Computational Non-coding RNA Biology by Yun Zheng

Author:Yun Zheng
Language: eng
Format: epub
ISBN: 9780128143667
Publisher: Elsevier Ltd.
Published: 2018-09-13T16:00:00+00:00

Part 3

MiRNA Targets

Outline

Introduction

Chapter 5. Identification of miRNA Targets in Animals

Chapter 6. Identification of miRNA and siRNA Targets in Plants

Introduction

Targets of microRNAs and siRNAs

MiRNAs realize their functions by regulating their target mRNAs. Thus, a critical step for revealing the functions of miRNAs is the correct identification of the targets of miRNAs. The miRNAs in plants and animals have different mechanism when regulating their targets. Plant miRNAs mainly induce the cleavage of their target mRNAs through fully or nearly fully matched complementary sites. However, miRNAs in animals normally have far fewer matched nucleotides in the complementary sites on their target mRNAs than plant miRNAs do. However, animal miRNAs also have some unique features when recognizing complementary sites. For example, of the first eight nucleotides of miRNAs, i.e., the seed region, normally at least seven are matched. Thus, different methods have been proposed for identifying miRNA targets in plants and animals.

With the development of sequencing-based technologies, advances were made in the identification of plant miRNA targets by using degradome sequencing profiles of polyadenylated transcripts. Chapter 6 introduces a computational pipeline for identifying plant miRNA and siRNA targets by using degradome sequencing profiles.

In comparison, CrossLinking ImmunoPrecipitation (CLIP) followed by high throughput sequencing was used to identify RNAs interacting with RNA binding proteins in animals. Several technologies, such as HITS-CLIP, PAR-CLIP, and iCLIP, were recently proposed to identify animal miRNA targets by using CLIP on Argonaute proteins. In Chapter 5, we introduce a new method called MiCPAR (identifying MiRNA targets using Corrected PAR-clip sequencing profiles) for the identification of animal miRNA targets.

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