ArticleNucleic acids research2016
Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 47 citations in OpenAlex.
- ASAR lncRNAs control DNA replication timing through interactions with multiple hnRNP/RNA binding proteins.eLife · 2024Article
- Article
- Long Non-Coding RNA Expression Profile Alteration Induced by Titanium Dioxide Nanoparticles in HepG2 Cells.Toxics · 2022Article
- Epigenetic control of chromosome-associated lncRNA genes essential for replication and stability.Nature communications · 2022Article
- Mammalian DNA Replication Timing.Cold Spring Harbor perspectives in biology · 2021Review
- Very long intergenic non-coding (vlinc) RNAs directly regulate multiple genes in cis and trans.BMC biology · 2021Article
- Review
- Complex Age- and Cancer-Related Changes in Human Blood Transcriptome-Implications for Pan-Cancer Diagnostics.Frontiers in genetics · 2021Article
- Reciprocal monoallelic expression of ASAR lncRNA genes controls replication timing of human chromosome 6.RNA (New York, N.Y.) · 2020Article
- A CRISPR/Cas13-based approach demonstrates biological relevance of vlinc class of long non-coding RNAs in anticancer drug response.Scientific reports · 2020Article
- Identification of novel GLI1 target genes and regulatory circuits in human cancer cells.Molecular oncology · 2018Article
- The State of Long Non-Coding RNA Biology.Non-coding RNA · 2018Article
- Noncoding RNAs in the Regulation of Pluripotency and Reprogramming.Stem cell reviews and reports · 2018Review
- Atlas of Schistosoma mansoni long non-coding RNAs and their expression correlation to protein-coding genes.Database : the journal of biological databases and curation · 2018Article
- Deep RNA Sequencing Uncovers a Repertoire of Human Macrophage Long Intergenic Noncoding RNAs Modulated by Macrophage Activation and Associated With Cardiometabolic Diseases.Journal of the American Heart Association · 2017Article
- Rapid Loss of RNA Detection by In Situ Hybridization in Stored Tissue Blocks and Preservation by Cold Storage of Unstained Slides.American journal of clinical pathology · 2017Article
- The Schistosoma mansoni genome encodes thousands of long non-coding RNAs predicted to be functional at different parasite life-cycle stages.Scientific reports · 2017Article
- Non-coding RNAs as drug targets.Nature reviews. Drug discovery · 2017Review
- Deep Sequencing Transcriptome Analysis of Murine Wound Healing: Effects of a Multicomponent, Multitarget Natural Product Therapy-Tr14.Frontiers in molecular biosciences · 2017Article
Corrections and comments
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Authors and funding
20 authors at 9 institutions in 6 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Functionality of the non-coding transcripts encoded by the human genome is the coveted goal of the modern genomics research. While commonly relied on the classical methods of forward genetics, integration of different genomics datasets in a global Systems Biology fashion presents a more productive avenue of achieving this very complex aim. Here we report application of a Systems Biology-based approach to dissect functionality of a newly identified vast class of very long intergenic non-coding (vlinc) RNAs. Using highly quantitative FANTOM5 CAGE dataset, we show that these RNAs could be grouped into 1542 novel human genes based on analysis of insulators that we show here indeed function as genomic barrier elements. We show that vlinc RNAs genes likely function in cisto activate nearby genes. This effect while most pronounced in closely spaced vlinc RNA-gene pairs can be detected over relatively large genomic distances. Furthermore, we identified 101 vlinc RNA genes likely involved in early embryogenesis based on patterns of their expression and regulation. We also found another 109 such genes potentially involved in cellular functions also happening at early stages of development such as proliferation, migration and apoptosis. Overall, we show that Systems Biology-based methods have great promise for functional annotation of non-coding RNAs.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.