Computational analysis of ribonomics datasets identifies long non-coding RNA targets of γ-herpesviral miRNAs

Nucleic Acids Research
Sunantha SethuramanRolf Renne

Abstract

Ribonomics experiments involving crosslinking and immuno-precipitation (CLIP) of Ago proteins have expanded the understanding of the miRNA targetome of several organisms. These techniques, collectively referred to as CLIP-seq, have been applied to identifying the mRNA targets of miRNAs expressed by Kaposi's Sarcoma-associated herpes virus (KSHV) and Epstein-Barr virus (EBV). However, these studies focused on identifying only those RNA targets of KSHV and EBV miRNAs that are known to encode proteins. Recent studies have demonstrated that long non-coding RNAs (lncRNAs) are also targeted by miRNAs. In this study, we performed a systematic re-analysis of published datasets from KSHV- and EBV-driven cancers. We used CLIP-seq data from lymphoma cells or EBV-transformed B cells, and a crosslinking, ligation and sequencing of hybrids dataset from KSHV-infected endothelial cells, to identify novel lncRNA targets of viral miRNAs. Here, we catalog the lncRNA targetome of KSHV and EBV miRNAs, and provide a detailed in silico analysis of lncRNA-miRNA binding interactions. Viral miRNAs target several hundred lncRNAs, including a subset previously shown to be aberrantly expressed in human malignancies. In addition, we identified thousands of ...Continue Reading

Citations

Sep 5, 2019·Endocrine, Metabolic & Immune Disorders Drug Targets·Dijie LiAirong Qian
Nov 15, 2018·Non-coding RNA·Lauren A GayRolf Renne
Oct 6, 2020·Frontiers in Pharmacology·Yali RenCheng Peng
Mar 9, 2021·Computational and Structural Biotechnology Journal·Petr V Nazarov, Stephanie Kreis
May 27, 2021·Cancer Cell International·Yitong LiuChengkun Wang

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Datasets Mentioned

BETA
SRP068881
SRP016130
GSE101978

Methods Mentioned

BETA
immunoprecipitation
HITS-CLIP
PAR-CLIP
CLASH
CLIP-seq
transfections
RNA-immunoprecipitation
PIPE-CLIP
PCR
CLIP

Software Mentioned

Bowtie
fastq
ANGIOGENES
R
HITS
Ago
Ago PAR - CLIP
Trimmomatic
FastQC
CLIPZ

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