Variable window binding for mutually exclusive alternative splicing

Genome Biology
Dimitris AnastassiouVinay Varadan

Abstract

Genes of advanced organisms undergo alternative splicing, which can be mutually exclusive, in the sense that only one exon is included in the mature mRNA out of a cluster of alternative choices, often arranged in a tandem array. In many cases, however, the details of the underlying biologic mechanisms are unknown. We describe 'variable window binding'--a mechanism used for mutually exclusive alternative splicing by which a segment ('window') of a conserved nucleotide 'anchor' sequence upstream of the exon 6 cluster in the pre-mRNA of the fruitfly Dscam gene binds to one of the introns, thereby activating selection of the exon directly downstream from the binding site. This mechanism is supported by the fact that the anchor sequence can be inferred solely from a comparison of the intron sequences using a genetic algorithm. Because the window location varies for each exon choice, regulation can be achieved by obstructing part of that sequence. We also describe a related mechanism based on competing pre-mRNA stem-loop structures that could explain the mutually exclusive choice of exon 17 of the Dscam gene. On the basis of comparative sequence analysis, we propose efficient biologic mechanisms of alternative splicing of the Drosoph...Continue Reading

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Citations

Jan 30, 2010·Nature·Timothy W Nilsen, Brenton R Graveley
Dec 6, 2012·Nature Communications·Xuebin WangYongfeng Jin
Jan 11, 2011·Nature Structural & Molecular Biology·Yun YangYongfeng Jin
Dec 1, 2007·Nature Structural & Molecular Biology·Sara OlsonBrenton R Graveley
Nov 21, 2007·Bioinformatics·Kuo-Ching LiangDimitris Anastassiou
Jul 24, 2012·Biochemical Society Transactions·Yash Hemani, Matthias Soller
Mar 11, 2017·Developmental and Comparative Immunology·Yu-Hsuan ChangHan-Ching Wang
Feb 10, 2018·Wiley Interdisciplinary Reviews. RNA·Yongfeng JinLina Bian
Sep 16, 2020·Wiley Interdisciplinary Reviews. RNA·Bingbing XuYongfeng Jin
Oct 22, 2018·Cellular and Molecular Life Sciences : CMLS·Yongfeng Jin, Hao Li
Jan 4, 2020·Cold Spring Harbor Perspectives in Biology·Marie Teng-Pei Wu, Victoria D'Souza
Apr 17, 2021·Frontiers in Genetics·Haiyang DongYongfeng Jin

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Datasets Mentioned

BETA
DQ317108
AF260530
AY686597

Software Mentioned

MATLAB

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Alternative splicing

Alternative splicing a regulated gene expression process that allows a single genetic sequence to code for multiple proteins. Here is that latest research.