Short interspersed DNA elements and miRNAs: a novel hidden gene regulation layer in zebrafish?

Chromosome Research

Volumn 23, Issue 3, 2015, Pages 533-544

  Scarpato, Margherita ^a   Angelini, Claudia ^b   Cocca, Ennio ^c   Pallotta, Maria M ^d   Morescalchi, Maria A ^d   Capriglione, Teresa ^d  

^a INSTITUTE OF GENETICS AND BIOPHYSICS ADRIANO BUZZATI TRAVERSO   (Italy)

^b CNR   (Italy)

^c CNR   (Italy)

^d UNIVERSITY OF NAPLES FEDERICO II   (Italy)

Author keywords

3 UTR; miRNA; Retrotransposons; SINEs

Indexed keywords

DNA; MICRORNA; MICRORNA 101; MICRORNA 128; MICRORNA 129; MICRORNA 141; MICRORNA 142A 3P; MICRORNA 142A 5P; MICRORNA 144; MICRORNA 17A; MICRORNA 181; MICRORNA 200A; MICRORNA 203; MICRORNA 204; MICRORNA 217; MICRORNA 2184; MICRORNA 2193; MICRORNA 223; MICRORNA 23; MICRORNA 30; MICRORNA 338; MICRORNA 3906; MICRORNA 429; MICRORNA 722; MICRORNA 724; MICRORNA 735; MICRORNA 737; MICRORNA 740; MICRORNA 9; MICRORNA148; UNCLASSIFIED DRUG; 3' UNTRANSLATED REGION; MESSENGER RNA;

3' UNTRANSLATED REGION; ARTICLE; CELL DIFFERENTIATION; CELL FUNCTION; CELL PROLIFERATION; COMPUTER MODEL; DNA HYBRIDIZATION; GENE LOCUS; GENE ONTOLOGY; GENE REGULATORY NETWORK; GENETIC CORRELATION; GENOME; GENOMICS; METABOLIC BALANCE; METABOLISM; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RETROPOSON; SHORT INTERSPERSED REPEAT; ZEBRA FISH; ANIMAL; BINDING SITE; BIOLOGY; CHEMISTRY; CHROMOSOMAL MAPPING; GENE EXPRESSION REGULATION; GENETICS; MULTIGENE FAMILY; PROCEDURES; RNA INTERFERENCE; SEQUENCE ANALYSIS;

3' UNTRANSLATED REGIONS; ANIMALS; BINDING SITES; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION; GENE ONTOLOGY; GENOME; GENOMICS; MICRORNAS; MULTIGENE FAMILY; RNA INTERFERENCE; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; SHORT INTERSPERSED NUCLEOTIDE ELEMENTS; ZEBRAFISH;

EID: 84947492228     PISSN: 09673849     EISSN: 15736849     Source Type: Journal    
DOI: 10.1007/s10577-015-9484-6     Document Type: Article

References (55)

1. Acunzo M, Croce CM (2015) MicroRNA in cancer and cachexia—a mini-review. J Infect Dis 212:S74–S77
2. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297
3. Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D (2006) A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 441:87–90
4. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B 57:289–300
5. Bohne A, Brunet F, Galiana-Arnoux D, Schultheis C, Volff JN (2008) Transposable elements as drivers of genomic and biological diversity in vertebrates. Chromosom Res 16:203–215
6. Caceres M, Puig M, Ruiz A (2001) Molecular characterization of two natural hotspots in the Drosophila buzzatii genome induced by transposon insertions. Genome Res 11:1353–1364
7. Capriglione T, Odierna G, Caputo V, Canapa A, Olmo E (2002) Characterization of a Tc1-like transposon in the Antarctic ice-fish, Chionodraco hamatus. Gene 295:193–198
8. Capriglione T, De Paolo S, Cocca E (2014) Helinoto, a Helitron2 transposon from the icefish Chionodraco hamatus, contains a region with three deubiquitinase-like domains that exhibit transcriptional activity. Comp Biochem Physiol Part D Genomics Proteomics 11:49–58
9. Carthew RW, Sontheimer EJ (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136:642–655
10. Chalopin D, Galiana D, Volff JN (2012) Genetic innovation in vertebrates: gypsy integrase genes and other genes derived from transposable elements. Int J Evol Biol 2012, 724519. doi:10.1155/2012/724519, 11 pages
11. Chalopin D, Naville M, Plard F, Galiana D, Volff JN (2015) Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates. Genome Biol Evol 7:567–580
12. Chen LL, Carmichael GG (2008) Gene regulation by SINEs and inosines: biological consequences of A-to-I editing of Alu element inverted repeats. Cell Cycle 7:3294–3301
13. Chen K, Rajewsky N (2007) The evolution of gene regulation by transcription factors and microRNAs. Nat Rev Genet 8:93–103
14. Chen CZ, Li L, Lodish HF, Bartel DP (2004) MicroRNAs modulate hematopoietic lineage differentiation. Science 303:83–86
15. Chénais B, Caruso A, Hiard S, Casse N (2012) The impact of transposable elements on eukaryotic genomes: from genome size increase to genetic adaptation to stressful environments. Gene 509:7–15
16. Cocca E, De Iorio S, Capriglione T (2011) Identification of a novel helitron transposon in the genome of Antarctic fish. Mol Phyl Evol 58:439–446
17. Daskalova E, Baev V, Rusinov V, Minkov I (2007) 3'UTR-located ALU elements: donors of potential miRNA target sites and mediators of network miRNA-based regulatory interactions. Evol Bioinformatics Online 2:103–120
18. Deininger PL, Moran JV, Batzer MA, Kazazian HH Jr (2003) Mobile elements and mammalian genome evolution. Curr Opin Genet Dev 13:651–658
19. Devor EJ, Peek AS, Lanier W, Samollow PB (2009) Marsupial-specific microRNAs evolved from marsupial-specific transposable elements. Gene 448:187–191
20. Eickbush TH, Jamburuthugoda VK (2008) The diversity of retrotransposons and the properties of their reverse transcriptases. Virus Res 134:221–234
21. Feschotte C, Pritham EJ (2007) DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet 41:331–368
22. Gallus S, Kumar V, Bertelsen MF, Janke A, M A (2015) A genome survey sequencing of the Java mouse deer (Tragulus javanicus) adds new aspects to the evolution of lineage specific retrotransposons in Ruminantia (Cetartiodactyla)
23. Gu TJ, Yi X, Zhao XW, Zhao Y, Yin JQ (2009) Alu-directed transcriptional regulation of some novel miRNAs. BMC Genomics 10:563
24. Ha M, Pang M, Agarwal V, Chen ZJ (2008) Interspecies regulation of miRNAs and their targets. BBA 1179:735–742
25. Hassan MQ, Tye CE, Stein GS, Lian JB (2015) Non-coding RNAs: epigenetic regulators of bone development and homeostasis. Bone
26. Heimberg AM, Sempere LF, Moy VN, Donoghue PC, Peterson KJ (2008) MicroRNAs and the advent of vertebrate morphological complexity. Proc Natl Acad Sci U S A 105:2946–2950
27. Hoffman Y, Pilpel Y, Oren M (2014) microRNAs and Alu elements in the p53-Mdm2-Mdm4 regulatory network. J Mol Cell Biol 6(3):192–197
28. Hsu K, Chang DY, Maraia RJ (1995) Human signal recognition particle (SRP) Alu-associated protein also binds Alu interspersed repeat sequence RNAs. Characterization of human SRP9. J Biol Chem 270:10179–10186
29. Jung YD, Ahn K, Kim YJ, Bae JH, Lee JR, Kim HS (2013) Retroelements: molecular features and implications for disease. Genes Genet Syst 88:31–43
30. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ (2004) The UCSC Table Browser data retrieval tool. Nucleic Acids Res 32(Database issue):D493-6
31. Kazazian HH Jr (2004) Mobile elements: drivers of genome evolution. Science 303:1626–1632
32. Kos A, Olde Loohuis NF, Wieczorek ML, Glennon JC, Martens GJ, Kolk SM, Aschrafi A (2012) A potential regulatory role for intronic microRNA-338-3p for its host gene encoding apoptosis-associated tyrosine kinase. PLoS One 7, e31022
33. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921.
34. Lehnert S, Van Loo P, Thilakarathne PJ, Marynen P, Verbeke G, Schuit FC (2009) Evidence for co-evolution between human microRNAs and Alu-repeats. PLoS One 4, e4456
35. Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15–20
36. Li Y, Zhang Z (2015) Computational Biology in microRNA. WIREs RNA 6:435–452
37. Liu C, Rennie WA, Mallick B, Kanoria S, Long D, Wolenc A, Carmack CS, Ding Y (2014) MicroRNA binding sites in C. elegans 3′ UTRs. RNA Biol 11:693–701
38. Matveev V, Okada N (2009) Retroposons of salmonoid fishes (Actinopterygii: Salmonoidei) and their evolution. Gene 434:16–28
39. Mi H, Muruganujan A, Casagrande JT, Thomas PD (2013) Large-scale gene function analysis with the PANTHER classification system. Nat Protoc 8:1551–1566
40. Nakanishi A, Kobayashi N, Suzuki-Hirano A, Nishihara H, Sasaki T, Hirakawa M, Sumiyama K, Shimogori T, Okada N (2012) A SINE-derived element constitutes a unique modular enhancer for mammalian diencephalic Fgf8. PLoS One 7, e43785
41. Nishimoto S, Nishida E (2006) MAPK signalling: ERK5 versus ERK1/2. EMBO Rep 7:782–786
42. O'Connell RM, Rao DS, Chaudhuri AA, Baltimore D (2010) Physiological and pathological roles for microRNAs in the immune system. Nat Rev Immunol 10:111–122
43. Ogiwara I, Miya M, Ohshima K, Okada N (2002) V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit. Genome Res 12:316–324
44. Ohshima K, Okada N (2005) SINEs and LINEs: symbionts of eukaryotic genomes with a common tail. Cytogenet. Genome Res 110:475–490
45. Pandey R, Mandal AK, Jha V, Mukerji M (2011) Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism. Genome Biol 12:R117
46. Piriyapongsa J, Jordan IK (2007) A family of human microRNA genes from miniature inverted-repeat transposable elements. PLoS One 2, e203
47. Piriyapongsa J, Rutledge MT, Patel S, Borodovsky M, Jordan IK (2007) Evaluating the protein coding potential of exonized transposable element sequences. Biol Direct 2:31
48. Platt RN, Vandewege MW, Kern C, Schmidt CJ, Hoffmann FG, Ray DA (2014) Large numbers of novel miRNAs originate from DNA transposons and are coincident with a large species radiation in bats. Mol Biol Evol 31:1536–1545
49. Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R (2004) Fast and effective prediction of microRNA/target duplexes. RNA 10:1507–1517
50. SanMiguel P, Gaut BS, Tiknonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20:43–45
51. Shedlock AM, Okada N (2000) SINE insertions: powerful tools for molecular systematics. Bioessays 22:148–160
52. Smalheiser NR, Torvik VI (2006) Alu elements within human mRNAs are probable microRNA targets. Trends Genet 22:532–536
53. Yang Z, Wan X, Gu Z, Zhang H, Yang X, He L, Miao R, Zhong Y, Zhao H (2014) Evolution of the mir-181 microRNA family. Comput Biol Med 52:82–87
54. Yu G, Wang LG, He QY (2015) ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics
55. Zhang L, Hammell M, Kudlow BA, Ambros V, Han M (2009) Systematic analysis of dynamic miRNA-target interactions during C. elegans development. Development 136:3043–3055