CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome

• Published in: Nucleic acids research Vol. 45; no. 16; pp. 9260 - 9271
• Main Authors: Zhang, Zijun, Xing, Yi
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 19.09.2017
• Subjects: Adenosine - analogs & derivatives; Adenosine - metabolism; Algorithms; Alternative Splicing; Argonaute Proteins - metabolism; Cell Line; Computational Biology; Gene Expression Regulation; Heterogeneous-Nuclear Ribonucleoprotein Group C - metabolism; High-Throughput Nucleotide Sequencing - methods; Humans; Immunoprecipitation; MicroRNAs - metabolism; Models, Statistical; Regulatory Sequences, Ribonucleic Acid; RNA Splicing Factors - metabolism; RNA Stability; RNA, Messenger - metabolism; Sequence Analysis, RNA - methods; Software; Transcriptome

Crosslinking or RNA immunoprecipitation followed by sequencing (CLIP-seq or RIP-seq) allows transcriptome-wide discovery of RNA regulatory sites. As CLIP-seq/RIP-seq reads are short, existing computational tools focus on uniquely mapped reads, while reads mapped to multiple loci are discarded. We pr...