SKIP controls flowering time via the alternative splicing of SEF pre-mRNA in Arabidopsis

Cui, Zhibo; Tong, Aizi; Huo, Yiqiong; Yan, Zhiqiang; Yang, Weiqi; Yang, Xiaojian; Wang, Xiaoxue

doi:10.1186/s12915-017-0422-2

Cited by 48 publications

(43 citation statements)

References 72 publications

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“…The bHLH and MYB transcription factors likely mediate transmission of the jasmonate signal to the splicing-related genes through splicing factors CIR (At2g44200), LSY1 (At3g18790), and SKIP (Ag1g77180; Figure 2). SKIP is an SNW domain-containing protein, which has conserved functions as both a transcriptional co-regulator (Li et al, 2016;Lim et al, 2009) and a splicing factor (Cui et al, 2017;Feng et al, 2015;Li et al, 2016;Wang, Wu, et al, 2012). In Arabidopsis, SKIP is a key regulator of AS across a broad collection of regulated processes, such as abiotic stress response (Feng et al, 2015;Lim et al, 2009), circadian clock (Wang, Wu, et al, 2012), light signaling (Zhang et al, 2014), and flowering time (Cui et al, 2017).…”

Section: Alternative Splicing Profiles and Networkmentioning

confidence: 99%

“…SKIP is an SNW domain-containing protein, which has conserved functions as both a transcriptional co-regulator (Li et al, 2016;Lim et al, 2009) and a splicing factor (Cui et al, 2017;Feng et al, 2015;Li et al, 2016;Wang, Wu, et al, 2012). In Arabidopsis, SKIP is a key regulator of AS across a broad collection of regulated processes, such as abiotic stress response (Feng et al, 2015;Lim et al, 2009), circadian clock (Wang, Wu, et al, 2012), light signaling (Zhang et al, 2014), and flowering time (Cui et al, 2017). SKIP is a spliceosome component that physically interacts with SR family splicing factors, such as SR45 (Wang, Wu, et al, 2012), and a variety of its target pre-mRNAs (Cui et al, 2017;Feng et al, 2015;Wang, Wu, et al, 2012).…”

Section: Alternative Splicing Profiles and Networkmentioning

confidence: 99%

“…In Arabidopsis, SKIP is a key regulator of AS across a broad collection of regulated processes, such as abiotic stress response (Feng et al, 2015;Lim et al, 2009), circadian clock (Wang, Wu, et al, 2012), light signaling (Zhang et al, 2014), and flowering time (Cui et al, 2017). SKIP is a spliceosome component that physically interacts with SR family splicing factors, such as SR45 (Wang, Wu, et al, 2012), and a variety of its target pre-mRNAs (Cui et al, 2017;Feng et al, 2015;Wang, Wu, et al, 2012). SKIP regulates AS by controlling recognition and cleavage of the 3' and 5' splicing sites (Feng et al, 2015) and the skip-1 mutant in Arabidopsis causes genome-wide splicing defects (Wang, Wu, et al, 2012).…”

Section: Alternative Splicing Profiles and Networkmentioning

confidence: 99%

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Jasmonate induced alternative splicing responses in Arabidopsis

et al. 2020

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Jasmonate is an essential phytohormone regulating plant growth, development, and defense. Alternative splicing (AS) in jasmonate ZIM‐domain (JAZ) repressors is well‐characterized and plays an important role in jasmonate signaling regulation. However, it is unknown whether other genes in the jasmonate signaling pathway are regulated by AS. We explore the potential for AS regulation in three Arabidopsis genotypes (WT, jaz2, jaz7) in response to methyl jasmonate (MeJA) treatment with respect to: (a) differential AS, (b) differential miRNA targeted AS, and (c) AS isoforms with novel functions. AS events identified from transcriptomic data were validated with proteomic data. Protein interaction networks identified two genes, SKIP and ALY4 whose products have both DNA‐ and RNA‐binding affinities, as potential key regulators mediating jasmonate signaling and AS regulation. We observed cases where AS alone, or AS and transcriptional regulation together, can influence gene expression in response to MeJA. Twenty‐one genes contain predicted miRNA target sites subjected to AS, which implies that AS is coupled to miRNA regulation. We identified 30 cases where alternatively spliced isoforms may have novel functions. For example, AS of bHLH160 generates an isoform without a basic domain, which may convert it from an activator to a repressor. Our study identified potential key regulators in AS regulation of jasmonate signaling pathway. These findings highlight the importance of AS regulation in the jasmonate signaling pathway, both alone and in collaboration with other regulators. Significance statement By exploring alternative splicing, we demonstrate its regulation in the jasmonate signaling pathway alone or in collaboration with other posttranscriptional regulations such as nonsense and microRNA‐mediated decay. A signal transduction network model for alternative splicing in jasmonate signaling pathway was generated, contributing to our understanding for this important, prevalent, but relatively unexplored regulatory mechanism in plants.

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Section: Alternative Splicing Profiles and Networkmentioning

confidence: 99%

Section: Alternative Splicing Profiles and Networkmentioning

confidence: 99%

Section: Alternative Splicing Profiles and Networkmentioning

confidence: 99%

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Jasmonate induced alternative splicing responses in Arabidopsis

et al. 2020

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“…Recently, SKIP protein in Arabidopsis was also shown to regulate the flowering time by directly binding to SWC6 pre-mRNA and splicing it. However, in skp-1 mutants, the unregulated splicing of SWC6 leads to a decrease in H2A.Z enrichment at FLC chromatin, in turn activating the flowering [39]. Moreover, the interaction of Arabidopsis SWC4 and SWC6 govern the deposition of H2A.Z that ultimately brings the changes in growth and developmental processes.…”

Section: Swr1-c and Flowering Time Regulationmentioning

confidence: 99%

SWR1 Chromatin Remodeling Complex: A Key Transcriptional Regulator in Plants

Aslam

Fakher

Jakada

et al. 2019

Cells

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The nucleosome is the structural and fundamental unit of eukaryotic chromatin. The chromatin remodeling complexes change nucleosome composition, packaging and positioning to regulate DNA accessibility for cellular machinery. SWI2/SNF2-Related 1 Chromatin Remodeling Complex (SWR1-C) belongs to the INO80 chromatin remodeling family and mainly catalyzes the exchange of H2A-H2B with the H2A.Z-H2B dimer. The replacement of H2A.Z into nucleosomes affects nucleosome stability and chromatin structure. Incorporation of H2A.Z into the chromatin and its physiochemical properties play a key role in transcriptional regulation during developmental and environmental responses. In Arabidopsis, various studies have uncovered several pivotal roles of SWR1-C. Recently, notable progress has been achieved in understanding the role of SWR1-C in plant developmental and physiological processes such as DNA damage repair, stress tolerance, and flowering time. The present article introduces the SWR1-C and comprehensively reviews recent discoveries made in understanding the function of the SWR1 complex in plants.

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“…Interestingly, the alternative splicing of genes was not consistent, but its occurrence and the expression pattern of alternatively spliced variants were reported to be regulated by various abiotic stresses 11–15 , at developmental stages 16 , or in different organs 17 . Although its exact mechanism hasn’t been well revealed yet 18 , a few reports indicated its importance during development, such as, the different alternative splicing variants of HAB1 play opposite roles during ABA signaling in Arabidopsis 19 .…”

Section: Introductionmentioning

confidence: 99%

An unexpected alternative splicing of SKU5-Similar3 in Arabidopsis

Zhou

2019

Preprint

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6Alternative splicing largely enhanced the diversity of transcriptome and proteome in eukaryas. Along with 7 technical development, more and more alternatively splicing was demonstrated. Here, we report an 8 unexpected alternative splicing of SKU5-Similar 3 (SKS3) within a special splicing site in Arabidopsis. 9Based on bioinformatics database, SKS3 was predicted to be alternatively transcribed into two variants, 10 SKS3.1 and SKS3.2, which encoded a GPI-anchored protein and a soluble secretory protein respectively. 11But, instead of SKS3.2, a novel variant, SKS3.3, which encoded a protein with transmembrane region at its 12 C-terminus, was demonstrated based on our experimental data. Interestingly, it exhibited a different organ-13 specific expression pattern from SKS3.1, and its intron splicing site did not follow 'GT-AG' rule or any 14 reported rules. 107Generally, due to the recognition and splicing from spliceosomes, the vast majority of intron splicing in 108 Arabidopsis followed the "GT-AG" rule, which means the spliced introns mostly start from "GT" and end 109 at "AG" 4,8-10 , with a few exceptions, such as "GC-AG" rule 5 . Interestingly, an unusual intron border was 110 identified in SKS3.3 which has not been reported. But due to the presence of the repeated "ATCCATC" 111 close to the splicing site of the unexpected intron, the exact splicing site of SKS3.3 could not be recognized, 112 but could only be limited within the short repeat "ATCCATC''. It would be not surprisingly if we found the 113 involvement of lncRNA in its alternative splicing through forming double strand RNA with 3'-terminus of 114 SKS3 pre-mRNA. 115 116 Acknowledgments 117 Ke ZHOU designed and performed the experiments, wrote and revised the manuscript.

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SKIP controls flowering time via the alternative splicing of SEF pre-mRNA in Arabidopsis

Cited by 48 publications

References 72 publications

Jasmonate induced alternative splicing responses in Arabidopsis

Jasmonate induced alternative splicing responses in Arabidopsis

SWR1 Chromatin Remodeling Complex: A Key Transcriptional Regulator in Plants

An unexpected alternative splicing of SKU5-Similar3 in Arabidopsis

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