Tag Archives: transcriptome

Comprehensive discovery of non-coding RNAs in acute myeloid leukemia cell transcriptomes

lncRNA

To comprehensively detect diverse and novel RNA species, researchers from Washington University, St. Louis compared deep small RNA and RNA sequencing (RNA-seq) methods applied to a primary acute myeloid leukemia (AML) sample. They were able to discover previously unannotated small RNAs using deep sequencing of a library method employing broader insert size selection. The researchers analyzed the long non-coding RNA (lncRNA) ...

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Identification and prioritization of long non-coding RNAs associated with autism

Genetic studies have identified many risk loci for autism spectrum disorder (ASD) although causal factors in the majority of cases are still unknown. Currently, known ASD risk genes are all protein-coding genes; however, the vast majority of transcripts in humans are non-coding RNAs (ncRNAs) which do not encode proteins. Recently, long non-coding RNAs (lncRNAs) were shown to be highly expressed ...

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In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome

The complexity of the tomato (Solanum lycopersicum) transcriptome has not yet been fully elucidated. To gain insights into the diversity and features of coding and non-coding RNA molecules of tomato fruits, researchers from the University of Naples Federico II generated strand-specific libraries from berries of two tomato cultivars grown in two open-field conditions with different soil type. Following high-throughput Illumina RNA-sequencing ...

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Identification and comparison of long non-coding RNAs in the silk gland between the domestic and wild silkworms

lncRNA

Under long-term artificial selection, the domestic silkworm (Bombyx mori) has increased its silk yield tremendously in comparison with its wild progenitor, Bombyx mandarina. However, the molecular mechanism of silk yield increase is still unknown. Comparative analysis of long non-coding RNAs (lncRNAs) may provide some insights into understanding this phenotypic variation. In this study, using the RNA-seq data of silk gland ...

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AnnoLnc – a web server for systematically annotating novel human lncRNAs

lncRNA

Long noncoding RNAs (lncRNAs) have been shown to play essential roles in almost every important biological process through multiple mechanisms. Although the repertoire of human lncRNAs has rapidly expanded, their biological function and regulation remain largely elusive, calling for a systematic and integrative annotation tool. Here researchers from Peking University present AnnoLnc, a one-stop portal for systematically annotating novel human ...

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The emerging role of long non-coding RNAs in endometrial cancer

lncRNA

The human genome is pervasively transcribed and approximately 98% of the genome is non-coding. Long non-coding RNAs (lncRNAs) are a heterogeneous group of RNA transcripts that are >200 nucleotides in length with minimal to no protein-coding potential. Similar to proteins, lncRNAs have important biological functions in both normal cells and disease states including many types of cancer. This review summarizes ...

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Mining long noncoding RNA in livestock

lncRNA

Genome-wide association studies in livestock based on high-resolution genotyping and sequencing have revealed that the majority of signals associated with complex phenotypic traits are located outside of annotated protein-coding regions in the genome. The approaches of next-generation sequencing applied to whole transcriptome and chromatin profiles have provided information about existing genome-wide transcriptional activity and have revealed that the genomes are ...

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Genomics 2.0: The Importance of RNA Biology

from the Rochester Democrat and Chronicle by Stephen Dewhurst – The ability to sequence the human genome has transformed the way we approach science and medicine.  But understanding our DNA is really only the first step in the Genomics revolution. The same DNA is present in each and every cell of our bodies – yet each of those cells is ...

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lncRNA prostate cancer associated transcript-14 (PCAT-14) is prognostic for metastatic disease and survival

lncRNA

Long noncoding RNAs (lncRNAs) are an emerging class of relatively underexplored oncogenic molecules with biological and clinical significance. Current inadequacies for stratifying patients with aggressive disease presents a strong rationale to systematically identify lncRNAs as clinical predictors in localized prostate cancer. To identify RNA biomarkers associated with aggressive prostate cancer researchers from the Washington University School of Medicine obtained radical ...

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