Monthly Archives: July 2016

Identification and function annotation of long intervening noncoding RNAs

RNA-seq technology offers the promise of rapid comprehensive discovery of long intervening noncoding RNAs (lincRNAs). Basic tools such as Tophat and Cufflinks have been widely used for RNA-seq assembly. However, advanced bioinformatics methodologies that allow in-depth analysis of lincRNAs are lacking. Here, researchers from the Chinese Academy of Sciences describe a computational protocol that is especially designed for the identification ...

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Post-doc Position Available – lncRNAs in Digestive Diseases

lncRNA

Job #JPF02413 DAVID GEFFEN SCHOOL OF MEDICINE – MEDICINE-GASTROENTEROLOGY Recruitment Period Open July 13th, 2016 through July 31st, 2016 Description The Padua lab has a keen interest in understanding gene regulation and signaling pathways in the context of complex biological phenomena. Our clinical interests are in inflammatory bowel disease (IBD) and colon cancer diagnosis. One focus of the lab will ...

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Genome regulation by long noncoding RNAs

lncRNA

NIH Director’s Wednesday Afternoon Lecture Series Dr. Chang’s research addresses how large sets of genes are turned on or off together, which is important in normal development, cancer, and aging. Chang discovered a new class of genes, termed long noncoding RNAs, can control gene activity throughout the genome, illuminating a new layer of biological regulation. He has invented new methods ...

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Functional annotation of noncoding variants and prioritization of cancer-associated lncRNAs in lung cancer

lncRNA

Multiple computational tools have been widely applied to the detection of coding driver mutations in cancer; however, the prioritization of pathogenic non-coding variants remains a difficult and demanding task. The present study was performed to distinguish non-coding disease-causing mutations from neutral ones, and to prioritize potential cancer-associated long non-coding RNAs (lncRNAs) with a logistic regression model in lung cancer. A ...

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Unraveling the oral cancer lncRNAome

lncRNA

The role of long non-coding RNA (lncRNA) expression in human head and neck squamous cell carcinoma (HNSCC) is still poorly understood. In this study, UCSD researchers aimed at establishing the onco-lncRNAome profiling of HNSCC and to identify lncRNAs correlating with prognosis and patient survival. The Atlas of Noncoding RNAs in Cancer (TANRIC) database was employed to retrieve the lncRNA expression ...

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Upcoming Webinar – RNA-ISH for Long non-coding RNAs – new game changers in pathology

lncRNA

August 11, 2016   –   11:00AM PST, 2:00PM ET, 7:00PM GMT Rohit Mehra, M.D. Assistant Professor of Pathology Member-Michigan Center for Translational Pathology MLabs Genitourinary Service Line Director Co-Director, University of Michigan Rapid Autopsy Discovery Program The central dogma that forms the backbone of molecular biology is that DNA codes for RNA (transcription) which then codes for proteins (translation). However, studies ...

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A correlation between Long noncoding RNA and unpaired DNA silencing in Drosophila

lncRNA

Hybrid transgenes are often recognized as foreign genetic material by cell surveillance mechanisms and are repressed in expression inversely to their copy numbers. Here, researchers from the Indian Institute of Chemical Technology compare the expression of multiple Adh-promoter-white reporter (Adh-w) inserts in paired and unpaired configurations in Drosophila somatic cells. The unpaired copies exhibit a clear repression at the transcriptional ...

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Developmentally regulated long non-coding RNAs in Xenopus tropicalis

lncRNA

Advances in RNA sequencing technologies have led to the surprising discovery that a vast number of transcripts emanate from regions of the genome that are not part of coding genes. Although some of the smaller ncRNAs such as microRNAs have well-characterized functions, the majority of long ncRNA (lncRNA) functions remain poorly understood. Understanding the significance of lncRNAs is an important ...

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Challenges in the analysis of long noncoding RNA functionality

lncRNA

Long noncoding RNAs (lncRNAs) are emerging as important regulators of diverse biological functions. Although mechanistic models are starting to emerge, it is also clear that the lncRNA field needs appropriate model systems in order to better elucidate the functions of lncRNAs and their roles in both physiological and pathological conditions. The field of lncRNAs is new, and the biochemical and ...

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DeepLNC, a long non-coding RNA prediction tool using a deep neural network

lncRNA

The significant role of long non-coding RNAs (lncRNAs) in various cellular functions, such as gene imprinting, immune response, embryonic pluripotency, tumorogenesis, and genetic regulations, has been widely studied and reported in recent years. Several experimental and computational methods involving genome-wide search and screenings of ncRNAs are being proposed utilizing sequence features-length, occurrence, and composition of bases with various limitations. Researchers ...

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