@article{10.11648/j.cbb.20231101.12,
  author = {Fangyu Zhang and Zhengfeng Zhang and Enci Wang and Chengqi Wang and Benze Xiao},
  title = {The Importance of Stiff Change of U(T) Content Around Splicing Sites in Efficient Plant Intron Splicing -- A Case Study in Rice},
  journal = {Computational Biology and Bioinformatics},
  volume = {11},
  number = {1},
  pages = {13-18},
  doi = {10.11648/j.cbb.20231101.12},
  url = {https://doi.org/10.11648/j.cbb.20231101.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.cbb.20231101.12},
  abstract = {Pre-mRNAs splicing is one of the fundamental process which generates multiple transcripts from a single gene, contributing to transcriptome and proteome diversity. AS is regulated by the cooperation of trans-factors and cis-elements. In plants, extensive alternative splicing occurs not only in tissue-specific manner but also in response to stress conditions. Intron retention is the most predominant splicing type. However, the cis-elements regulating intron retention are still ambiguous in plants, especially under environmental stresses. This study aimed to elucidate the cis-elements underlying intron retention in plants under adverse enrironments. Using RNA-seq data of rice cultivars IRAT109 and ZS97 under drought environments, we compared the sequence characteristics between constitutive and retained introns. The results show that the main AS types include intron retention (IR), alternative acceptor sites (AA), alternative donor sites (AD) and cassette exon (exon skipping, ES). Among of them, IR was the prevelent pattern with frequencies of 30.8-31.2%. Motif analysis of 5' and 3' 200bp intron sequences found rich U(T) in the motifs for both constitutive and retained introns. By further analysis of base composition of sequences flanking splice sites, we detected a notable difference in U(T) content between introns and their neighboring exons in constitutive introns, but not in retained introns. The results in this study suggested that the lack of significant changes in U(T) content between retained introns and neighboring exons might be a potential cis feature of intron retention.},
 year = {2023}
}

Copy | Download

TY  - JOUR
T1  - The Importance of Stiff Change of U(T) Content Around Splicing Sites in Efficient Plant Intron Splicing -- A Case Study in Rice
AU  - Fangyu Zhang
AU  - Zhengfeng Zhang
AU  - Enci Wang
AU  - Chengqi Wang
AU  - Benze Xiao
Y1  - 2023/06/05
PY  - 2023
N1  - https://doi.org/10.11648/j.cbb.20231101.12
DO  - 10.11648/j.cbb.20231101.12
T2  - Computational Biology and Bioinformatics
JF  - Computational Biology and Bioinformatics
JO  - Computational Biology and Bioinformatics
SP  - 13
EP  - 18
PB  - Science Publishing Group
SN  - 2330-8281
UR  - https://doi.org/10.11648/j.cbb.20231101.12
AB  - Pre-mRNAs splicing is one of the fundamental process which generates multiple transcripts from a single gene, contributing to transcriptome and proteome diversity. AS is regulated by the cooperation of trans-factors and cis-elements. In plants, extensive alternative splicing occurs not only in tissue-specific manner but also in response to stress conditions. Intron retention is the most predominant splicing type. However, the cis-elements regulating intron retention are still ambiguous in plants, especially under environmental stresses. This study aimed to elucidate the cis-elements underlying intron retention in plants under adverse enrironments. Using RNA-seq data of rice cultivars IRAT109 and ZS97 under drought environments, we compared the sequence characteristics between constitutive and retained introns. The results show that the main AS types include intron retention (IR), alternative acceptor sites (AA), alternative donor sites (AD) and cassette exon (exon skipping, ES). Among of them, IR was the prevelent pattern with frequencies of 30.8-31.2%. Motif analysis of 5' and 3' 200bp intron sequences found rich U(T) in the motifs for both constitutive and retained introns. By further analysis of base composition of sequences flanking splice sites, we detected a notable difference in U(T) content between introns and their neighboring exons in constitutive introns, but not in retained introns. The results in this study suggested that the lack of significant changes in U(T) content between retained introns and neighboring exons might be a potential cis feature of intron retention.
VL  - 11
IS  - 1
ER  - 

Copy | Download