Search Results for: incrna

A deep learning method for lincRNA detection using auto-encoder algorithm

lncRNA

RNA sequencing technique (RNA-seq) enables scientists to develop novel data-driven methods for discovering more unidentified lincRNAs. Meantime, knowledge-based technologies are experiencing a potential revolution ignited by the new deep learning methods. By scanning the newly found data set from RNA-seq, scientists have found that: (1) the expression of lincRNAs appears to be regulated, that is, the relevance exists along the ...

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Neat1 is a p53-inducible lincRNA essential for transformation suppression

lncrna

The p53 gene is mutated in over half of all cancers, reflecting its critical role as a tumor suppressor. Although p53 is a transcriptional activator that induces myriad target genes, those p53-inducible genes most critical for tumor suppression remain elusive. Here, researchers at Stanford University School of Medicine leveraged p53 ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) and RNA-seq ...

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De novo RNA sequence assembly during in vivo inflammatory stress reveals hundreds of unannotated lincRNAs in human blood

lncrna

Long intergenic noncoding RNAs (lincRNAs) have emerged as key regulators of cellular functions and physiology. Yet functional lincRNAs often have low, context-specific and tissue-specific expression. Researchers from Columbia University Medical Center hypothesized that many human monocyte and adipose lincRNAs would be absent in current public annotations due to lincRNA tissue specificity, modest sequencing depth in public data, limitations of transcriptome assembly ...

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Novel lincRNA SLINKY is a prognostic biomarker in kidney cancer

lncRNA

Clear cell renal cell carcinomas (ccRCC) show a broad range of clinical behavior, and prognostic biomarkers are needed to stratify patients for appropriate management. Stanford University researchers  sought to determine whether long intergenic non-coding RNAs (lincRNAs) might predict patient survival. Candidate prognostic lincRNAs were identified by mining The Cancer Genome Atlas (TCGA) transcriptome (RNA-seq) data on 466 ccRCC cases (randomized ...

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cis-Acting Complex-Trait-Associated lincRNA Expression Correlates with Modulation of Chromosomal Architecture

lncRNA

Intergenic long noncoding RNAs (lincRNAs) are the largest class of transcripts in the human genome. Although many have recently been linked to complex human traits, the underlying mechanisms for most of these transcripts remain undetermined. Researchers from the University of Lausanne investigated the regulatory roles of a high-confidence and reproducible set of 69 trait-relevant lincRNAs (TR-lincRNAs) in human lymphoblastoid cells ...

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Bioinformatics for Novel Long Intergenic Noncoding RNA (lincRNA) Identification

lncRNA

Long intergenic noncoding RNAs (lincRNAs) , which are larger than 200 nucleotides and transcribed from the intergenic regions of protein coding genes, have been shown by accumulating findings to be widely expressed and extensively functional in many cellular processes. Nevertheless, given their cell/tissue-specificity, there is a need of identifying novel lincRNAs in a given system. To fulfill this purpose, researchers ...

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lincRNAs Display Distinctive Patterns of Transcription and RNA Processing

lncRNA

Numerous long intervening noncoding RNAs (lincRNAs) are generated from the mammalian genome by RNA polymerase II (Pol II) transcription. Although multiple functions have been ascribed to lincRNAs, their synthesis and turnover remain poorly characterized. Here, University of Oxford researchers define systematic differences in transcription and RNA processing between protein-coding and lincRNA genes in human HeLa cells. This is based on ...

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Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs

lncRNA

While long intergenic noncoding RNAs (lincRNAs) and mRNAs share similar biogenesis pathways, these transcript classes differ in many regards. LincRNAs are less evolutionarily conserved, less abundant, and more tissue-specific, suggesting that their pre- and post-transcriptional regulation is different from that of mRNAs. Here, researchers from Harvard University performed an in-depth characterization of the features that contribute to lincRNA regulation in ...

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Long noncoding RNA (lincRNA), a new paradigm in gene expression control

lncRNA

Long intergenic non-coding RNAs (lincRNAs) are defined as RNA transcripts that are longer than 200 nucleotides. By definition, these RNAs must not have open reading frames that encode proteins. Many of these transcripts are encoded by RNA polymerase II, are spliced, and are poly-adenylated. This final fact indicates that there is a trove of information about lincRNAs in databases such ...

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