Differences in alternative splicing and their potential underlying factors between animals and plants

Yunfei Du; Lu Cao; Shuo Wang; Liangyu Guo; Lingling Tan; Hua Liu; Ying Feng; Wenwu Wu

doi:10.1016/j.jare.2023.11.017

Differences in alternative splicing and their potential underlying factors between animals and plants

J Adv Res. 2023 Nov 20:S2090-1232(23)00354-5. doi: 10.1016/j.jare.2023.11.017. Online ahead of print.

Authors

Yunfei Du¹, Lu Cao¹, Shuo Wang¹, Liangyu Guo¹, Lingling Tan¹, Hua Liu¹, Ying Feng², Wenwu Wu³

Affiliations

¹ State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China.
² Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health (SINH), Chinese Academy of Sciences (CAS), Shanghai 200032, China. Electronic address: fengying@sibs.ac.cn.
³ State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China. Electronic address: wwwu@zafu.edu.cn.

PMID: 37981087
DOI: 10.1016/j.jare.2023.11.017

Abstract

Background: Alternative splicing (AS), a posttranscriptional process, contributes to the complexity of transcripts from a limited number of genes in a genome, and AS is considered a great source of genetic and phenotypic diversity in eukaryotes. In animals, AS is tightly regulated during the processes of cell growth and differentiation, and its dysregulation is involved in many diseases, including cancers. Likewise, in plants, AS occurs in all stages of plant growth and development, and it seems to play important roles in the rapid reprogramming of genes in response to environmental stressors. To date, the prevalence and functional roles of AS have been extensively reviewed in animals and plants. However, AS differences between animals and plants, especially their underlying molecular mechanisms and impact factors, are anecdotal and rarely reviewed.

Aim of review: This review aims to broaden our understanding of AS roles in a variety of biological processes and provide insights into the underlying mechanisms and impact factors likely leading to AS differences between animals and plants.

Key scientific concepts of review: We briefly summarize the roles of AS regulation in physiological and biochemical activities in animals and plants. Then, we underline the differences in the process of AS between plants and animals and especially analyze the potential impact factors, such as gene exon/intron architecture, 5'/3' untranslated regions (UTRs), spliceosome components, chromatin dynamics and transcription speeds, splicing factors [serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs)], noncoding RNAs, and environmental stimuli, which might lead to the differences. Moreover, we compare the nonsense-mediated mRNA decay (NMD)-mediated turnover of the transcripts with a premature termination codon (PTC) in animals and plants. Finally, we summarize the current AS knowledge published in animals versus plants and discuss the potential development of disease therapies and superior crops in the future.

Keywords: Alternative splicing; Chromatin dynamics; Cotranscriptional splicing; NMD pathway; SR proteins; Splicing factors.

Publication types

Review