Alternative splicing and translation play important roles in hypoxic germination in rice

Chen, Mo Xian; Zhu, Fu Yuan; Wang, Fengzhu; Ye, Nenghui; Gao, Bei; Chen, Xi; Zhao, Shan Shan; Fan, Tao; Cao, Yun; Liu, Tie Yuan; Su, Ze Zhuo; Xie, Li; Hu, Qi; Wu, Hui Jie; Xiao, Shi; Zhang, Jianhua; Liu, Ying Gao

doi:10.1093/jxb/ery393

Cited by 58 publications

(39 citation statements)

References 92 publications

(142 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In humans, YTHDC1 mediates pre-mRNA splicing by interacting with splicing factor [26]. Pre-mRNA splicing is involved in the regulation of plant development, sexual reproduction, and abiotic stress responses [27][28][29][30][31][32][33][34][35]. Thus, the functions of plant YTHDCs in pre-mRNA splicing merit further study.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat

et al. 2020

View full text Add to dashboard Cite

Background: N6-Methyladenosine (m6A) is the most widespread RNA modification that plays roles in the regulation of genes and genome stability. YT521-B homology (YTH) domain-containing RNA-binding proteins are important RNA binding proteins that affect the fate of m6A-containing RNA by binding m6A. Little is known about the YTH genes in common wheat (Triticum aestivum L.), one of the most important crops for humans. Results: A total of 39 TaYTH genes were identified in common wheat, which are comprised of 13 homologous triads, and could be mapped in 18 out of the 21 chromosomes. A phylogenetic analysis revealed that the TaYTHs could be divided into two groups: YTHDF (TaDF) and YTHDC (TaDC). The TaYTHs in the same group share similar motif distributions and domain organizations, which indicates functional similarity between the closely related TaYTHs. The TaDF proteins share only one domain, which is the YTH domain. In contrast, the TaDCs possess three C3H1-type zinc finger repeats at their N-termini in addition to their central YTH domain. In TaDFs, the predicated aromatic cage pocket that binds the methylysine residue of m6A is composed of tryptophan, tryptophan, and tryptophan (WWW). In contrast, the aromatic cage pocket in the TaDCs is composed of tryptophan, tryptophan, and tyrosine (WWY). In addition to the general aspartic acid or asparagine residue used to form a hydrogen bond with N 1 of m6A, histidine might be utilized in some TaDFb proteins. An analysis of the expression using both online RNA-Seq data and quantitative real-time PCR verification revealed that the TaDFa and TaDFb genes are highly expressed in various tissues/organs compared with that of TaDFcs and TaDCs. In addition, the expression of the TaYTH genes is changed in response to various abiotic stresses. Conclusions: In this study, we identified 39 TaYTH genes from common wheat. The phylogenetic structure, chromosome distribution, and patterns of expression of these genes and their protein structures were analyzed. Our results provide a foundation for the functional analysis of TaYTHs in the future.

show abstract

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat

et al. 2020

View full text Add to dashboard Cite

show abstract

“…In human, nearly all annotated protein-coding genes undergo alternative splicing [ 56 , 75 ]. In plants, over 80% of intron-containing genes exhibit splicing isoforms [ 11 , 82 ]. Furthermore, the process of splicing is tightly regulated by initial recognition of the splice site during early spliceosome assembly.…”

Section: Discussionmentioning

confidence: 99%

Systematic characterization of the branch point binding protein, splicing factor 1, gene family in plant development and stress responses

et al. 2020

Self Cite

View full text Add to dashboard Cite

Background: Among eukaryotic organisms, alternative splicing is an important process that can generate multiple transcripts from one same precursor messenger RNA, which greatly increase transcriptome and proteome diversity. This process is carried out by a super-protein complex defined as the spliceosome. Specifically, splicing factor 1/ branchpoint binding protein (SF1/BBP) is a single protein that can bind to the intronic branchpoint sequence (BPS), connecting the 5′ and 3′ splice site binding complexes during early spliceosome assembly. The molecular function of this protein has been extensively investigated in yeast, metazoa and mammals. However, its counterpart in plants has been seldomly reported. Results: To this end, we conducted a systematic characterization of the SF1 gene family across plant lineages. In this work, a total of 92 sequences from 59 plant species were identified. Phylogenetic relationships of these sequences were constructed, and subsequent bioinformatic analysis suggested that this family likely originated from an ancient gene transposition duplication event. Most plant species were shown to maintain a single copy of this gene. Furthermore, an additional RNA binding motif (RRM) existed in most members of this gene family in comparison to their animal and yeast counterparts, indicating that their potential role was preserved in the plant lineage. Conclusion: Our analysis presents general features of the gene and protein structure of this splicing factor family and will provide fundamental information for further functional studies in plants.

show abstract

“…In human, nearly all the annotated protein-coding genes undergo alternative splicing (Qun et al, 2008;Wang et al, 2008). And in plants, over 80% of intron-containing genes exhibit splicing isoforms (Zhu et al, 2017;Chen et al, 2019). Furthermore, the process of splicing is tightly regulated by initial recognition of splice site during early spliceosome assembly.…”

Section: Discussionmentioning

confidence: 99%

Systematic characterization of branch point binding protein, splicing factor 1, gene family in plant development and stress responses

Zhang

Feng

Yang

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

Among eukaryotic organisms, the splicing of nuclear precursor messenger RNA (pre-mRNA) is a process of introns excision and sequentially joining of exons, leading multi-exonic genes to generate multiple splicing isoforms at transcription level. This process is carried out by a super-protein complex defined as spliceosome. Specifically, splicing factor 1/branchpoint binding protein (SF1/BBP) is a single protein that can bind to the intronic branchpoint sequence (BPS), connecting 5’ and 3’ splice site binding complexes during early spliceosome assembly. The molecular function of this protein has been extensively investigated in yeast, metazoan and mammals. However, their counterparts in plants are seldomly reported. To this end, we conducted a systematic characterization of SF1 gene family across plant lineage. In this work, a total of 92 sequences from 59 plant species were identified. Phylogenetic relationships of these sequences were constructed and subsequent bioinformatic analysis suggested that this family is likely originated from an ancient gene transposition duplication event. Most plant species were shown to maintain a single copy of this gene. Furthermore, an additional RNA binding motif (RRM) existed in most members of this gene family in comparison to their animal and yeast counterparts, indicating their potential role conserved in plant lineage. Our analysis presents general feature of gene and protein structure of this splicing factor family and will provide fundamental information for further functional studies in plants.

show abstract

Alternative splicing and translation play important roles in hypoxic germination in rice

Abstract: Using RNA sequencing and qualitative and quantitative proteomics, we unravel alternative spliced isoforms and new ‘frame’ proteins during hypoxic germination in rice.

Cited by 58 publications

References 92 publications

Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat

Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat

Systematic characterization of the branch point binding protein, splicing factor 1, gene family in plant development and stress responses

Systematic characterization of branch point binding protein, splicing factor 1, gene family in plant development and stress responses

Contact Info

Product

Resources

About