Community Curated Database For LncRNA

A wiki-style database hopes to serve as an online encyclopedia of lncRNA by and for the scientific community. Scientists have More »

Finding the function of long noncoding RNA

Mouse experiments suggest that a noncoding RNA can be vital for successful pregnancy The proteins that underlie nearly all biological More »

Human long noncoding RNAs are substantially less folded than messenger RNAs

Long noncoding RNAs (lncRNAs) do not code for proteins but function as RNAs. Because the functions of an RNA rely More »

Long noncoding RNAs – A Novel Prognostic Marker In AML

COLUMBUS, Ohio – A new study led by researchers at The Ohio State University Comprehensive Cancer Center – Arthur G. More »

New Angelman syndrome therapy proposed

from UT San Diego by Bradley J. Fikes Isis Pharma approach helps mouse models of genetic disease A potential therapy More »

 

Review Paper

Discovery and annotation of long noncoding RNAs

lncRNARecent advances in RNA-sequencing technologies have led to the discovery of thousands of previously unannotated noncoding transcripts, including many long noncoding RNAs (lncRNAs) whose functions remain largely unknown. Discussed here are considerations and best practices in lncRNA identification and annotation, which we hope will foster functional and mechanistic exploration.

Perhaps the biggest surprise of the postgenomic era has been the enormous number and diversity of transcriptional products arising from the previously presumed wastelands of the non-protein-coding genome. These include a plethora of small regulatory RNAs and tens of thousands of polyadenylated and nonpolyadenylated lncRNAs that are antisense, intronic, intergenic and overlapping with respect to protein-coding loci. The functions of these transcripts are largely unknown, although there is increasing in vitro and in vivo evidence that lncRNAs have key roles across diverse biological processes, with an emerging theme of interfacing with epigenetic regulatory pathways. Thus, the sheer number and the increasing pace of discovery of new lncRNAs are accompanied by the growing challenge of their definition and annotation.

The broad term lncRNA refers to a transcript >200 nt in length that does not appear to contain a protein-coding sequence. The size threshold is an arbitrary but convenient biophysical cutoff that excludes most known, although still poorly understood, classes of small infrastructural and regulatory RNAs, such as tRNAs, small nuclear RNAs, small nucleolar RNAs and their derivatives, microRNAs, short interfering RNAs, Piwi-interacting RNAs, transcription-initiation RNAs and small RNAs that regulate splicing. Occasionally other terminology, such as transcripts of unknown function (TUFs) and transcriptionally active regions (TARs), has been suggested, but the consensus has settled on the generic descriptor lncRNA, at least for the time being. (read more…)

  • Mattick JS, Rinn JL. (2015) Discovery and annotation of long noncoding RNAs. Nat Struct Mol Biol 22(1):5-7. [abstract]

Incoming search terms:

  • intronic mirna database

A pathophysiological view of the long non-coding RNA world

Because cells are constantly exposed to micro-environmental changes, they require the ability to adapt to maintain a dynamic equilibrium. Proteins are considered critical for the regulation of gene expression, which is a fundamental process in determining the cellular responses to stimuli. Recently, revolutionary findings in RNA research and the advent of high-throughput genomic technologies have revealed a pervasive transcription of the human genome, which generates many long non-coding RNAs (lncRNAs) whose roles are largely undefined. However, there is evidence that lncRNAs are involved in several cellular physiological processes such as adaptation to stresses, cell differentiation, maintenance of pluripotency and apoptosis. The correct balance of lncRNA levels is crucial for the maintenance of cellular equilibrium, and the dysregulation of lncRNA expression is linked to many disorders; certain transcripts are useful prognostic markers for some of these pathologies. This review revisits the classic concept of cellular homeostasis from the perspective of lncRNAs specifically to understand how this novel class of molecules contributes to cellular balance and how its dysregulated expression can lead to the onset of pathologies such as cancer.

lncRNA

  • Di Gesualdo F, Capaccioli S, Lulli M. (2014) A pathophysiological view of the long non-coding RNA world. Oncotarget [Epub ahead of print]. [article]

The functional role of long non-coding RNAs and epigenetics

Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides. The post-transcriptional regulation is influenced by these lncRNAs by interfering with the microRNA pathways, involving in diverse cellular processes. The regulation of gene expression by lncRNAs at the epigenetic level, transcriptional and post-transcriptional level have been well known and widely studied. Recent recognition that lncRNAs make effects in many biological and pathological processes such as stem cell pluripotency, neurogenesis, oncogenesis and etc. This review focuses on the functional roles of lncRNAs in epigenetics and related research progress are summarized.

lncRNA

  • Cao J. (2014) The functional role of long non-coding RNAs and epigenetics. Biol Proced Online 16:11. [article]

Long non-coding RNAs in cancer: implications for personalized therapy

lncRNA

Long non-coding RNAs (lncRNAs, pseudogenes and circRNAs) have recently come into light as powerful players in cancer pathogenesis and it is becoming increasingly clear that they have the potential of greatly contributing to the spread and success of personalized cancer medicine. In this concise review, the authors briefly:

  1. Introduce these three classes of long non-coding RNAs.
  2. Discuss their applications as diagnostic and prognostic biomarkers.
  3. Describe their appeal as targets and as drugs,
  4. Point out the limitations that still lie ahead of their definitive entry into clinical practice.
  • Vitiello M, Tuccoli A, Poliseno L. (2014) Long non-coding RNAs in cancer: implications for personalized therapy. Cell Oncol (Dordr) [Epub ahead of print]. [abstract]

Long non-coding RNAs in cancer: implications for personalized therapy

Long non-coding RNAs (lncRNAs, pseudogenes and circRNAs) have recently come into light as powerful players in cancer pathogenesis and it is becoming increasingly clear that they have the potential of greatly contributing to the spread and success of personalized cancer medicine. In this concise review, the authors briefly introduce these three classes of long non-coding RNAs. We then discuss their applications as diagnostic and prognostic biomarkers. Finally, we describe their appeal as targets and as drugs, while pointing out the limitations that still lie ahead of their definitive entry into clinical practice.

lncRNA

  • Vitiello M, Tuccoli A, Poliseno L. (2014) Long non-coding RNAs in cancer: implications for personalized therapy. Cell Oncol (Dordr). [Epub ahead of print]. [abstract]