{{protein-stub}}
[[Category:Genes mutated in mice]]
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Revision as of 06:10, 11 September 2017

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Identifiers
Aliases
External IDsGeneCards: [1]
Orthologs
SpeciesHumanMouse
Entrez

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Ensembl

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UniProt

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RefSeq (mRNA)

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RefSeq (protein)

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Wikidata
View/Edit Human

Histone-lysine N-methyltransferase SETMAR is an enzyme that in humans is encoded by the SETMAR gene.[1][2]


Model organisms

Model organisms have been used in the study of SETMAR function. A conditional knockout mouse line, called Setmartm1a(EUCOMM)Wtsi[9][10] 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.[11][12][13]

Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion.[7][14] Twenty five tests were carried out on mutant mice and two significant abnormalities were observed.[7] Homozygous mutant animals of both sex had abnormal retinal pigmentation and morphology, while males also had atypical peripheral blood lymphocyte parameters.[7]

References

  1. ↑ Robertson HM; Zumpano KL (Feb 1998). "Molecular evolution of an ancient mariner transposon, Hsmar1, in the human genome". Gene. 205 (1–2): 203–17. doi:10.1016/S0378-1119(97)00472-1. PMID 9461395.
  2. ↑ "Entrez Gene: SETMAR SET domain and mariner transposase fusion gene".
  3. ↑ "Eye morphology data for Setmar". Wellcome Trust Sanger Institute.
  4. ↑ "Peripheral blood lymphocytes data for Setmar". Wellcome Trust Sanger Institute.
  5. ↑ "Salmonella infection data for Setmar". Wellcome Trust Sanger Institute.
  6. ↑ "Citrobacter infection data for Setmar". Wellcome Trust Sanger Institute.
  7. ↑ 7.0 7.1 7.2 7.3 Gerdin, AK (2010). "The Sanger Mouse Genetics Programme: High throughput characterisation of knockout mice". Acta Ophthalmologica. 88: 925–7. doi:10.1111/j.1755-3768.2010.4142.x.
  8. ↑ Mouse Resources Portal, Wellcome Trust Sanger Institute.
  9. ↑ "International Knockout Mouse Consortium".
  10. ↑ "Mouse Genome Informatics".
  11. ↑ 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.
  12. ↑ Dolgin, Elie (2011). "Mouse library set to be knockout". Nature. 474 (7351): 262–3. doi:10.1038/474262a. PMID 21677718.
  13. ↑ International Mouse Knockout Consortium; Collins, FS; Rossant, J; Wurst, W (2007). "A Mouse for All Reasons". Cell. 128 (1): 9–13. doi:10.1016/j.cell.2006.12.018. PMID 17218247.
  14. ↑ 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.

Further reading

Retrieved from "https://www.wikidoc.org/index.php?title=SETMAR&oldid=1413256"