Tag Archives: lncrna

Profiling long noncoding RNA of multi-tissue transcriptome enhances porcine noncoding genome annotation

lncRNA

To construct a comprehensive pig noncoding transcriptome and further enhance porcine noncoding genome annotation, researchers at China Agricultural University performed tissue-based long noncoding RNA (lncRNA) profiling. They identified 32,212 nonredundant lncRNA isoforms corresponding to 18,676 lncRNA loci across 34 normal pig tissues using high-throughput sequencing. Furthermore, they globally assessed the potential relationship between these identified lncRNAs and known protein-coding genes ...

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RNA-seq-based genome annotation and identification of long-noncoding RNAs in the winegrape Riesling

lncRNA

The technological advances of RNA-seq and de novo transcriptome assembly have enabled genome annotation and transcriptome profiling in highly heterozygous species such as grapevine (Vitis vinifera L.). This work is an attempt to utilize a de novo-assembled transcriptome of the V. vinifera cultivar ‘Riesling’ to improve annotation of the grapevine reference genome sequence. Here researchers from Missouri State University and the ...

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Circulating lncRNAs Serve as Diagnostic Markers for Hepatocellular Carcinoma

lncRNA

Circulating (serous or plasmic) long non-coding RNA (lncRNA) as biomarkers for predicting the diagnosis or prognosis of human disease have been well documented. Due to the sensibility or specificity limitation of Alpha Fetoprotein (AFP), a cluster lncRNAs were revealed as fingerprints for hepatocellular carcinoma (HCC). In this study, researchers at Huai’an First People’s Hospital enrolled all the reported circulating lncRNAs ...

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The Dark Side of the Epitranscriptome – Chemical Modifications in Long Non-Coding RNAs

lncrna

The broad application of next-generation sequencing technologies in conjunction with improved bioinformatics has helped to illuminate the complexity of the transcriptome, both in terms of quantity and variety. In humans, 70-90% of the genome is transcribed, but only ~2% carries the blueprint for proteins. Hence, there is a huge class of non-translated transcripts, called long non-coding RNAs (lncRNAs), which have ...

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Prediction of clinical outcome and survival in soft-tissue sarcoma using a ten-lncRNA signature

lncRNA

The prognostic value of long non-coding RNAs (lncRNAs) in patients with soft-tissue sarcoma has rarely been unraveled. Researchers from Guangxi Medical University set out to find a lncRNA signature to predict the clinical outcome and survival in soft-tissue sarcoma based on the high-throughput RNA-seq data from The Cancer Genome Atlas (TCGA) database. The lncRNAs which closely correlated with overall survival ...

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Elucidating the role of host long non-coding RNA during viral infection

lncrna

Research over the past decade has clearly shown that long non-coding RNAs (lncRNAs) are functional. Many lncRNAs can be related to immunity and the host response to viral infection, but their specific functions remain largely elusive. The vast majority of lncRNAs are annotated with extremely limited knowledge and tend to be expressed at low levels, making ad hoc experimentation difficult. ...

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Analysis of lncRNA-Protein Interactions by RNA-Protein Pull-Down Assays and RNA Immunoprecipitation (RIP)

lncrna

Long noncoding RNAs (lncRNAs) have important roles in shaping chromatin by targeting chromatin-modifying enzymes to distinct genomic sites. This section covers two methods to analyze lncRNA-protein interactions. The RNA-protein pull-down assays use either bead-bound proteins to capture in vitro transcripts, or immobilized synthetic RNAs to bind proteins from cell lysates. In the RNA immunoprecipitation (RIP) assay, endogenous RNAs are co-immunoprecipitated ...

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lncRNAs and immunity – watchdogs for host pathogen interactions

lncRNA

Immune responses combat various infectious agents by inducing inflammatory responses, antimicrobial pathways and adaptive immunity. The polygenic responses to these external stimuli are temporally and coordinately regulated. Specific lncRNAs are induced to modulate innate and adaptive immune responses which can function through various target interactions like RNA-DNA, RNA-RNA, and RNA-protein interaction and hence affect the immunogenic regulation at various stages ...

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Regulated expression of the lncRNA TERRA and its impact on telomere biology

lncrna

The telomere protects against genomic instability by minimizing the accelerated end resection of the genetic material, a phenomenon that results in severe chromosome instability that could favor the transformation of a cell by enabling the emergence of tumor-promoting mutations. Some mechanisms that avoid this fate, such as capping and loop formation, have been very well characterized; however, telomeric non-coding transcripts, ...

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