Epigenetic coordination of embryonic heart transcription by dynamically regulated long noncoding RNAs

The role of noncoding RNAs in mammalian biology is of great interest, especially since the Encyclopedia of DNA Elements results More »

The Long Noncoding RNA Expression Profile of Hepatocellular Carcinoma Identified by Microarray Analysis

Thousands of long noncoding RNAs (lncRNAs) have been reported in mammalian genomes. These RNAs represent an important subset of pervasive More »

lnCeDB: Database of Human Long Noncoding RNA Acting as Competing Endogenous RNA

Long noncoding RNA (lncRNA) influences post-transcriptional regulation by interfering with the microRNA (miRNA) pathways, acting as competing endogenous RNA (ceRNA). More »

Long non-coding RNAs: evolution of new epigenetic and post-transcriptional functions

9:00 am on Monday 28 September 2015 — 5:00 pm on Tuesday 29 September 2015 at The Royal Society at More »

Featured long non-coding RNA – meiRNA

Long non-coding RNAs (lncRNAs) play key roles in the formation of nuclear bodies. In the fission yeast Schizosaccharomyces pombe, a More »

 

A long non-coding RNA signature to improve prognosis prediction of colorectal cancer

Increasing evidence suggests long non-coding RNAs (lncRNAs) are frequently aberrantly expressed in cancers, however, few related lncRNA signatures have been established for prediction of cancer prognosis.

Researchers from the Shanghai Institution of Digestive Disease aimed to develop a lncRNA signature to improve prognosis prediction of colorectal cancer (CRC). Using a lncRNA-mining approach, they performed lncRNA expression profiling in large CRC cohorts from Gene Expression Ominus (GEO) (N=436), internal validation series (N=117); and two independent validation series GSE14333 (N=197) and GSE17536(N=145). They established a set of six lncRNAs that were significantly correlated with the disease free survival (DFS) in the test series. Based on this six-lncRNA signature, the test series patients could be classified into high-risk and low-risk subgroups with significantly different DFS (HR=2.670; P<0.0001). The prognostic value of this six-lncRNA signature was confirmed in the internal validation series and another two independent CRC sets. Gene set enrichment analysis (GSEA) analysis suggested that risk score positively correlated with several cancer metastasis related pathways. Functional experiments demonstrated three dysregulated lncRNAs, AK123657, BX648207 and BX649059 were required for efficient invasion and proliferation suppression in CRC cell lines. Our results might provide an efficient classification tool for clinical prognosis evaluation of CRC.

lncRNA

  • Hu Y1, Chen HY, Yu CY, Xu J, Wang JL, Qian J, Zhang X, Fang JY. (2014) A long non-coding RNA signature to improve prognosis prediction of colorectal cancer. Oncotarget 5(8):2230-42. [article]

Epigenetic coordination of embryonic heart transcription by dynamically regulated long noncoding RNAs

lncRNA

The role of noncoding RNAs in mammalian biology is of great interest, especially since the Encyclopedia of DNA Elements results were published. Many have studied microRNAs in the heart, but little is known about their larger cousins, long noncoding RNAs (lncRNAs). Here, researchers from the Washington University School of Medicine used genome-wide sequencing and improved bioinformatics to quantify lncRNA expression in mouse hearts, define a subset of cardiac-specific lncRNAs, and measure dynamic lncRNA regulation during the transition between embryo and adult, and in the adult heart after experimental pressure overload (a model resembling human hypertensive cardiomyopathy). They linked specific regulated lncRNAs to cardiac-expressed mRNAs that they target and, through network analyses, discovered a broader role of regulated cardiac lncRNAs as modulators of key cardiac transcriptional pathways.

  • Matkovich SJ, Edwards JR, Grossenheider TC, de Guzman Strong C, Dorn GW 2nd. (2014) Epigenetic coordination of embryonic heart transcription by dynamically regulated long noncoding RNAs. Proc Natl Acad Sci U S A 111(33):12264-9. [abstract]

Postdoc Position Available – University of Copenhagen

lncRNADeadline for application is September 22, 2014

The fellowship is part of a newly established European non‐coding RNA training network, ‘RNatrain’ funded by th European Commission as a Marie Curie Initial Training Network (FP7). We are looking for a researcher to join the programme and the Lund Group at BRIC from January 1st 2015 or after agreement. (find out more…)

Researchers obtain key insights into how the internal body clock is tuned

DALLAS – August 18, 2014 – Researchers at UT Southwestern Medical Center have found a new way that internal body clocks are regulated by a type of molecule known as long non-coding RNA.

Dr. Yi Liu

The internal body clocks, called circadian clocks, regulate the daily “rhythms” of many bodily functions, from waking and sleeping to body temperature and hunger. They are largely “tuned” to a 24-hour cycle that is influenced by external cues such as light and temperature.

“Although we know that long non-coding RNAs are abundant in many organisms, what they do in the body, and how they do it, has not been clear so far,” said Dr. Yi Liu, Professor of Physiology. “Our work establishes a role for long non-coding RNAs in ‘tuning’ the circadian clock, but also shows how they control gene expression.”

Determining how circadian clocks work is crucial to understanding several human diseases, including sleep disorders and depression in which the clock malfunctions. The influence of a functional clock is evident in the reduced performance of shift workers and the jet lag felt by long-distance travellers.

Long Noncoding RNA Regulating Apoptosis Discovered

from Genetic Engineering News

Scientists from the University of São Paulo (USP) have identified an RNA molecule known as INXS that, although containing no instructions for the production of a protein, modulates the action of an important gene that impacts apoptosis.

According to Sergio Verjovski-Almeida, Ph.D., professor at the USP Chemistry Institute, INXS expression is generally diminished in cancer cells, and methods that are capable of stimulating the production of this noncoding RNA can be used to treat tumors. In experiments on mice, the USP scientists were able to effect a 10-fold reduction in the volume of subcutaneous malignant tumors by administering local injections of a plasmid containing INXS.

The team’s findings (“Long noncoding RNA INXS is a critical mediator of BCL-XS induced apoptosis”) were published in Nucleic Acids Research.

The group headed by Dr. Verjovski-Almeida at USP has been investigating the regulatory role of so-called intronic nonprotein-coding genes—those found in the same region of the genome as a coding gene but on the opposite DNA strand. INXS, for example, is an RNA expressed on the opposite strand of a gene coding for  the BCL-X protein.

“We were studying several protein-coding genes involved in cell death in search of evidence that one of them was regulated by intronic noncoding RNA. That was when we found the gene for BCL-X, which is located on chromosome 20,” he explained.

(read more…)