zflncRNApedia: A comprehensive online resource for zebrafish long non-coding RNAs

PLoS ONE

Volumn 10, Issue 6, 2015, Pages

  Dhiman, Heena ^a   Kapoor, Shruti ^a,b   Sivadas, Ambily ^a   Sivasubbu, Sridhar ^a   Scaria, Vinod ^a,b  

^a CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

^b ACADEMY OF SCIENTIFIC AND INNOVATIVE RESEARCH ACSIR   (India)

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA; TRANSCRIPTOME;

ANIMAL TISSUE; ARTICLE; EPIGENETICS; GENE EXPRESSION; GENE INSERTION; GENE MUTATION; GENETIC ANALYSIS; GENETIC CODE; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOMICS; INTRON; MOLECULAR GENETICS; NONHUMAN; ONLINE SYSTEM; PROMOTER REGION; PROTEIN DATABASE; WEB BROWSER; ZEBRA FISH; ZFLNCRNAPEDIA DATABASE; ANIMAL; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; INTERNET; NUCLEIC ACID DATABASE; PROCEDURES; SEQUENCE ANALYSIS; SOFTWARE;

DANIO RERIO;

ANIMALS; DATABASES, NUCLEIC ACID; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INTERNET; MOLECULAR SEQUENCE ANNOTATION; PROMOTER REGIONS, GENETIC; RNA, LONG NONCODING; SEQUENCE ANALYSIS, RNA; SOFTWARE; TRANSCRIPTOME; ZEBRAFISH;

EID: 84935082239     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0129997     Document Type: Article

References (39)

1. Soshnev AA, Ishimoto H, McAllister BF, Li X, Wehling MD, Kitamoto T, et al. A conserved long noncoding RNA affects sleep behavior in Drosophila. Genetics. 2011; 189(2):455-68. doi: 10.1534/genetics. 111.131706 PMID: 21775470; PubMed Central PMCID: PMC3189806.
2. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, et al. The transcriptional landscape of the mammalian genome. Science. 2005; 309(5740):1559-63. doi: 10.1126/science.1112014 PMID: 16141072.
3. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome research. 2012; 22(9):1775-89. doi: 10.1101/gr.132159.111 PMID: 22955988; PubMed Central PMCID: PMC3431493.
4. Kapranov P, Drenkow J, Cheng J, Long J, Helt G, Dike S, et al. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome research. 2005; 15(7):987-97. doi: 10.1101/gr.3455305 PMID: 15998911; PubMed Central PMCID: PMC1172043.
5. Yan B, Wang ZH, Guo JT. The research strategies for probing the function of long noncoding RNAs. Genomics. 2012; 99(2):76-80. doi: 10.1016/j.ygeno.2011.12.002 PMID: 22210346.
6. Kurokawa R, Rosenfeld MG, Glass CK. Transcriptional regulation through noncoding RNAs and epigenetic modifications. Rna Biol. 2009; 6(3):233-6. PMID: WOS:000273716700005.
7. Guttman M, Rinn JL. Modular regulatory principles of large non-coding RNAs. Nature. 2012; 482 (7385):339-46. doi: 10.1038/Nature10887 PMID: WOS:000300287100035.
8. Martianov I, Ramadass A, Barros AS, Chow N, Akoulitchev A. Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature. 2007; 445(7128):666-70. doi: 10.1038/ Nature05519 PMID: WOS:000244039400048.
9. Neguembor MV, Jothi M, Gabellini D. Long noncoding RNAs, emerging players in muscle differentiation and disease. Skeletal muscle. 2014; 4(1):8. doi: 10.1186/2044-5040-4-8 PMID: 24685002; PubMed Central PMCID: PMC3973619.
10. Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, et al. Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes. Science. 2010; 329(5992):689-93. doi: 10.1126/ science.1192002 PMID: WOS:000280602700041.
11. Bhartiya D, Kapoor S, Jalali S, Sati S, Kaushik K, Sachidanandan C, et al. Conceptual approaches for lncRNA drug discovery and future strategies. Expert Opin Drug Dis. 2012; 7(6):503-13. doi: 10.1517/ 17460441.2012.682055 PMID: WOS:000304522600006.
12. Qi P, Du X. The long non-coding RNAs, a new cancer diagnostic and therapeutic gold mine. Modern Pathol. 2013; 26(2):155-65. doi: 10.1038/modpathol.2012.160 PMID: WOS:000314444000001.
13. Varshney GK, Huang H, Zhang S, Lu J, Gildea DE, Yang Z, et al. The Zebrafish Insertion Collection (ZInC): a web based, searchable collection of zebrafish mutations generated by DNA insertion. Nucleic acids research. 2013; 41(Database issue):D861-4. doi: 10.1093/nar/gks946 PMID: 23180778; PubMed Central PMCID: PMC3531054.
14. Quek XC, Thomson DW, Maag JL, Bartonicek N, Signal B, Clark MB, et al. lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. Nucleic acids research. 2014. doi: 10. 1093/nar/gku988 PMID: 25332394.
15. Park C, Yu N, Choi I, Kim W, Lee S. lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs. Bioinformatics. 2014; 30(17):2480-5. doi: 10.1093/bioinformatics/btu325 PMID: 24813212.
16. Pauli A, Valen E, Lin MF, Garber M, Vastenhouw NL, Levin JZ, et al. Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome research. 2012; 22(3):577-91. doi: 10.1101/gr.133009.111 PMID: 22110045; PubMed Central PMCID: PMC3290793.
17. Kaushik K, Leonard VE, Kv S, Lalwani MK, Jalali S, Patowary A, et al. Dynamic expression of long noncoding RNAs (lncRNAs) in adult zebrafish. PloS one. 2013; 8(12):e83616. doi: 10.1371/journal.pone. 0083616 PMID: 24391796; PubMed Central PMCID: PMC3877055.
18. Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP. Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell. 2011; 147(7):1537-50. doi: 10.1016/j.cell. 2011.11.055 PMID: 22196729; PubMed Central PMCID: PMC3376356.
19. Haque S, Kaushik K, Leonard VE, Kapoor S, Sivadas A, Joshi A, et al. Short stories on zebrafish long noncoding RNAs. Zebrafish. 2014; 11(6):499-508. doi: 10.1089/zeb.2014.0994 PMID: 25110965; PubMed Central PMCID: PMC4248245.
20. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009; 25(9):1105-11. doi: 10.1093/bioinformatics/btp120 PMID: 19289445; PubMed Central PMCID: PMC2672628.
21. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome research. 2008; 18(11):1851-8. doi: 10.1101/gr.078212.108 PMID: WOS:000260536100017.
22. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol. 2008; 9(9). doi: Artn R137 doi: 10.1186/Gb-2008-9-9-R137 PMID: WOS:000260586900015.
23. Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome research. 2012; 22(9):1813-31. doi: 10.1101/gr.136184.111 PMID: 22955991; PubMed Central PMCID: PMC3431496.
24. Aday AW, Zhu LJ, Lakshmanan A, Wang J, Lawson ND. Identification of cis regulatory features in the embryonic zebrafish genome through large-scale profiling of H3K4me1 and H3K4me3 binding sites. Dev Biol. 2011; 357(2):450-62. doi: 10.1016/j.ydbio.2011.03.007 PMID: WOS:000294834400016.
25. Bogdanovic O, Fernandez-Minan A, Tena JJ, de la Calle-Mustienes E, Hidalgo C, van Kruysbergen I, et al. Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis. Genome research. 2012; 22(10):2043-53. doi: 10.1101/gr.134833.111 PMID: WOS:000309325900020.
26. Irimia M, Tena JJ, Alexis MS, Fernandez-Minan A, Maeso I, Bogdanovic O, et al. Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints. Genome research. 2012; 22(12):2356-67. doi: 10.1101/gr.139725.112 PMID: WOS:000311895500004.
27. Pauli A, Valen E, Lin MF, Garber M, Vastenhouw NL, Levin JZ, et al. Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome research. 2012; 22(3):577-91. doi: 10.1101/gr.133009.111 PMID: WOS:000300962600017.
28. Chew GL, Pauli A, Rinn JL, Regev A, Schier AF, Valen E. Ribosome profiling reveals resemblance between long non-coding RNAs and 5 ' leaders of coding RNAs. Development. 2013; 140(13):2828-34. doi: 10.1242/Dev.098343 PMID: WOS:000320168300021.
29. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009; 10(3). doi: Artn R25 doi: 10.1186/Gb-2009-10-3-R25 PMID: WOS:000266544500005.
30. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013; 14(4). doi: Artn R36 doi: 10.1186/Gb-2013-14-4-R36 PMID: WOS:000322521300006.
31. Rice P, Longden I, Bleasby A. EMBOSS: The European molecular biology open software suite. Trends Genet. 2000; 16(6):276-7. doi: 10.1016/S0168-9525(00)02024-2 PMID: WOS:000087457200010.
32. Kondrychyn I, Teh C, Garcia-Lecea M, Guan Y, Kang A, Korzh V. Zebrafish Enhancer TRAP transgenic line database ZETRAP 2.0. Zebrafish. 2011; 8(4):181-2. doi: 10.1089/zeb.2011.0718 PMID: 22181660.
33. Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, et al. The UCSC Genome Browser database: 2014 update. Nucleic acids research. 2014; 42(Database issue):D764-70. doi: 10. 1093/nar/gkt1168 PMID: 24270787; PubMed Central PMCID: PMC3964947.
34. Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. JBrowse: A next-generation genome browser. Genome research. 2009; 19(9):1630-8. doi: 10.1101/gr.094607.109 PMID: WOS:000269482200014.
35. Sati S, Ghosh S, Jain V, Scaria V, Sengupta S. Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci. Nucleic acids research. 2012; 40(20):10018-31. doi: 10. 1093/Nar/Gks776 PMID: WOS:000310970700013.
36. Ganis JJ, Hsia N, Trompouki E, de Jong JL, DiBiase A, Lambert JS, et al. Zebrafish globin switching occurs in two developmental stages and is controlled by the LCR. Dev Biol. 2012; 366(2):185-94. doi: 10. 1016/j.ydbio.2012.03.021 PMID: 22537494; PubMed Central PMCID: PMC3378398.
37. Leichsenring M, Maes J, Mossner R, Driever W, Onichtchouk D. Pou5f1 transcription factor controls zygotic gene activation in vertebrates. Science. 2013; 341(6149):1005-9. doi: 10.1126/science.1242527 PMID: 23950494.
38. Paik EJ, Mahony S, White RM, Price EN, Dibiase A, Dorjsuren B, et al. A Cdx4-Sall4 regulatory module controls the transition from mesoderm formation to embryonic hematopoiesis. Stem cell reports. 2013; 1(5):425-36. doi: 10.1016/j.stemcr.2013.10.001 PMID: 24286030; PubMed Central PMCID: PMC3841246.
39. Xu C, Fan ZP, Muller P, Fogley R, DiBiase A, Trompouki E, et al. Nanog-like regulates endoderm formation through the Mxtx2-Nodal pathway. Developmental cell. 2012; 22(3):625-38. doi: 10.1016/j. devcel.2012.01.003 PMID: 22421047; PubMed Central PMCID: PMC3319042.