LncRNAdb V2.0: Expanding the Reference Database for Functional Long Noncoding RNAs

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2014 Oct 22

PMID 25332394

Citations 298

Authors

Xiu Cheng Quek

Daniel W Thomson

Jesper L V Maag

Nenad Bartonicek

Bethany Signal

Michael B Clark

Brian S Gloss

Marcel E Dinger

Affiliations

Soon will be listed here.

Abstract

Despite the prevalence of long noncoding RNA (lncRNA) genes in eukaryotic genomes, only a small proportion have been examined for biological function. lncRNAdb, available at http://lncrnadb.org, provides users with a comprehensive, manually curated reference database of 287 eukaryotic lncRNAs that have been described independently in the scientific literature. In addition to capturing a great proportion of the recent literature describing functions for individual lncRNAs, lncRNAdb now offers an improved user interface enabling greater accessibility to sequence information, expression data and the literature. The new features in lncRNAdb include the integration of Illumina Body Atlas expression profiles, nucleotide sequence information, a BLAST search tool and easy export of content via direct download or a REST API. lncRNAdb is now endorsed by RNAcentral and is in compliance with the International Nucleotide Sequence Database Collaboration.

Citing Articles

ncRNA Editing: Functional Characterization and Computational Resources.

Marceca G, Romano G, Acunzo M, Nigita G Methods Mol Biol. 2024; 2883:455-495.

PMID: 39702721 DOI: 10.1007/978-1-0716-4290-0_20.

Biological Insights and Recent Advances in Plant Long Non-Coding RNA.

Zhao Z, Yang Y, Iqbal A, Wu Q, Zhou L Int J Mol Sci. 2024; 25(22).

PMID: 39596034 PMC: 11593582. DOI: 10.3390/ijms252211964.

Transcriptome-scale RNA-targeting CRISPR screens reveal essential lncRNAs in human cells.

Liang W, Muller S, Hart S, Wessels H, Mendez-Mancilla A, Sookdeo A Cell. 2024; 187(26):7637-7654.e29.

PMID: 39532094 PMC: 11682925. DOI: 10.1016/j.cell.2024.10.021.

Long Non-Coding RNAs in Cardiac Hypertrophy.

Mangraviti N, De Windt L Front Mol Med. 2024; 2:836418.

PMID: 39086960 PMC: 11285587. DOI: 10.3389/fmmed.2022.836418.

Hierarchical lncRNA regulatory network in early-onset severe preeclampsia.

Liu H, Wang Z, Li Y, Chen Q, Jiang S, Gao Y BMC Biol. 2024; 22(1):159.

PMID: 39075446 PMC: 11287949. DOI: 10.1186/s12915-024-01959-1.

References

Liu G, Mattick J, Taft R . A meta-analysis of the genomic and transcriptomic composition of complex life. Cell Cycle. 2013; 12(13):2061-72. PMC: 3737309. DOI: 10.4161/cc.25134. View

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley D . Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012; 7(3):562-78. PMC: 3334321. DOI: 10.1038/nprot.2012.016. View

Banfai B, Jia H, Khatun J, Wood E, Risk B, Gundling Jr W . Long noncoding RNAs are rarely translated in two human cell lines. Genome Res. 2012; 22(9):1646-57. PMC: 3431482. DOI: 10.1101/gr.134767.111. View

Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H . The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012; 22(9):1775-89. PMC: 3431493. DOI: 10.1101/gr.132159.111. View

Rinn J, Kertesz M, Wang J, Squazzo S, Xu X, Brugmann S . Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell. 2007; 129(7):1311-23. PMC: 2084369. DOI: 10.1016/j.cell.2007.05.022. View

Paraskevopoulou M, Georgakilas G, Kostoulas N, Reczko M, Maragkakis M, Dalamagas T . DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. Nucleic Acids Res. 2012; 41(Database issue):D239-45. PMC: 3531175. DOI: 10.1093/nar/gks1246. View

Dinger M, Gascoigne D, Mattick J . The evolution of RNAs with multiple functions. Biochimie. 2011; 93(11):2013-8. DOI: 10.1016/j.biochi.2011.07.018. View

Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi P . A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?. Cell. 2011; 146(3):353-8. PMC: 3235919. DOI: 10.1016/j.cell.2011.07.014. View

Harrow J, Frankish A, Gonzalez J, Tapanari E, Diekhans M, Kokocinski F . GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012; 22(9):1760-74. PMC: 3431492. DOI: 10.1101/gr.135350.111. View

10.

Das S, Ghosal S, Sen R, Chakrabarti J . lnCeDB: database of human long noncoding RNA acting as competing endogenous RNA. PLoS One. 2014; 9(6):e98965. PMC: 4057149. DOI: 10.1371/journal.pone.0098965. View

11.

Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W . Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25(17):3389-402. PMC: 146917. DOI: 10.1093/nar/25.17.3389. View

12.

Kim T, Hemberg M, Gray J, Costa A, Bear D, Wu J . Widespread transcription at neuronal activity-regulated enhancers. Nature. 2010; 465(7295):182-7. PMC: 3020079. DOI: 10.1038/nature09033. View

13.

Dinger M, Pang K, Mercer T, Mattick J . Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLoS Comput Biol. 2008; 4(11):e1000176. PMC: 2518207. DOI: 10.1371/journal.pcbi.1000176. View

14.

Gascoigne D, Cheetham S, Cattenoz P, Clark M, Amaral P, Taft R . Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes. Bioinformatics. 2012; 28(23):3042-50. DOI: 10.1093/bioinformatics/bts582. View

15.

Mercer T, Mattick J . Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol. 2013; 20(3):300-7. DOI: 10.1038/nsmb.2480. View

16.

Xia J, Joyce C, Bowcock A, Zhang W . Noncanonical microRNAs and endogenous siRNAs in normal and psoriatic human skin. Hum Mol Genet. 2012; 22(4):737-48. PMC: 3554200. DOI: 10.1093/hmg/dds481. View

17.

Askarian-Amiri M, Crawford J, French J, Smart C, Smith M, Clark M . SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA. 2011; 17(5):878-91. PMC: 3078737. DOI: 10.1261/rna.2528811. View

18.

Wang K, Chang H . Molecular mechanisms of long noncoding RNAs. Mol Cell. 2011; 43(6):904-14. PMC: 3199020. DOI: 10.1016/j.molcel.2011.08.018. View

19.

Cabili M, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A . Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011; 25(18):1915-27. PMC: 3185964. DOI: 10.1101/gad.17446611. View

20.

Engreitz J, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C . The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science. 2013; 341(6147):1237973. PMC: 3778663. DOI: 10.1126/science.1237973. View