Positive selection on the nonhomologous end-joining factor Cernunnos-XLF in the human lineage

Biology Direct

Volumn 1, Issue , 2006, Pages

  Pavlicek, Adam ^a   Jurka, Jerzy ^a  

^a Genetic Information Research Institute   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BOVINAE; MACACA; MACACA MULATTA; PAN;

EID: 34248334698     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-1-15     Document Type: Review

References (41)

1. Rich T Allen RL Wyllie AH Defying death after DNA damage Nature 2000 407 777-783 10.1038/35037717 11048728
2. Haber JE Partners and pathways repairing a double-strand break Trends Genet 2000 16 259-264 10.1016/S0168-9525(00)02022-9 10827453
3. Dai Y Kysela B Hanakahi LA Manolis K Riballo E Stumm M Harville TO West SC Oettinger MA Jeggo PA Nonhomologous end joining and V(D)J recombination require an additional factor Proc Natl Acad Sci USA 2003 100 2462-2467 151363 12604777 10.1073/pnas.0437964100
4. Buck D Malivert L de Chasseval R Barraud A Fondaneche MC Sanal O Plebani A Stephan JL Hufnagel M le Deist F Fischer A Durandy A de Villartay JP Revy P Cernunnos, a novel nonhomologous end-joining factor, is mutated in human immunodeficiency with microcephaly Cell 2006 124 287-299 10.1016/j.cell.2005.12.030 16439204
5. Ahnesorg P Smith P Jackson SP XLF interacts with the XRCC4-DNA ligase IV complex to promote DNA nonhomologous end-joining Cell 2006 124 301-313 10.1016/j.cell.2005.12.031 16439205
6. Callebaut I Malivert L Fischer A Mornon JP Revy P de Villartay JP Cernunnos interacts with the XRCC4/DNA-ligase IV complex and is homologous to the yeast nonhomologous end-joining factor NEJ1 J Biol Chem 2006
7. Zhang J Evolution of the human ASPM gene, a major determinant of brain size Genetics 2003 165 2063-2070 14704186
8. Evans PD Anderson JR Vallender EJ Gilbert SL Malcom CM Dorus S Lahn BT Adaptive evolution of ASPM, a major determinant of cerebral cortical size in humans Hum Mol Genet 2004 13 489-494 10.1093/hmg/ddh055 14722158
9. Kouprina N Pavlicek A Mochida GH Solomon G Gersch W Yoon YH Collura R Ruvolo M Barrett JC Woods CG Walsh CA Jurka J Larionov V Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion PLoS Biol 2004 2 E126 374243 15045028 10.1371/ journal.pbio.0020126
10. Evans PD Anderson JR Vallender EJ Choi SS Lahn BT Reconstructing the evolutionary history of microcephalin, a gene controlling human brain size Hum Mol Genet 2004 13 1139-1145 10.1093/hmg/ddh126 15056607
11. Wang YQ Su B Molecular evolution of microcephalin, a gene determining human brain size Hum Mol Genet 2004 13 1131-1137 10.1093/hmg/ddh127 15056608
12. Dorus S Vallender EJ Evans PD Anderson JR Gilbert SL Mahowald M Wyckoff GJ Malcom CM Lahn BT Accelerated evolution of nervous system genes in the origin of Homo sapiens Cell 2004 119 1027-1040 10.1016/ j.cell.2004.11.040 15620360
13. Mekel-Bobrov N Gilbert SL Evans PD Vallender EJ Anderson JR Hudson RR Tishkoff SA Lahn BT Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens Science 2005 309 1720-1722 10.1126/ science.1116815 16151010
14. Evans PD Gilbert SL Mekel-Bobrov N Vallender EJ Anderson JR Vaez-Azizi LM Tishkoff SA Hudson RR Lahn BT Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans Science 2005 309 1717-1720 10.1126/science.1113722 16151009
15. Ponting C Jackson AP Evolution of primary microcephaly genes and the enlargement of primate brains Curr Opin Genet Dev 2005 15 241-248 10.1016/j.gde.2005.04.009 15917198
16. Voight BF Kudaravalli S Wen X Pritchard JK A map of recent positive selection in the human genome PLoS Biol 2006 4 e72 1382018 16494531 10.1371/journal.pbio.0040072
17. Bustamante CD Fledel-Alon A Williamson S Nielsen R Hubisz MT Glanowski S Tanenbaum DM White TJ Sninsky JJ Hernandez RD Civello D Adams MD Cargill M Clark AG Natural selection on protein-coding genes in the human genome Nature 2005 437 1153-1157 10.1038/nature04240 16237444
18. Grawunder U Zimmer D Leiber MR DNA ligase IV binds to XRCC4 via a motif located between rather than within its BRCT domains Curr Biol 1998 8 873-876 10.1016/S0960-9822(07)00349-1 9705934
19. Junop MS Modesti M Guarne A Ghirlando R Gellert M Yang W Crystal structure of the Xrcc4 DNA repair protein and implications for end joining EMBO J 2000 19 5962-5970 305814 11080143 10.1093/emboj/19.22.5962
20. Sibanda BL Critchlow SE Begun J Pei XY Jackson SP Blundell TL Pellegrini L Crystal structure of an Xrcc4-DNA ligase IV complex Nat Struct Biol 2001 8 1015-1019 10.1038/nsb725 11702069
21. Clark AG Glanowski S Nielsen R Thomas PD Kejariwal A Todd MA Tanenbaum DM Civello D Lu F Murphy B Ferriera S Wang G Zheng X White TJ Sninsky JJ Adams MD Cargill M Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios Science 2003 302 1960-1963 10.1126/ science.1088821 14671302
22. Nielsen R Bustamante C Clark AG Glanowski S Sackton TB Hubisz MJ Fledel-Alon A Tanenbaum DM Civello D White TJ Sninsky J Adams MD Cargill M A scan for positively selected genes in the genomes of humans and chimpanzees PLoS Biol 2005 3 e170 1088278 15869325 10.1371/ journal.pbio.0030170
23. Kornack DR Rakic P Changes in cell-cycle kinetics during the development and evolution of primate neocortex Proc Natl Acad Sci USA 1998 95 1242-1246 18732 9448316 10.1073/pnas.95.3.1242
24. Kouprina N Pavlicek A Collins NK Nakano M Noskov VN Ohzeki J Mochida GH Risinger JI Goldsmith P Gunsior M Solomon G Gersch W Kim JH Barrett JC Walsh CA Jurka J Masumoto H Larionov V The microcephaly ASPM gene is expressed in proliferating tissues and encodes for a mitotic spindle protein Hum Mol Genet 2005 14 2155-2165 10.1093/hmg/ddi220 15972725
25. Xu X Lee J Stern DF Microcephalin is a DNA damage response protein involved in regulation of CHK1 and BRCA1 J Biol Chem 2004 279 34091-34094 10.1074/jbc.C400139200 15220350
26. Lin SY Rai R Li K Xu ZX Elledge SJ BRIT1/MCPH1 is a DNA damage responsive protein that regulates the Brca1-Chk1 pathway, implicating checkpoint dysfunction in microcephaly Proc Natl Acad Sci USA 2005 102 15105-15109 1257745 16217032 10.1073/pnas.0507722102
27. Abner CW McKinnon PJ The DNA double-strand break response in the nervous system DNA Repair (Amst) 2004 3 1141-1147 10.1016/j.dnarep.2004.03.009 15279803
28. Huttley GA Easteal S Southey MC Tesoriero A Giles GG McCredie MR Hopper JL Venter DJ Adaptive evolution of the tumour suppressor BRCA1 in humans and chimpanzees. Australian Breast Cancer Family Study Nat Genet 2000 25 410-413 10.1038/78092 10932184
29. Pavlicek A Noskov VN Kouprina N Barrett JC Jurka J Larionov V Evolution of the tumor suppressor BRCA1 locus in primates: Implications for cancer predisposition Hum Mol Genet 2004 13 2737-2751 10.1093/hmg/ddh301 15385441
30. Wheeler DL Barrett T Benson DA Bryant SH Canese K Chetvernin V Church DM DiCuccio M Edgar R Federhen S Geer LY Helmberg W Kapustin Y Kenton DL Khovayko O Lipman DJ Madden TL Maglott DR Ostell J Pruitt KD Schuler GD Schriml LM Sequeira E Sherry ST Sirotkin K Souvorov A Starchenko G Suzek TO Tatusov R Tatusova TA Wagner L Yaschenko E Database resources of the National Center for Biotechnology Information Nucleic Acids Res 2006 34 D173-180 1347520 16381840 10.1093/nar/gkj158
31. Kent WJ BLAT-the BLAST-like alignment tool Genome Res 2002 12 656-664 187518 11932250 10.1101/gr.229202. Article published online before March 2002
32. Subramanian AR Weyer-Menkhoff J Kaufmann M Morgenstern B DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment BMC Bioinformatics 2005 6 66 1087830 15784139 10.1186/1471-2105-6-66
33. Nicholas KB Nicholas HB Jr Deerfield DW GeneDoc: Analysis and Visualization of Genetic Variation EMBNEW.NEWS 1997 4 14
34. Korber B HIV Signature and Sequence Variation Analysis Computational Analysis of HIV Molecular Sequences Kluwer Academic Publishers, Dordrecht, Netherlands Rodrigo AG, Learn GH 2000 55-72
35. Gonnet GH Cohen MA Benner SA Exhaustive matching of the entire protein sequence database Science 1992 256 1443-1145 1604319
36. Yang Z PAML: A program package for phylogenetic analysis by maximum likelihood Comput Appl Biosci 1997 13 555-556 9367129
37. Page RD TREEVIEW: An application to display phylogenetic trees on personal computers Comput Appl Biosci 1996 12 357-358 8902363
38. Yang Z Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution Mol Biol Evol 1998 15 568-573 9580986
39. Kelley LA MacCallum RM Sternberg MJ Enhanced Genome Annotation using Structural Profiles in the Program 3D-PSSM J Mol Biol 2000 299 499-520 10.1006/jmbi.2000.3741 10860755
40. Schwede T Kopp J Guex N Peitsch MC SWISS-MODEL: An automated protein homology-modeling server Nucleic Acids Res 2003 31 3381-3385 168927 12824332 10.1093/nar/gkg520
41. PyMOL, DeLano Scientific, San Carlos CA http://www.pymol.org