Genome-wide identification and functional analysis of the splicing component SYF2/NTC31/p29 across different plant species

Tian, Yuan; Chen, Mo Xian; Yang, Jing; Achala, H. H.K.; Gao, Bei; Yang, Guang; Dian, Zhi Yong; Hu, Qi; Zhang, Di; Zhang, Jianhua; Liu, Ying Gao

doi:10.1007/s00425-018-3026-3

Cited by 8 publications

(2 citation statements)

References 59 publications

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“…There are several RNase H proteins with unknown function in plants, but with pivotal roles in mammalian cell physiology and health, related to genome stability and cell viability [48,49]. Other upregulated genes were a RNA-binding protein encoding for a chloroplast enzyme involved in rRNA maturation and intron recycling (At3g13740, [50]), a gene involved in splicing (At2g16860, [51]) and several rRNA intron-encoded homing endonucleases (Table 1, Fig. 5, Table S2).…”

Section: Discussionmentioning

confidence: 99%

Silencing of StRIK in potato suggests a role in periderm related to RNA processing and stress

et al. 2021

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Background The periderm is a protective barrier crucial for land plant survival, but little is known about genetic factors involved in its development and regulation. Using a transcriptomic approach in the cork oak (Q. suber) periderm, we previously identified an RS2-INTERACTING KH PROTEIN (RIK) homologue of unknown function containing a K homology (KH)-domain RNA-binding protein, as a regulatory candidate gene in the periderm. Results To gain insight into the function of RIK in the periderm, potato (S. tuberosum) tuber periderm was used as a model: the full-length coding sequence of RIK, hereafter referred to as StRIK, was isolated, the transcript profile analyzed and gene silencing in potato performed to analyze the silencing effects on periderm anatomy and transcriptome. The StRIK transcript accumulated in all vegetative tissues studied, including periderm and other suberized tissues such as root and also in wounded tissues. Downregulation of StRIK in potato by RNA interference (StRIK-RNAi) did not show any obvious effects on tuber periderm anatomy but, unlike Wild type, transgenic plants flowered. Global transcript profiling of the StRIK-RNAi periderm did show altered expression of genes associated with RNA metabolism, stress and signaling, mirroring the biological processes found enriched within the in silico co-expression network of the Arabidopsis orthologue. Conclusions The ubiquitous expression of StRIK transcript, the flower associated phenotype and the differential expression of StRIK-RNAi periderm point out to a general regulatory role of StRIK in diverse plant developmental processes. The transcriptome analysis suggests that StRIK might play roles in RNA maturation and stress response in the periderm.

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Section: Discussionmentioning

confidence: 99%

Silencing of StRIK in potato suggests a role in periderm related to RNA processing and stress

et al. 2021

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“…The U1-70K protein sequence (ENSP00000472998.1) of Homo sapiens was used as a query to carry out BLASTp search with e -value cutoff = 1 e −10 against all available animal genome sequences from Ensembl database http://asia.ensembl.org/index.html ) as described previously 27 , 28 . The obtained sequences consisting of both PF00076.22 (RNA recognition motif, RRM_1) and PF12220.8 (U1 small nuclear ribonucleoprotein of 70 kDa MW N terminal, U1snRNP70_N) protein domains were further screened by HMMER ( https://www.ebi.ac.uk/Tools/hmmer/search/phmmer ).…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic comparison and splice site conservation of eukaryotic U1 snRNP-specific U1-70K gene family

Fan

Zhao

Yang

et al. 2021

Sci Rep

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Eukaryotic cells can expand their coding ability by using their splicing machinery, spliceosome, to process precursor mRNA (pre-mRNA) into mature messenger RNA. The mega-macromolecular spliceosome contains multiple subcomplexes, referred to as small nuclear ribonucleoproteins (snRNPs). Among these, U1 snRNP and its central component, U1-70K, are crucial for splice site recognition during early spliceosome assembly. The human U1-70K has been linked to several types of human autoimmune and neurodegenerative diseases. However, its phylogenetic relationship has been seldom reported. To this end, we carried out a systemic analysis of 95 animal U1-70K genes and compare these proteins to their yeast and plant counterparts. Analysis of their gene and protein structures, expression patterns and splicing conservation suggest that animal U1-70Ks are conserved in their molecular function, and may play essential role in cancers and juvenile development. In particular, animal U1-70Ks display unique characteristics of single copy number and a splicing isoform with truncated C-terminal, suggesting the specific role of these U1-70Ks in animal kingdom. In summary, our results provide phylogenetic overview of U1-70K gene family in vertebrates. In silico analyses conducted in this work will act as a reference for future functional studies of this crucial U1 splicing factor in animal kingdom.

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

Du,

Cao,

Wang

et al. 2024

Journal of Advanced Research

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Genome-wide identification and functional analysis of the splicing component SYF2/NTC31/p29 across different plant species

Cited by 8 publications

References 59 publications

Silencing of StRIK in potato suggests a role in periderm related to RNA processing and stress

Silencing of StRIK in potato suggests a role in periderm related to RNA processing and stress

Phylogenetic comparison and splice site conservation of eukaryotic U1 snRNP-specific U1-70K gene family

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

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