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New lncRNA Products
from Biocompare by Jeffrey M. Perkel
There’s an old saying that you can judge a man by the company he keeps. The same can be said of biomolecules. If you want to know what a protein is doing, you can get a hint from the functions of its interaction partners.
These days, there is considerable research interest in the class of molecules called long noncoding RNAs (lncRNAs). Many have been identified, but few have had functions assigned. One way to approach that problem is—you guessed it—to ask which proteins these molecules call friends. A growing set of tools enables researchers to determine precisely that.
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from Genetic Engineering News 2013 (Vol. 33, No. 19) by Jeanene Swanson
RNAi screens for functional genomics typically look for loss- or gain-of-function phenotypes. They currently have many applications, including target discovery and validation, lead identification and optimization, mechanism of action discovery, predictive toxicology, and biomarker identification.
While reagents are gaining ground, technical difficulties remain in how best to perform and analyze these assays.
“RNAi reagents are being used ubiquitously,” says David Root, Ph.D., director of the RNAi Platform and project leader of the RNAi Consortium (TRC) at the Broad Institute. Dr. Root was among a handful of scientists and corporate partners who created one of the early genome-wide libraries of shRNA constructs (called TRC1). As of 2011, TRC2 has expanded the library (to 300,000 shRNAs) and has measured the knockdown performance of 100,000 of those constructs.
To perform RNAi screens, researchers can choose among a growing variety of reagents, including siRNA, shRNA, miRNA, and lncRNA constructs, as well as pooled libraries and constructs coupled to inducers. Synthetic siRNA has a transient effect, and it is eventually degraded. shRNA can be introduced into a cell within a lentiviral backbone, which allows the construct to be incorporated into the host cell’s genome and then stably expressed. This means the gene is always expressing the shRNA.
“Our philosophy has always been ‘siRNA if you can, shRNA if you must,’” says Christophe Echeverri, Ph.D., CEO and CSO of Cenix BioScience USA. “If the chosen cell system allows for good target knockdown by siRNA transfection, and the timeline needed for the experiments and assays is compatible with the duration of the siRNA effects, then it’ll almost certainly be an siRNA-based study.”
Khalil, Ahmad M.; Coller, Jeff (Eds.)
2014, VI, 166 p. 18 illus., 16 illus. in color.
About this book
- Brings together key experts in the field of lncRNAs
- Has appeal for basic scientists and clinicians
- Focuses on the recently discovered, and less understood, class of long non-coding RNAs
Long non-coding RNAs (lnc)RNAs have emerged as a new paradigm in epigenetic regulation of the genome. Thousands of lncRNAs have been identified and observed in a wide range of organisms. Unlike mRNA, lncRNA have no protein-coding capacity. So, while their function is not entirely clear, they may serve as key organizers of protein complexes that allow for higher order regulatory events. Discovering these functions has been the result of intense research done of the last few years, and lncRNA research has had several critical developments during that time. This book consolidates these ideas and models to better examine the most important issues in lncRNA biology. This includes critical studies that have led to the discovery and annotation of lncRNAs in numerous species, and the molecular mechanisms for a few lncRNA that have begun to emerge.
Table of contents
Preface.- Chromatin regulation by long non-coding RNAs.- Regulation of Eukaryotic Cell Differentiation by Long Noncoding RNAs.- Roles of long non-coding RNAs in X-chromosome inactivation.- Roles of Long Non-Coding RNAs in Genomic Imprinting.- Dysregulation of long noncoding RNAs in human disease.- Functions of long non-coding RNAs in non-mammalian systems.- Emerging technologies to study long non-coding RNAs.- Long non coding RNAs and nuclear body formation and function.- Index.
It was traditionally thought that the transcriptome would be mostly comprised of mRNAs, however advances in high-throughput RNA sequencing technologies have revealed the complexity of our genome. Non-coding RNA is now known to make up the majority of transcribed RNAs and in addition to those that carry out well-known housekeeping functions (e.g. tRNA, rRNA etc), many different types of regulatory RNAs have been and continue to be discovered. Many of these non-coding RNAs are thought to have a wide range of functions in cellular and developmental processes.
Long noncoding RNAs (lncRNAs) are a large and diverse class of transcribed RNA molecules with a length of more than 200 nucleotides that do not encode proteins. Their expression is developmentally regulated and lncRNAs can be tissue- and cell-type specific. A significant proportion of lncRNAs are located exclusively in the nucleus. They are comprised of many types of transcripts that can structurally resemble mRNAs, and are sometimes transcribed as whole or partial antisense transcripts to coding genes. LncRNAs are thought to carry out important regulatory functions, adding yet another layer of complexity to our understanding of genomic regulation.
Functions of lncRNA
LncRNAs may exert their functions…
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We have created a custom lncRNA expression array design (gencode.v15.lncrna.2probe.version1) with probes targeting the Gencode v15 human lncRNA annotation.
The design file is for the standard Agilent 8x60k expression array format, with two 60mer probes targeting each of 22,001 lncRNA transcripts.
The array also contains 17,535 catalogue probes targeting protein-coding genes. Similar arrays designed against an earlier version of Gencode lncRNA annotations were described in Derrien et al (Genome Res. 2012 Sep;22(9):1775-89).
We are making this design freely available to the scientific community – interested researchers may contact Rory Johnson for more information (firstname.lastname@example.org).
Because the design is a standard custom Agilent format, researchers can freely order microarray slides for their own projects, or else can employ hybridisation services such as that offered by the Centre for Genomic Regulation Genomics Core Facility.