Comprehensive Identification and Alternative Splicing of Microexons in Drosophila

Ting-Lin Pang; Zhan Ding; Shao-Bo Liang; Liang Li; Bei Zhang; Yu Zhang; Yu-Jie Fan; Yong-Zhen Xu

doi:10.3389/fgene.2021.642602

Comprehensive Identification and Alternative Splicing of Microexons in Drosophila

Front Genet. 2021 Mar 30:12:642602. doi: 10.3389/fgene.2021.642602. eCollection 2021.

Authors

Ting-Lin Pang^{1

2

3}, Zhan Ding^{1

2

3}, Shao-Bo Liang³, Liang Li^{1

2

3}, Bei Zhang^{1

2}, Yu Zhang^{1

2}, Yu-Jie Fan³, Yong-Zhen Xu³

Affiliations

¹ University of Chinese Academy of Sciences, Beijing, China.
² Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
³ RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, China.

Abstract

Interrupted exons in the pre-mRNA transcripts are ligated together through RNA splicing, which plays a critical role in the regulation of gene expression. Exons with a length ≤ 30 nt are defined as microexons that are unique in identification. However, microexons, especially those shorter than 8 nt, have not been well studied in many organisms due to difficulties in mapping short segments from sequencing reads. Here, we analyzed mRNA-seq data from a variety of Drosophila samples with a newly developed bioinformatic tool, ce-TopHat. In addition to the Flybase annotated, 465 new microexons were identified. Differentially alternatively spliced (AS) microexons were investigated between the Drosophila tissues (head, body, and gonad) and genders. Most of the AS microexons were found in the head and two AS microexons were identified in the sex-determination pathway gene fruitless.

Keywords: Drosophila; alternative splicing; ce-Tophat; microexon; sex determination.