Evolutionary origin and genomic organization of Micro-RNA genes in immunoglobulin lambda variable region gene family

Molecular Biology and Evolution

Volumn 26, Issue 5, 2009, Pages 1179-1189

  Das, Sabyasachi ^a,b  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Immunoglobulin lambda variable region genes; Micro RNA evolution; Micro RNA host genes; Micro RNA transcription; Multigene family; Overlapping genes

Indexed keywords

IMMUNOGLOBULIN LAMBDA CHAIN; MICRORNA;

ARTICLE; CONTROLLED STUDY; EXON; GENE DELETION; GENE DUPLICATION; GENE EXPRESSION; GENE NUMBER; GENE SEQUENCE; GENE STRUCTURE; GENETIC VARIABILITY; HUMAN; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PROTEIN SECONDARY STRUCTURE; SEQUENCE ALIGNMENT;

ANIMALS; BASE SEQUENCE; CHROMOSOMES, MAMMALIAN; EVOLUTION, MOLECULAR; EXONS; GENOME; HUMANS; IMMUNOGLOBULIN LAMBDA-CHAINS; IMMUNOGLOBULIN VARIABLE REGION; MICRORNAS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; NUCLEIC ACID CONFORMATION; PHYLOGENY; PRIMATES; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID;

PRIMATES;

EID: 65349130771     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msp035     Document Type: Article

References (56)

1. Ambros V, Bartel B, Bartel DP, et al. 2003. A uniform system for microRNA annotation. RNA. 9:277-279 (13 co-authors).
2. Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B, Gaasterland T, Meyer J, Tuschl T. 2003. The small RNA profile during Drosophila melanogaster development. Dev Cell. 5:337-350.
3. Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 116:281-297.
4. Bartel DP, Chen CZ. 2004. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat Rev Genet. 5:396-400.
5. Bentwich I, Avniel A, Karov Y, et al. 2005. Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet. 37:766-770 (13 co-authors).
6. Cullen BR. 2004. Transcription and processing of human microRNA precursors. Mol Cell. 16:861-865.
7. Cummins JM, He Y, Leary RJ, et al. 2006. The colorectal microRNAome. Proc Natl Acad Sci USA. 103:3687-3692 (16 co-authors).
8. Das S, Nikolaidis N, Klein J, Nei M. 2008. Evolutionary redefinition of immunoglobulin light chain isotypes in tetrapods using molecular markers. Proc Natl Acad Sci USA. 105:16647-16652.
9. Das S, Nozawa M, Klein J, Nei M. 2008. Evolutionary dynamics of the immunoglobulin heavy chain variable region genes in vertebrates. Immunogenetics. 60:47-55.
10. Denli AM, Tops BB, Plasterk RH, Ketting RF, Hannon GJ. 2004. Processing of primary microRNAs by the microprocessor complex. Nature. 432:231-235.
11. Ding Y, Chan CY, Lawrence CE. 2005. RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA. 11:1157-1166.
12. Eis PS, Tam W, Sun L, Chadburn A, Li Z, Gomez MF, Lund E, Dahlberg JE. 2005. Accumulation of miR-155 and BIC RNA in human B cell lymphomas. Proc Natl Acad Sci USA. 102:3627-3632.
13. Glazov EA, McWilliam S, Barris WC, Dalrymple BP. 2008. Origin, evolution, and biological role of miRNA cluster in DLK-DIO3 genomic region in placental mammals. Mol Biol Evol. 25:939-948.
14. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. 2008. miRBase: tools for microRNA genomics. Nucleic Acids Res. 36:D154-D158.
15. Gruber AR, Lorenz R, Bernhart SH, Neubock R, Hofacker IL. 2008. The Vienna RNA website. Nucleic Acids Res. 36:W70-W74.
16. Han J, Lee Y, Yeom KH, Kim YK, Jin H, Kim VN. 2004. The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev. 18:3016-3027.
17. Hoefig KP, Heissmeyer V. 2008. MicroRNAs grow up in the immune system. Curr Opin Immunol. 20:281-287.
18. Houbaviy HB, Dennis L, Jaenisch R, Sharp PA. 2005. Characterization of a highly variable eutherian microRNA gene. RNA. 11:1245-1257.
19. Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, Zamore PD. 2001. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science. 293:834-838.
20. Kawasaki H, Taira K. 2003. Hes1 is a target of microRNA-23 during retinoic-acid-induced neuronal differentiation of NT2 cells. Nature. 423:838-842.
21. Kim VN, Nam JW. 2006. Genomics of microRNA. Trends Genet. 22:165-173.
22. Kim YK, Kim VN. 2007. Processing of intronic microRNAs. Embo J. 26:775-783.
23. Klein J, Hořejš́í V. 1997. Immunology. Oxford: Blackwell Science Ltd.
24. Kohany O, Gentles AJ, Hankus L, Jurka J. 2006. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics. 7:474.
25. Kyte J, Doolittle RF. 1982. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 157:105-132.
26. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T. 2001. Identification of novel genes coding for small expressed RNAs. Science. 294:853-858.
27. Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T. 2002. Identification of tissue-specific microRNAs from mouse. Curr Biol. 12:735-739.
28. Landgraf P, Rusu M, Sheridan R, et al. 2007. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell. 129:1401-1414 (51 co-authors).
29. Lau NC, Lim LP, Weinstein EG, Bartel DP. 2001. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science. 294:858-862.
30. Lawrie CH, Saunders NJ, Soneji S, et al. 2008. MicroRNA expression in lymphocyte development and malignancy. Leukemia. 22:1440-1446 (14 co-authors).
31. Lee RC, Ambros V. 2001. An extensive class of small RNAs in Caenorhabditis elegans. Science. 294:862-864.
32. Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP. 2003. Vertebrate microRNA genes. Science. 299:1540.
33. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM. 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature. 433:769-773.
34. Lindsay MA. 2008. microRNAs and the immune response. Trends Immunol. 29:343-351.
35. Liu CG, Calin GA, Meloon B, et al. 2004. An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc Natl Acad Sci USA. 101:9740-9744 (14 co-authors).
36. Lu J, Getz G, Miska EA, et al. 2005. MicroRNA expression profiles classify human cancers. Nature. 435:834-838 (14 coauthors).
37. Lu J, Shen Y, Wu Q, Kumar S, He B, Shi S, Carthew RW, Wang SM, Wu CI. 2008. The birth and death of microRNA genes in Drosophila. Nat Genet. 40:351-355.
38. McCaskill JS. 1990. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers. 29:1105-1119.
39. Nei M, Kumar S. 2000. Molecular evolution and phylogenetics. Oxford: Oxford University Press.
40. Ota T, Sitnikova T, Nei M. 2000. Evolution of vertebrate immunoglobulin variable gene segments. Curr Top Microbiol Immunol. 248:221-245.
41. Piriyapongsa J, Marino-Ramirez L, Jordan IK. 2007. Origin and evolution of human microRNAs from transposable elements. Genetics. 176:1323-1337.
42. Prestridge DS. 1991. SIGNAL SCAN: a computer program that scans DNA sequences for eukaryotic transcriptional elements. Comput Appl Biosci. 7:203-206.
43. Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A. 2004. Identification of mammalian microRNA host genes and transcription units. Genome Res. 14:1902-1910.
44. SaitouN,NeiM.1987. The neighbor-joining method:anew method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406-425.
45. Sibley CG, Ahlquist JE. 1987. DNA hybridization evidence of hominoid phylogeny: results from an expanded data set. J Mol Evol. 26:99-121.
46. Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M. 2007. Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res. 17:1865-1879.
47. Svoboda P, Di Cara A. 2006. Hairpin RNA: a secondary structure of primary importance. Cell Mol Life Sci. 63:901-908.
48. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 24:1596-1599.
49. Tanzer A, Stadler PF. 2004. Molecular evolution of a microRNA cluster. J Mol Biol. 339:327-335.
50. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
51. Vasicek TJ, Leder P. 1990. Structure and expression of the human immunoglobulin lambda genes. J Exp Med. 172:609-620.
52. Verdel A, Moazed D. 2005. RNAi-directed assembly of heterochromatin in fission yeast. FEBS Lett. 579:5872-5878.
53. Wienholds E, Kloosterman WP, Miska E, Alvarez-Saavedra E, Berezikov E, de Bruijn E, Horvitz HR, Kauppinen S, Plasterk RH. 2005. MicroRNA expression in zebrafish embryonic development. Science. 309:310-311.
54. Zhang R, Peng Y, Wang W, Su B. 2007. Rapid evolution of an X-linked microRNA cluster in primates. Genome Res. 17:612-617.
55. Zhang R, Wang YQ, Su B. 2008. Molecular evolution of a primate-specific microRNA family. Mol Biol Evol. 25: 1493-1502.
56. Zuker M, Stiegler P. 1981. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9:133-148.