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Apr
4
RNA: The genome’s rising stars
Filed Under News, Publications, Review | Leave a Comment
from Nature by Amy Maxmen
When Saba Valadkhan lingered in the hallways at conferences, absorbed in discussions about the strands of ‘junk’ DNA that litter the human genome, she was not looking for work. She was consumed with curiosity about the possibility that long RNA sequences that do not encode proteins nevertheless have a function — enhancing or suppressing gene expression. Valadkhan’s enthusiasm about the budding field of long non-coding RNA (lncRNA) did not go unnoticed: senior investigators were on the hunt for young researchers willing to pursue the topic. “Before I was even looking for job opportunities, I was told about people who were hiring,” says Valadkhan. Soon after receiving her PhD for studies on small nuclear RNA — a type of non-coding RNA — at Columbia University in New York in 2003, she took a position as an assistant professor at Case Western Reserve University in Cleveland, Ohio.
John Rinn, now a molecular biologist at Harvard University and the Broad Institute of MIT and Harvard in Cambridge, Massachusetts, also had a rapid career launch; as a postdoc at Stanford University in California, he was noticed at meetings where he spoke about his research on how lncRNA silences genes involved in embryonic development. Rinn was offered several faculty positions, but was sold on the Cambridge post when Stuart Schreiber, a chemical biologist and a founding member of the Broad Institute, told him: “Every day I come to work dreaming of how I will bend the genome to my will.” Rinn wanted to bend the genome with lncRNA to learn how to prevent and cure diseases.
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Apr
3
Predicting long non-coding RNAs with RNA-Seq
Filed Under Analysis Pipelines, Other Tools | Leave a Comment
The advent of next-generation sequencing, and in particular RNA-sequencing (RNA-Seq), technologies has expanded our knowledge of the transcriptional capacity of human and other animal, genomes. In particular, recent RNA-Seq studies have revealed that transcription is widespread across the mammalian genome, resulting in a large increase in the number of putative transcripts from both within, and intervening between, known protein-coding genes. Long transcripts that appear to lack protein-coding potential (long non-coding RNAs, lncRNAs) have been the focus of much recent research, in part owing to observations of their cell-type and developmental time-point restricted expression patterns. A variety of sequencing protocols are currently available for identifying lncRNAs including RNA polymerase II occupancy, chromatin state maps and – the focus of this review – deep RNA sequencing. In addition, there are numerous analytical methods available for mapping reads and assembling transcript models that predict the presence and structure of lncRNAs from RNA-Seq data. Here the authors review current methods for identifying lncRNAs using large-scale sequencing data from RNA-Seq experiments and highlight analytical considerations that are required when undertaking such projects.
- Ilott NE, Ponting CP. (2013) Predicting long non-coding RNAs using RNA sequencing. Methods [Epub ahead of print]. [abstract]
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Feb
19
lncRScan – Prediction of novel long non-coding RNAs based on RNA-Seq data
Filed Under Analysis Pipelines, Other Tools | Leave a Comment
Study on long non-coding RNAs (lncRNAs) has been promoted by high-throughput RNA sequencing (RNA-Seq). However, it is still not trivial to identify lncRNAs from the RNA-Seq data and it remains a challenge to uncover their functions.
Now, a team led by researchers at China University of Mining and Technology have developed a computational pipeline for detecting novel lncRNAs from the RNA-Seq data. First, the genome-guided transcriptome reconstruction is used to generate initially assembled transcripts. The possible partial transcripts and artefacts are filtered according to the quantified expression level. After that, novel lncRNAs are detected by further filtering known transcripts and those with high protein coding potential, using a newly developed program called lncRScan.
They applied our pipeline to a mouse Klf1 knockout dataset, and discussed the plausible functions of the novel lncRNAs they detected by differential expression analysis. The team identified 308 novel lncRNA candidates, which have shorter transcript length, fewer exons, shorter putative open reading frame, compared with known protein-coding transcripts. Of the lncRNAs, 52 large intergenic ncRNAs (lincRNAs) show lower expression level than the protein-coding ones and 13 lncRNAs represent significant differential expression between the wild-type and Klf1 knockout conditions.
Their method can predict a set of novel lncRNAs from the RNA-Seq data. Some of the lncRNAs are showed differentially expressed between the wild-type and Klf1 knockout strains, suggested that those novel lncRNAs can be given high priority in further functional studies.
- Sun L, Zhang Z, Bailey TL, Perkins AC, Tallack MR, Xu Z, Liu H. (2012) Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study. BMC Bioinformatics [Epub ahead of print]. [abstract]
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Feb
15
iSeeRNA – identification of long intergenic non-coding RNA transcripts from RNA-Seq data
Filed Under Analysis Pipelines, Other Tools | Leave a Comment
Long intergenic non-coding RNAs (lincRNAs) are emerging as a novel class of non-coding RNAs and potent gene regulators. High-throughput RNA-sequencing combined with de novo assembly promises quantity discovery of novel transcripts. However, the identification of lincRNAs from thousands of assembled transcripts is still challenging due to the difficulties of separating them from protein coding transcripts (PCTs).
A team of scientists at The Chinese University of Hong Kong have developed iSeeRNA, a support vector machine (SVM)-based classifier for the identification of lincRNAs. iSeeRNA shows better performance compared to other software.
iSeeRNA demonstrates high prediction accuracy and runs several magnitudes faster than other similar programs. It can be integrated into the transcriptome data analysis pipelines or run as a web server, thus offering a valuable tool for lincRNA study.
Availability – iSeeRNA is available as a user-friendly web server with free accessibility at http://www.myogenesisdb.org/iSeeRNA
- Sun K, Chen X, Jiang P, Song X, Wang H, Sun H. (2013) iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data. BMC Genomics 14(supp 2). [article]
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Dec
17
A computational pipeline for detecting novel lncRNAs from the RNA-Seq data
Filed Under Analysis Pipelines | Leave a Comment
Study on long non-coding RNAs (lncRNAs) has been promoted by high-throughput RNA sequencing (RNA-Seq). However, it is still not trivial to identify lncRNAs from the RNA-Seq data and it remains a challenge to uncover their functions.
Now, researchers at China University of Mining and Technology, Xuzhou present a computational pipeline for detecting novel lncRNAs from the RNA-Seq data. First, the genome-guided transcriptome reconstruction is used to generate initially assembled transcripts. The possible partial transcripts and artefacts are filtered according to the quantified expression level. After that, novel lncRNAs are detected by further filtering known transcripts and those with high protein coding potential, using a newly developed program called lncRScan.
They applied the pipeline to a mouse Klf1 knockout dataset, and discussed the plausible functions of the novel lncRNAs they detected by differential expression analysis. The researchers identified 308 novel lncRNA candidates, which have shorter transcript length, fewer exons, shorter putative open reading frame, compared with known protein-coding transcripts. Of the lncRNAs, 52 large intergenic ncRNAs (lincRNAs) show lower expression level than the protein-coding ones and 13 lncRNAs represent significant differential expression between the wild-type and Klf1 knockout conditions.
This method can predict a set of novel lncRNAs from the RNA-Seq data. Some of the lncRNAs are showed differentially expressed between the wild-type and Klf1 knockout strains, suggested that those novel lncRNAs can be given high priority in further functional studies.
- Sun L, Zhang Z, Bailey TL, Perkins AC, Tallack MR, Xu Z, Liu H.(2012) Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study. BMC Bioinformatics [Epub ahead of print]. [abstract] [provisional PDF]
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Nov
23
Expression profiles of mRNAs and lncRNAs from RNA-Seq data across 22 human tissues
Filed Under Web Tools | Leave a Comment
from yjhua2110 at seqanswers.com
We have constructed expression profiles of long noncoding RNAs (lncRNAs, lincRNAs) and protein-coding genes (mRNAs) from RNA-Seq data across 22 normal tissues (Human BodyMap 2.0 data from Illumina) generated by Cabili et al. (Cabili et al. 2011, Genes Dev., 25, 1915-1927.). We hope it will help your research.
(1) User can find tissue-specific lncRNAs and mRNAs and expression pattern of each gene by viewing heatmap constructed by us. (2)Move mouse cursor on heatmap to see details or click lncRNA or mRNA name to launch detail page. (3) Click the title of the heatmap (e.g. gene symbol, lncRNA name, nearest gene, gene symbol, tissues(e.g. liver, lung…)), to sort whole heatmap.
Examples:
(a) access lncRNA expression profiles.
(b) access protein-coding expression profiles:
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Nov
5
Long noncoding RNAs in pathogenesis
Filed Under Publications | Leave a Comment
LncRNAs (pronounced “link”) are long non-coding RNAs that are emerging as important regulators of gene expression in biological processes and diseases. In this issue of the Journal of Clinical Investigation, two papers connect lncRNAs to inherited conditions in humans.
Sylvia B-hring and colleagues at the Experimental and Clinical Research Center in Berlin found a chromosomal translocation that disrupts the expression of a lncRNA. This disruption alters the expression of the genes PTHLH and SOX9 and results in brachydactyly, an inherited malformation of the fingers and toes. HELLP syndrome, a group of symptoms occurring in pregnant women that lead to pre-term delivery, was also found to be caused by a lncRNA.
Researchers led by Cees Oudejans at the VU University Medical Center in Amsterdam identified a lncRNA on chromosome 12 that activated a set of genes which control the development of the placenta. In a companion commentary, Norman Sharpless of the University of North Carolina at Chapel Hill provides an overview of lncRNA biology and discusses the role of lncRNAs in heritable human diseases.
(read more at News-Medical.net)
(read more at: Journal of Clinical Investigation)
- van Dijk M, Thulluru HK, Mulders J, Michel OJ, Poutsma A, Windhorst S, Kleiverda G, Sie D, Lachmeijer AM, Oudejans CB. (2012) HELLP babies link a novel lincRNA to the trophoblast cell cycle. J Clin Invest 122(11):4003-11. [article]
- Maass PG, Rump A, Schulz H, Stricker S, Schulze L, Platzer K, Aydin A, Tinschert S, Goldring MB, Luft FC, Bähring S. (2012) A misplaced lncRNA causes brachydactyly in humans. J Clin Invest 122(11):3990-4002. [article]
Incoming search terms:
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Aug
16
Long ncRNA processed to small ncRNA?
Filed Under Publications | Leave a Comment
Contrary to the previous assumption that large tracts of the eukaryotic genomes are not transcriptionally active, recent evidence from transcriptome sequencing approaches have revealed pervasive transcription in many genomes of higher eukaryotes. Many of these loci encode transcripts that have no obvious protein-coding potential and are designated as non-coding RNA (ncRNA). Noncoding RNAs are classified empirically as small and long non-coding RNAs based on the size of the functional RNAs. Each of these classes is further classified into functional subclasses.
Although microRNAs (miRNA), one of the major subclass of ncRNAs, have been extensively studied for their roles in regulation of gene expression and involvement in a large number of patho-physiological processes, the functions of a large proportion of long noncoding RNAs (lncRNA) still remains elusive.
Researchers at the CSIR Institute of Genomics and Integrative Biology, India hypothesized that some lncRNAs could potentially be processed to small RNA and thus could have a dual regulatory output.
- Jalali S, Jayaraj GG, Scaria V. (2012) Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs. Biol Direct 7(1), 25. [abstract]
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May
24
The Emergence of lncRNA
Filed Under Information | 3 Comments
lncRNA Database
Most (~75%) of the catalogued lncRNAs are from mammals, for which more transcriptomic data is available and which have been more intensively studied, but lncRNAs from vertebrates to single-celled eukaryotes have been included. In addition, lncRNAdb has links to the UCSC Genome Browser for visualization and NRED (ncRNA Expression Database) for expression information from a variety of sources.
Macro lncRNAs: A new layer of cis-regulatory information in the mammalian genome.
Guenzl P, Barlow D.
RNA Biol. 2012 Jun 1;9(6). [Epub ahead of print]
Long Noncoding RNA: Its Physiological and Pathological Roles.
Yan B, Wang Z.
DNA Cell Biol. 2012 May 21. [Epub ahead of print]
Regulatory long non-coding RNA and its functions.
Huang Y, Liu N, Wang JP, Wang YQ, Yu XL, Wang ZB, Cheng XC, Zou Q.
J Physiol Biochem. 2012 Apr 26. [Epub ahead of print]
Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs.
Moran VA, Perera RJ, Khalil AM.
Nucleic Acids Res. 2012 Apr 5. [Epub ahead of print]
Exploring long non-coding RNAs through sequencing.
Atkinson SR, Marguerat S, Bähler J.
Semin Cell Dev Biol. 2012 Apr;23(2):200-5. Epub 2011 Dec 20.
The Emergence of lncRNAs in Cancer Biology.
Prensner JR, Chinnaiyan AM.
Cancer Discov. 2011 Oct;1(5):391-407.
Long noncoding RNAs and human disease.
Wapinski O, Chang HY.
Trends Cell Biol. 2011 Jun;21(6):354-61. Epub 2011 May 6.
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- Biostar – RNA-Seq
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