Search Results for: incrna

Seminar – Measurement and analysis of mRNAs and long non-coding RNAs using RNA-Seq

lncRNA

H3ABioNet – Pan African Bioinformatics Network for H3Africa

These one day courses are designed for scientists and clinicians with little or no experience in next generation sequencing. The courses aim to provide the experimental and bioinformatics skills required to prepare samples, quantify the levels of mRNA/long-non-coding RNA (RNAseq) or exon/DNA (DNAseq) expresion. We assume that sequencing will be performed by an external provider and will provide advice in this area. The courses are computer based and will involve a combination of presentations/exercises to analysis ‘actual’ next generation sequencing data using publically (free) available programmes.
Content:

  • Overview on mRNAs and long non-coding RNAs
  • Introduction to RNA databases (Ensembl, RefSeq, GenBank and human lincRNA catalogue)
  • RNA isolation techniques and quality assessment
  • Overview of next generation sequencing platforms (ABI Solid, Illumina Solexa, Life Technologies Ion Torrent)
  • Introduction to data file formats (FASTA, FASTQ, SAM, BAM, GTF and BED files)
  • Mapping of RNA data onto a reference genome using Tophat
  • Quantification of known RNA species using CuffDiff
  • Identification and quantification of novel RNA transcripts using CuffLinks
  • Visualisation and analysis of sequencing data using the IGV genome browsers
  • Functional annotation using DAVID pathway analysis

Course Trainers: Dr Nick Ilott (University of Oxford) and Prof Mark Lindsay (University of Bath)
Dates and location:
Tuesday 9th July 2013 – IMG Training Rooms, Near Liverpool Street Station, London

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Incoming search terms:

  • lncrna isolation

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

lncRNA

Known protein coding gene exons compose less than 3% of the human genome. The remaining 97% is largely uncharted territory, with only a small fraction characterized. The recent observation of transcription in this intergenic territory has stimulated debate about the extent of intergenic transcription and whether these intergenic RNAs are functional.

Here, researchers at the University of California, San Francisco directly observed with a large set of RNA-seq data covering a wide array of human tissue types that the majority of the genome is indeed transcribed, corroborating recent observations by the ENCODE project. Furthermore, using de novo transcriptome assembly of this RNA-seq data, they found that intergenic regions encode far more long intergenic noncoding RNAs (lincRNAs) than previously described, helping to resolve the discrepancy between the vast amount of observed intergenic transcription and the limited number of previously known lincRNAs. In total, they identified tens of thousands of putative lincRNAs expressed at a minimum of one copy per cell, significantly expanding upon prior lincRNA annotation sets. These lincRNAs are specifically regulated and conserved rather than being the product of transcriptional noise. In addition, lincRNAs are strongly enriched for trait-associated SNPs suggesting a new mechanism by which intergenic trait-associated regions may function. These findings will enable the discovery and interrogation of novel intergenic functional elements.

  • Hangauer MJ, Vaughn IW, McManus MT. (2013) Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs. PLoS Genet 9(6), e1003569. [article]

The Intertwining of Transposable Elements and Non-Coding RNAs

lncRNA

Growing evidence shows a close association of transposable elements (TE) with non-coding RNAs (ncRNA), and a significant number of small ncRNAs originate from TEs. Further, ncRNAs linked with TE sequences participate in a wide-range of regulatory functions. Alu elements in particular are critical players in gene regulation and molecular pathways. Alu sequences embedded in both long non-coding RNAs (lncRNA) and mRNAs form the basis of targeted mRNA decay via short imperfect base-pairing. Imperfect pairing is prominent in most ncRNA/target RNA interactions and found throughout all biological kingdoms. The piRNA-Piwi complex is multifunctional, but plays a major role in protection against invasion by transposons. This is an RNA-based genetic immune system similar to the one found in prokaryotes, the CRISPR system. Thousands of long intergenic non-coding RNAs (lincRNAs) are associated with endogenous retrovirus LTR transposable elements in human cells. These TEs can provide regulatory signals for lincRNA genes. A surprisingly large number of long circular ncRNAs have been discovered in human fibroblasts. These serve as “sponges” for miRNAs. Alu sequences, encoded in introns that flank exons are proposed to participate in RNA circularization via Alu/Alu base-pairing. Diseases are increasingly found to have a TE/ncRNA etiology. A single point mutation in a SINE/Alu sequence in a human long non-coding RNA leads to brainstem atrophy and death. On the other hand, genomic clusters of repeat sequences as well as lncRNAs function in epigenetic regulation. Some clusters are unstable, which can lead to formation of diseases such as facioscapulohumeral muscular dystrophy. The future may hold more surprises regarding diseases associated with ncRNAs andTEs.

  • Hadjiargyrou M, Delihas N. (2013) The Intertwining of Transposable Elements and Non-Coding RNAs. Int J Mol Sci 14(7), 13307-28. [article]

No Junk DNA…It’s All Good!

from Zone in With Zon

A Short Walk in the Wondrous, Wacky World of Long—and now Circular—Noncoding RNAs

I’m pleased by how much I learn when researching topics for new content, and this was certainly the case for long noncoding RNA (lncRNA), which was briefly mentioned in my last blog post, “Ripples from the 2013 TIDES Conference.”  The topic piqued my interest so I set out to find out more. Plowing through lncRNA (aka lincRNA = large intergenic non-coding RNA) literature I quickly realized that there was an enormous amount of information, and the big challenge would be to capture some intriguing aspects without getting bogged down in “technical weeds” or being overly simplistic. In what follows there is a super brief introduction to what lncRNAs are and what they do—the latter is controversial—along with an appreciation for why lncRNAs are indeed a structurally and functionally wondrous class of nucleic acids that now encompass circular molecules. Maybe—to borrow from Forrest Gump—lncRNAs are like “a box of chocolates” for molecular biologists.

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Incoming search terms:

  • incrnas

Induction of long intergenic non-coding RNA HOTAIR in lung cancer cells by type I collagen

lncRNA

The tumor microenvironment is a crucial determinant in tumor progression. Interstitial extracellular matrix (ECM), such as type I collagen (Col-1), is aberrantly enriched in the tumor microenvironment and promotes tumor progression. Long intergenic non-coding RNAs (lincRNA) are a new family of regulatory RNAs that modulate fundamental cellular processes via diverse mechanisms.

Researchers at Tulane University School of Medicine investigated whether the expression of lincRNAs was regulated by the tumor promoting Col-1. In a three-dimensional organotypic culture model using the reconstituted basement membrane ECM Matrigel (rBM 3-D), supplementation of Col-1 disrupted acini, a differentiation feature of well-differentiated lung adenocarcinoma cells, and concurrently induced the expression of a tumor-promoting lincRNA, HOX transcript antisense RNA (HOTAIR). Induction of HOTAIR by Col-1 was diminished by a neutralizing antibody against the Col-1 receptor alpha2beta1 integrin. Col-1 activates the expression of a reporter gene controlled by the human HOTAIR promoter. Moreover the expression of HOTAIR and Col-1 was concurrently up-regulated in human non-small cell lung cancer.

These findings indicate that tumor-promoting Col-1 up-regulates the expression of HOTAIR in NSCLC cells. These initial results warrant further investigation of HOTAIR and other lincRNA genes in lung tumorigenesis.

  • Zhuang Y, Wang X, Nguyen HT, Zhuo Y, Cui X, Fewell C, Flemington EK, Shan B. (2013) Induction of long intergenic non-coding RNA HOTAIR in lung cancer cells by type I collagen. J Hematol Oncol 6(1), 35. [Epub ahead of print]. [article]