Search Results for: long noncoding rna expression

ALDB – a domestic-animal long noncoding RNA database

The domestic-animal lncRNA database (ALDB) is the first comprehensive database with a focus on the domestic-animal lncRNAs. ALDB currently comprises 12,103 pig lincRNAs, 8,923 chicken lincRNAs, and 8,250 cow lincRNAs, which have been identified using computational pipeline in this study. Moreover, ALDB provides related useful data, such as genome-wide expression profile and animal quantitative trait loci (QTLs), that is not available in the existing lncRNA database (lncRNAdb and NONCODE), along with convenient tools, such as BLAST, GBrowse and flexible search functionalities.

lncRNA

  • Li, Aimin (2015): ALDB: a domestic-animal long noncoding RNA database. figshare.

 

Long Noncoding RNAs in Cardiovascular Diseases

lncRNA

In recent years, increasing evidence suggests that noncoding RNAs play important roles in the regulation of tissue homeostasis and pathophysiological conditions. Besides small noncoding RNAs (eg, microRNAs), >200-nucleotide long transcripts, namely long noncoding RNAs (lncRNAs), can interfere with gene expressions and signaling pathways at various stages. In the cardiovascular system, studies have detected and characterized the expression of lncRNAs under normal physiological condition and in disease states. Several lncRNAs are regulated during acute myocardial infarction (eg, Novlnc6) and heart failure (eg, Mhrt), whereas others control hypertrophy, mitochondrial function and apoptosis of cardiomyocytes. In the vascular system, the endothelial-expressed lncRNAs (eg, MALAT1 and Tie-1-AS) can regulate vessel growth and function, whereas the smooth-muscle-expressed lncRNA smooth muscle and endothelial cell-enriched migration/differentiation-associated long noncoding RNA was recently shown to control the contractile phenotype of smooth muscle cells.

This review article summarizes the data on lncRNA expressions in mouse and human and highlights identified cardiovascular lncRNAs that might play a role in cardiovascular diseases. Although our understanding of lncRNAs is still in its infancy, these examples may provide helpful insights how lncRNAs interfere with cardiovascular diseases.

  • Uchida S, Dimmeler S. (2015) Long Noncoding RNAs in Cardiovascular Diseases. Circ Res 116(4):737-750. [article]

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  • transcribed noncoding rna

The landscape of long noncoding RNAs in the human transcriptome

Long noncoding RNAs (lncRNAs) are emerging as important regulators of tissue physiology and disease processes including cancer. To delineate genome-wide lncRNA expression, researchers at the University of Michigan curated 7,256 RNA sequencing (RNA-seq) libraries from tumors, normal tissues and cell lines comprising over 43 Tb of sequence from 25 independent studies. They applied ab initio assembly methodology to this data set, yielding a consensus human transcriptome of 91,013 expressed genes.

rna-seq

Over 68% (58,648) of genes were classified as lncRNAs, of which 79% were previously unannotated. About 1% (597) of the lncRNAs harbored ultraconserved elements, and 7% (3,900) overlapped disease-associated SNPs. To prioritize lineage-specific, disease-associated lncRNA expression, the reseaechers employed non-parametric differential expression testing and nominated 7,942 lineage- or cancer-associated lncRNA genes. The lncRNA landscape characterized here may shed light on normal biology and cancer pathogenesis and may be valuable for future biomarker development.

rna-seq

Iyer MK, Niknafs YS, Malik R, Singhal U, Sahu A, Hosono Y, Barrette TR, Prensner JR, Evans JR, Zhao S, Poliakov A, Cao X, Dhanasekaran SM, Wu YM, Robinson DR, Beer DG, Feng FY, Iyer HK, Chinnaiyan AM. (2015) The landscape of long noncoding RNAs in the human transcriptome. Nat Genet [Epub ahead of print]. [abstract]

Long noncoding RNAs – A Novel Prognostic Marker In AML

From Drug Discovery News

A new study led by researchers at The Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute (OSUCCC – James) describes a novel marker that might help doctors choose the least toxic, most effective treatment for many older patients with acute myeloid leukemia (AML). AML occurs mainly in older patients and has a three-year survival rate of 5 to 15 percent.

lncRNAThe researchers investigated patterns of molecules called long noncoding RNAs (lncRNAs), a class of RNA molecules more than 200 nucleotide units long that are involved in regulating genes. The researchers examined the abundance, or expression, of lncRNAs in patients who were 60 years and older and who had cytogenetically normal (CN) AML.

The study is published online in the Proceedings of the National Academy of Sciences.

Incoming search terms:

  • CE hypothesis

Human long noncoding RNAs are substantially less folded than messenger RNAs

lncRNA

Long noncoding RNAs (lncRNAs) do not code for proteins but function as RNAs. Because the functions of an RNA rely on either its sequence or secondary structure, lncRNAs should be folded at least as strongly as messenger RNAs (mRNAs), which serve as messengers for translation and are generally thought to lack secondary structure-dependent RNA-level functions. Contrary to this prediction, analysis of genome-wide experimental data of human RNA folding reveals that lncRNAs are substantially less folded than mRNAs even after the control of expression level and GC%, although both lncRNAs and mRNAs are more strongly folded than expected by chance. In contrast to mRNAs, lncRNAs show neither the positive correlation between folding strength and expression level nor the negative correlation between folding strength and evolutionary rate. These and other results support that, while RNA folding undoubtedly plays a role in RNA biology, it is also important in translation and/or protein biology.

  • Yang J, Zhang J. (2014) Human long noncoding RNAs are substantially less folded than messenger RNAs. Mol Biol Evol [Epub ahead of print]. [abstract]