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LncRNA Research

Towards systematic and functional annotation of LncRNAs

 
Importantly, systematic and detailed lncRNA annotations, subclassification and analyses are packaged in our sample-to-results microarray services to gain insight into the complex biology of lncRNAs. All the reported LncRNAs involved in biological processes, such as apoptosis, differentiation and development, or associated with human diseases, such as cancers, neurodegenerative diseases, and cardiovascular diseases, are comprehensively annotated and cross referenced. This rich source of information helps to unravel functional roles and molecular mechanisms of the LncRNAs.
 
Genomic context. LncRNAs are systematically classified based on their genomic relationships with the protein coding genes into Intergenic (LincRNA), Intronic, Bidirectional, Sense-overlapping, Antisense and Pseudogene LncRNAs (Fig 1), to help dissect potential regulatory functions in cis or trans, at transcriptional or post-transcriptional levels.
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Figure 1. LncRNA classification and subgroups in various genomic context with the protein coding gene (Top). LncRNAs may regulate gene expression by various mechanisms, such as recruiting chromatin modifiers/remodelers to epigenetically regulate gene expression; by enhancer RNAs; by nuclear substructures; by nuclear-cytoplasmic transport; by competing endogenous RNAs via miRNAs; or by mRNA stability and translation; in cis or in trans, at transcription or post-transcriptional levels (Bottom).

Highly conserved LncRNAs. LncRNA genes containing ultraconserved regions (UCR) or harboring ultraconserved non-coding elements (UCNEs) are represented as sequence conserved to be biologically important. Human lncRNAs syntenic to stringent lncRNAs in other species are also collected even with only modest homology, as genomic context rather than overall sequence conservation may be more relevant in gene regulation [1].

Tissue specific lncRNAs. LncRNAs displaying restricted tissue or development specificities may indicate related functions [1]. In particular, 6,059 cell lineage or cancer associated lncRNAs are annotated [2].

Disease lncRNAs. LncRNAs known to be associated with diseases as compiled in LncRNADisease [3].

Disease SNP associated lncRNAs. LncRNAs overlapping with disease-associated SNPs that may be associated with or contribute to human diseases.

LncRNAs correlated with mRNA expression in biological functions. The correlated LncRNAs are related to biological process or functional gene sets (e.g. angiogenesis, hypoxia, metastasis, proliferation, cell cycle, cell adhesion, DNA damage and repair) [2].

Cancer associated LncRNAs. LncRNAs potentially driving different cancer types, displaying altered or cancer specific expression in large scale lncRNA studies in thousands of cancer samples [4-5].

Very long intergenic lncRNAs (vlincRNA), with sizes ranging from 50 kb to 1 Mb, that are implicated in biological processes, such as pluripotency, cancer, apoptosis, cell cycle progression, and cellular senescence [6-7, 8].

Miscellaneous. For example, Hypoxia-induced noncoding ultraconserved transcripts (HINCUTs) [9], and long stress-induced noncoding transcripts (LSINCTs) [10].


Related Services
LncRNA Array Service
LncPath™ Array Service
T-UCR Array Service



Reference1.Cabili, M.N. et al. (2011) Genes Dev 25(18):1915-27 [PMID: 21890647]
2.Iyer M.K. et al. (2015) Nat. Genet. 47(3):199-208 [PMID: 25599403]
3.Chen G. et al. (2013) Nucleic Acids Res. 41(Database issue):D983-6 [PMID: 23175614]
4.St Laurent G. et al. (2015) Trends Genet. 31(5):239-51 [PMID: 25869999]
5.Yan X. et al. (2015) Cancer Cell 28(4):529-40 [PMID: 26461095]
6.Hackermuller J. et al. (2014) Genome Biol. 15(3):R48 [PMID: 24594072]
7.St Laurent G. et al. (2013) Genome Biol. 14(7):R73 [PMID: 23876380]
8.Clark M.B. et al. (2015) Nat. Methods 12(4):339-42 [PMID: 25751143]
9.Ferdin J. et al. (2013) Cell Death Differ. 20(12):1675-87 [PMID: 24037088]
10.Silva J.M. et al. (2010) Genomics 95(6):355-62 [PMID: 20214974]

 

 

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