The whole-organism heavy chain B cell repertoire from Zebrafish self-organizes into distinct network features

BMC Systems Biology

Volumn 5, Issue , 2011, Pages

  Ben Hamo, Rotem ^a   Efroni, Sol ^a  

^a BAR ILAN UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

DANIO RERIO;

IMMUNOGLOBULIN MU CHAIN;

ADAPTIVE IMMUNITY; ANIMAL; ARTICLE; B LYMPHOCYTE; BIOLOGY; GENE REGULATORY NETWORK; GENETICS; IMMUNOLOGY; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN MOTIF; SEQUENCE ALIGNMENT; ZEBRA FISH;

ADAPTIVE IMMUNITY; AMINO ACID MOTIFS; ANIMALS; B-LYMPHOCYTES; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DNA MUTATIONAL ANALYSIS; GENE REGULATORY NETWORKS; IMMUNOGLOBULIN MU-CHAINS; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT; ZEBRAFISH;

EID: 79751537038     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-27     Document Type: Article

References (43)

1. Richard A, Goldsby TJK, Barbara A, Osborne. KUBY IMMUNOLOGY. 2000, W.H. Freeman & Company.
2. Cohen IR. Tending Adam's garden: evolving the cognitive immune self. 2000, San Diego, CA: Academic Press.
3. Parham P. The immune System. 2009, New York, Garland Publishing Press.
4. Andersson E, Matsunaga T. Evolutionary stability of the immunoglobulin heavy chain variable region gene families in teleost. Immunogenetics 1998, 47(3):272-277. 10.1007/s002510050357, 9435346.
5. Hansen JD, McBlane JF. Recombination-activating genes, transposition, and the lymphoid-specific combinatorial immune system: a common evolutionary connection. Curr Top Microbiol Immunol 2000, 248:111-135.
6. Li Z, Chang Y. V(D)J recombination in zebrafish: Normal joining products with accumulation of unresolved coding ends and deleted signal ends. Mol Immunol 2007, 44(7):1793-1802. 10.1016/j.molimm.2006.07.295, 1785108, 17005252.
7. Clark LA, Ganesan S, Papp S, van Vlijmen HW. Trends in antibody sequence changes during the somatic hypermutation process. J Immunol 2006, 177(1):333-340.
8. Kepler TB, Perelson AS. Somatic hypermutation in B cells: an optimal control treatment. J Theor Biol 1993, 164(1):37-64. 10.1006/jtbi.1993.1139, 8264243.
9. Foster SJ, Dorner T, Lipsky PE. Somatic hypermutation of VkappaJkappa rearrangements: targeting of RGYW motifs on both DNA strands and preferential selection of mutated codons within RGYW motifs. Eur J Immunol 1999, 29(12):4011-4021. 10.1002/(SICI)1521-4141(199912)29:12<4011::AID-IMMU4011>3.0.CO;2-W, 10602011.
10. Berek C, Milstein C. The dynamic nature of the antibody repertoire. Immunol Rev 1988, 105:5-26. 10.1111/j.1600-065X.1988.tb00763.x, 3058579.
11. Kleinstein SH, Louzoun Y, Shlomchik MJ. Estimating hypermutation rates from clonal tree data. J Immunol 2003, 171(9):4639-4649.
12. Jolly CJ, Wagner SD, Rada C, Klix N, Milstein C, Neuberger MS. The targeting of somatic hypermutation. Semin Immunol 1996, 8(3):159-168. 10.1006/smim.1996.0020, 8738915.
13. Yoder JA, Nielsen ME, Amemiya CT, Litman GW. Zebrafish as an immunological model system. Microbes Infect 2002, 4(14):1469-1478. 10.1016/S1286-4579(02)00029-1, 12475637.
14. Willett CE, Cherry JJ, Steiner LA. Characterization and expression of the recombination activating genes (rag1 and rag2) of zebrafish. Immunogenetics 1997, 45(6):394-404. 10.1007/s002510050221, 9089097.
15. Trede NS, Langenau DM, Traver D, Look AT, Zon LI. The use of zebrafish to understand immunity. Immunity 2004, 20(4):367-379. 10.1016/S1074-7613(04)00084-6, 15084267.
16. Weinstein JA, Jiang N, White RA, Fisher DS, Quake SR. High-throughput sequencing of the zebrafish antibody repertoire. Science 2009, 324(5928):807-810. 10.1126/science.1170020, 19423829.
17. Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM. Systematic determination of genetic network architecture. Nat Genet 1999, 22(3):281-285. 10.1038/10343, 10391217.
18. Jeong H, Mason SP, Barabasi AL, Oltvai ZN. Lethality and centrality in protein networks. Nature 2001, 411(6833):41-42. 10.1038/35075138, 11333967.
19. Ozier O, Amin N, Ideker T. Global architecture of genetic interactions on the protein network. Nat Biotechnol 2003, 21(5):490-491. 10.1038/nbt0503-490, 12721566.
20. Barabasi AL. Scale-free networks: a decade and beyond. Science 2009, 325(5939):412-413. 10.1126/science.1173299, 19628854.
21. Girvan M, Newman ME. Community structure in social and biological networks. Proc Natl Acad Sci USA 2002, 99(12):7821-7826. 10.1073/pnas.122653799, 122977, 12060727.
22. Zotenko E, Mestre J, O'Leary DP, Przytycka TM. Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLoS Comput Biol 2008, 4(8):e1000140. 10.1371/journal.pcbi.1000140, 2467474, 18670624.
23. He XL, Zhang JZ. Why do hubs tend to be essential in protein networks?. Plos Genetics 2006, 2(6):826-834.
24. Jeong H, Mason SP, Barabasi AL, Oltvai ZN. Lethality and centrality in protein networks. Nature 2001, 411(6833):41-42. 10.1038/35075138, 11333967.
25. Park JY, Barabasi AL. Distribution of node characteristics in complex networks. Proceedings of the National Academy of Sciences of the United States of America 2007, 104(46):17916-17920. 10.1073/pnas.0705081104, 2084271, 17989231.
26. Yook SH, Oltvai ZN, Barabasi AL. Functional and topological characterization of protein interaction networks. Proteomics 2004, 4(4):928-942. 10.1002/pmic.200300636, 15048975.
27. Mora T, Walczak AM, Bialek W, Callan CG. Maximum entropy models for antibody diversity. Proc Natl Acad Sci USA 2010, 107(12):5405-5410. 10.1073/pnas.1001705107, 20212159.
28. Zheng NY, Wilson K, Jared M, Wilson PC. Intricate targeting of immunoglobulin somatic hypermutation maximizes the efficiency of affinity maturation. J Exp Med 2005, 201(9):1467-1478. 10.1084/jem.20042483, 2213188, 15867095.
29. Papavasiliou FN, Schatz DG. The activation-induced deaminase functions in a postcleavage step of the somatic hypermutation process. J Exp Med 2002, 195(9):1193-1198. 10.1084/jem.20011858, 2193708, 11994424.
30. Muramatsu M, Sankaranand VS, Anant S, Sugai M, Kinoshita K, Davidson NO, Honjo T. Specific expression of activation-induced cytidine deaminase (AID), a novel member of the RNA-editing deaminase family in germinal center B cells. J Biol Chem 1999, 274(26):18470-18476. 10.1074/jbc.274.26.18470, 10373455.
31. Tanaka A, Shen HM, Ratnam S, Kodgire P, Storb U. Attracting AID to targets of somatic hypermutation. J Exp Med 207(2):405-415. 10.1084/jem.20090821, 2822603, 20100870.
32. Hershberg U, Shlomchik MJ. Differences in potential for amino acid change after mutation reveals distinct strategies for kappa and lambda light-chain variation. Proc Natl Acad Sci USA 2006, 103(43):15963-15968. 10.1073/pnas.0607581103, 1635110, 17038496.
33. Barbazuk WB, Korf I, Kadavi C, Heyen J, Tate S, Wun E, Bedell JA, McPherson JD, Johnson SL. The syntenic relationship of the zebrafish and human genomes. Genome Res 2000, 10(9):1351-1358. 10.1101/gr.144700, 310919, 10984453.
34. Postlethwait JH, Woods IG, Ngo-Hazelett P, Yan YL, Kelly PD, Chu F, Huang H, Hill-Force A, Talbot WS. Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res 2000, 10(12):1890-1902. 10.1101/gr.164800, 11116085.
35. Liu TX, Zhou Y, Kanki JP, Deng M, Rhodes J, Yang HW, Sheng XM, Zon LI, Look AT. Evolutionary conservation of zebrafish linkage group 14 with frequently deleted regions of human chromosome 5 in myeloid malignancies. Proc Natl Acad Sci USA 2002, 99(9):6136-6141. 10.1073/pnas.072560099, 122915, 11983906.
36. Andersson E, Matsunaga T. Evolution of immunoglobulin heavy chain variable region genes: a VH family can last for 150-200 million years or longer. Immunogenetics 1995, 41(1):18-28. 10.1007/BF00188428, 7806270.
37. Kabat EA. The paucity of species-specific amino acid residues in the variable regions of human and mouse Bence-Jones proteins and its evolutionary and genetic implications. Proc Natl Acad Sci USA 1967, 57(5):1345-1349. 10.1073/pnas.57.5.1345, 224478, 5231739.
38. Andersson E, Tormanen V, Matsunaga T. Evolution of a VH gene family in low vertebrates. Int Immunol 1991, 3(6):527-533. 10.1093/intimm/3.6.527, 1716145.
39. Rast JP, Litman GW. T-cell receptor gene homologs are present in the most primitive jawed vertebrates. Proc Natl Acad Sci USA 1994, 91(20):9248-9252. 10.1073/pnas.91.20.9248, 44789, 7937749.
40. Mora T, Walczak AM, Bialek W, Callan CG. Maximum entropy models for antibody diversity. Proc Natl Acad Sci USA 107(12):5405-5410. 10.1073/pnas.1001705107, 2851784, 20212159.
41. Danilova N, Bussmann J, Jekosch K, Steiner LA. The immunoglobulin heavy-chain locus in zebrafish: identification and expression of a previously unknown isotype, immunoglobulin Z. Nat Immunol 2005, 6(3):295-302. 10.1038/ni1166, 15685175.
42. McGinnis S, Madden TL. BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 2004, (32 Web Server):W20-25. 10.1093/nar/gkh435, 441573, 15215342.
43. Batagelj VMA. Pajek: A program for large network analysis. Connections 1998, 47-57.