Data/hora: 08/06/2024 18:24:23

Provedor de dados: | Brazilian Archives of Biology and Technology
País: | Brazil
Título: | Optimized Exon-Exon Junction Library and its Application on Rodents' Brain Transcriptome Analysis
Autores: | Dou,Tong-Hai; Gao,Yuan; Chen,Cheng-Wen; Xu,Min-Jie; Fu,Mao-Bin; Zhang,Liang; Zhou,Yan.
Data: | 2017-01-01
Ano: | 2017
Palavras-chave: | RNA-seq; Exon-exon junction; Alternative splicing; Cerebrum; Cerebellum.
Resumo: | ABSTRACT  Background: Alternative splicing (AS), which plays an important role in gene expression and functional regulation, has been analyzed on genome-scale by various bioinformatic approaches based on RNA-seq data. Compared with the huge number of studies on mouse, the AS researches approaching the rat, whose genome is intermedia between mouse and human, were still limited. To enrich the knowledge on AS events in rodents' brain, we perfomed a comprehensive analysis on four transcriptome libraries (mouse cerebrum, mouse cerebellum, rat cerebrum, and rat cerebellum), recruiting high-throughput sequencing technology. An optimized exon-exon junction library approach was introduced to adapt the longer RNA-seq reads and to improve mapping efficiency.  Results: In total, 7,106 mouse genes and 2,734 rat genes were differentially expressed between cerebrum and cerebellum, while 7,125 mouse genes and 1,795 rat genes exhibited varieties on transcript variant level. Only half of the differentially expressed exon-exon junctions could be reflected at gene expression level. Functional cluster analysis showed that 32 pathways in mouse and 9 pathways in rat were significantly enriched, and 6 of them were in both. Interestingly, some differentially expressed transcript variants did not show difference on gene expression level, such as PLCβ1 and Kcnma1.  Conclusion: Our work provided a case study of a novel exon-exon junction strategy to analyze the expression of genes and isoforms, helping us understand which transcript contributes to the overall expression and further functional change.
Tipo: | Info:eu-repo/semantics/article
Idioma: | Inglês
Identificador: | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132017000100400
Editor: | Instituto de Tecnologia do Paraná - Tecpar
Relação: | 10.1590/1678-4324-2016160240
Formato: | text/html
Fonte: | Brazilian Archives of Biology and Technology  v.60 2017
Fonte: | info:eu-repo/semantics/openAccess