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Distribution of alternative splicing events with significant changes in alternative splicing profiles in the cbp mutants.
Source publication
The nuclear cap-binding protein complex (CBC) participates in 5′ splice site selection of introns that are proximal to the
mRNA cap. However, it is not known whether CBC has a role in alternative splicing. Using an RT–PCR alternative splicing panel,
we analysed 435 alternative splicing events in Arabidopsis thaliana genes, encoding mainly transcrip...
Contexts in source publication
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... the 252 remaining different AS events 101 showed significant (P 0.10) changes in the ratio of alternatively spliced isoforms of over 3% between wild type plants and the cbp20, cbp80(abh1) or cbp20/80 mutants. Of these events, 41 were common to all three mutants, nine were found in both the cbp80(abh1) and cbp20/80 mutants, four were common to cbp20 and cbp20/80, five were common to cbp20 and cbp80(abh1), 15 were found only in the double mutant, and 6 and 21 only in the single cbp20 and cbp80(abh1) mutants, respectively ( Figure 1). Different types of alternative splicing events were affected in the cbp mutants ( Table 1). ...
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... standard errors derived from two or three repeat experiments are given with the ratios. Significant changes between the wild type and mutants is measured at P 0. 10 changes in either two out of three mutants or only in one of them (Figure 1), only six events involved the cbp20 mutant while 21 and 15 events involved either the cbp80(abh1) or the cbp20/80 mutants, respectively (Figure 1). In addition, nine events with significant changes in alternative splicing were common to the cbp80 and cbp20/80 mutants such that the majority of events affected in the cbp mutants were found in the cbp80 and cbp20/80 double mutants. ...
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... standard errors derived from two or three repeat experiments are given with the ratios. Significant changes between the wild type and mutants is measured at P 0. 10 changes in either two out of three mutants or only in one of them (Figure 1), only six events involved the cbp20 mutant while 21 and 15 events involved either the cbp80(abh1) or the cbp20/80 mutants, respectively (Figure 1). In addition, nine events with significant changes in alternative splicing were common to the cbp80 and cbp20/80 mutants such that the majority of events affected in the cbp mutants were found in the cbp80 and cbp20/80 double mutants. ...
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... CBC in animal and yeast systems promotes an effi- cient interaction between U1snRNP and the first intron, and enhances production of spliced mRNAs (29,30). To examine whether Arabidopsis nuclear cap-binding proteins also affected the first intron of transcripts, we compared the position of the introns affected by alternative splicing in the total number of events (252), the events which showed a significant change at least one of the mutants (101) (Figure 1) and those events which showed a signif- icant change in alternative splicing in all three mutants (41). Among the 252 events showing alternative splicing on the RT-PCR panel, 107 events (42%) involved the first intron in the gene transcript, 102 (40%) involved an internal intron and 43 (17%) involved the last intron in the transcript (Figure 3). ...
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Citations
... Alternative splicing events, including alternative 5' and 3' splice site selection, exon skipping, and intron retention [21], are widespread mechanisms in eukaryotes [22]. In alternative splicing, a single gene produces different protein variants through different splice site combinations [23][24][25]. ...
The Asteraceae are widely distributed throughout the world, with diverse functions and large genomes. Many of these genes remain undiscovered and unstudied. In this study, we discovered a new gene ClNUM1 in Chrysanthemum lavandulifolium and studied its function. In this study, bioinformatics, RT-qPCR, paraffin sectioning, and tobacco transgenics were utilized to bioinformatically analyze and functionally study the three variable splice variants of the unknown gene ClNUM1 cloned from C. lavandulifolium. The results showed that ClNUM1.1 and ClNUM1.2 had selective 3′ splicing and selective 5′ splicing, and ClNUM1.3 had selective 5′ splicing. When the corresponding transgenic tobacco plants were subjected to abiotic stress treatment, in the tobacco seedlings, the ClNUM1.1 gene and the ClNUM1.2 gene enhanced salt and low-temperature tolerance and the ClNUM1.3 gene enhanced low-temperature tolerance; in mature tobacco plants, the ClNUM1.1 gene was able to enhance salt and low-temperature tolerance, and the ClNUM1.2 and ClNUM1.3 genes were able to enhance low-temperature tolerance. In summary, there are differences in the functions of the different splice variants and the different seedling stages of transgenic tobacco, but all of them enhanced the resistance of tobacco to a certain extent. The analysis and functional characterization of the ClNUM1 gene provided new potential genes and research directions for abiotic resistance breeding in Chrysanthemum.
... Previous studies have reported many splicing regulators in plant responses to abiotic stress (Zhan et al., 2015;Zhang F. et al., 2016). The cap-binding protein CBP20 modulated salt stress response in Arabidopsis (Kong et al., 2014) and is part of a subunit of dimeric nuclear cap-binding complex (CBC) which combines with the cap structure of RNA polymerase II to influence AS of first introns (Raczynska et al., 2010). In the root tissue in the present study, we identified TSS and TTS at 6 and 24 h in the salttolerant strain for Ta.CBP20. ...
Background: Salinity stress is a major adverse environmental factor that can limit crop yield and restrict normal land use. The selection of salt-tolerant strains and elucidation of the underlying mechanisms by plant breeding scientists are urgently needed to increase agricultural production in arid and semi-arid regions.
Results: In this study, we selected the salt-tolerant wheat (Triticum aestivum) strain ST9644 as a model to study differences in expression patterns between salt-tolerant and salt-sensitive strains. High-throughput RNA sequencing resulted in more than 359.10 Gb of clean data from 54 samples, with an average of 6.65 Gb per sample. Compared to the IWGSC reference annotation, we identified 50,096 new genes, 32,923 of which have functional annotations. Comparisons of abundances between salt-tolerant and salt-sensitive strains revealed 3,755, 5,504, and 4,344 genes that were differentially expressed at 0, 6, and 24 h, respectively, in root tissue under salt stress. KEGG pathway analysis of these genes showed that they were enriched for phenylpropanoid biosynthesis (ko00940), cysteine and methionine metabolism (ko00270), and glutathione metabolism (ko00480). We also applied weighted gene co-expression network analysis (WGCNA) analysis to determine the time course of root tissue response to salt stress and found that the acute response lasts >6 h and ends before 12 h. We also identified key alternative splicing factors showing different splicing patterns in salt-sensitive and salt-tolerant strains; however, only few of them were differentially expressed in the two groups.
Conclusion: Our results offer a better understanding of wheat salt tolerance and improve wheat breeding.
... The CAP-BINDING PROTEIN 20 (CBP20) and CAP-BINDING PRO-TEIN 80/ABSCISIC ACID HYPERSENSITIVE1 (CBP80/ABH1) genes were found to affect plant sensitivity to ABA and the ABA signaling pathway (Hugouvieux et al., 2001(Hugouvieux et al., , 2002Pieczynski et al., 2013). CBP20 and CBP80 form a nuclear cap-binding complex that binds to the cap structure and affects pre-mRNA splicing, mRNA stability, and micro-RNA biogenesis (Flaherty et al., 1997;Izaurralde et al., 1994;Kmieciak & Jarmolowski, 2002;Lewis et al., 1996;Pieczynski et al., 2013;Raczynska et al., 2010;Szarzynska et al., 2009). Arabidopsis cbp20 and cbp80/abh1 mutants were found to be hypersensitive to ABA during germination (Hugouvieux et al., 2001;Reyes & Chua, 2007), moreover, adult cbp20 and cbp80/abh1 mutants exhibit drought tolerance (Pieczynski et al., 2013). ...
Drought is one of the main climate threats limiting crop production. Potato is one of the four most important food crop species worldwide and is sensitive to water shortage. The CBP80 gene was shown to affect Arabidopsis and potato responses to drought by regulating the level of microRNA159 and, consequently, the levels of the MYB33 and MYB101 transcription factors. Here, we show that three MYB transcription factors, MYB33, MYB65, and MYB101, are involved in plant responses to water shortage. Their downregulation in Arabidopsis causes stomatal hyposensitivity to ABA, leading to reduced tolerance to drought. Transgenic Arabidopsis and potato plants overexpressing these genes, with a mutated recognition site in miR159, show hypersensitivity to ABA and relatively high tolerance to drought conditions. Thus, the MYB33, MYB65, and MYB101 genes may be potential targets for innovative breeding to obtain crops with relatively high tolerance to drought. This article is protected by copyright. All rights reserved.
... Although CBC has been considered to control these processes by functioning in pre-mRNA splicing and microRNA biogenesis (F. Zhang et al., 2016;Kim et al., 2008;Kong et al., 2014;Laubinger et al., 2008;Raczynska et al., 2010;Y. Li et al., 2021), it has also been found to directly interact with chromatin modifiers and impact on chromatin modifications (Z. ...
... CBC regulates pre-mRNA processing, particularly intron splicing (Laubinger et al., 2008;Raczynska et al., 2010Raczynska et al., , 2014, and it has also been reported to regulate intron splicing in plant salt stress response Y. Li et al., 2021). To investigate whether ELF7 coregulates intron splicing with CBP20, we analysed the RNA-seq data to screen for IR changes in cbp20 and elf7-3 compared with WT (Supporting Information: Data set 2). Salt treatment induced a strong change in intron splicing in WT, with 2389 introns exhibiting significant IR changes (Supporting Information: Figure 7A). ...
Adaptive response to stress involves an extensive reprogramming of gene expression. Under stressful conditions, the induction of efficient changes in mRNA production is crucial for maximized plant survival. Transcription and pre‐mRNA processing are two closely related steps in mRNA biogenesis, yet how they are controlled in plant stress response remains elusive. Here, we show that the Arabidopsis nuclear cap‐binding complex (CBC) component CBP20 directly interacts with ELF7, a subunit of the transcription elongation factor RNA Pol II‐associated factor 1 complex (PAF1c) to promote RNA Pol II transcription in plant response to salt stress. CBP20 and ELF7 co‐regulate the expression of a large number of genes including those crucial for salt tolerance. Both CBP20 and ELF7 are required for enhanced RNA Pol II elongation at salt‐activated genes. Though CBP20 also regulates intron splicing, this function is largely independent of ELF7. Our study reveals the function of an RNA processing regulator CBC in assisting efficient RNA Pol II transcription and pinpoints the complex roles of CBC on mRNA production in plant salt stress resistance. This article is protected by copyright. All rights reserved.
... The CBC can bind to the cap structure of transcripts produced by RNA polymerase II. In Arabidopsis (Arabidopsis thaliana), the CBC participates in the biogenesis of microRNAs (miRNAs) and splicing of cap-proximal introns in pre-mRNAs (Kim et al., 2008;Laubinger et al., 2008;Raczynska et al., 2009). The CBC coordinates its various roles with the C 2 H 2 zinc-finger protein SERRATE (SE; Grigg et al., 2005;Laubinger et al., 2008;Raczynska et al., 2014). ...
... The first and last introns appeared to be more sensitive to loss of Du13 activity than internal introns (Figure 6b). In addition, alternative 5 0 and 3 0 splice site selection by du13 greatly increased within the first intron (Figure 6c, d), suggesting that Du13 might affect splice site choice mostly within the first intron, similar to SE and Arabidopsis CBPs (Raczynska et al., 2009(Raczynska et al., , 2014. Isshiki et al. (2000) proposed that Du1 (OsCBP20) and Du2 may be essential for recognizing the two weak splice sites activated in Wx b exon 1 and stabilizing the spliceosomes assembled at both sites. ...
Amylose content is a crucial physicochemical property responsible for the eating and cooking quality of rice (Oryza sativa L.) grain and is mainly controlled by the Waxy (Wx) gene. Previous studies have identified several Dull genes that modulate the expression of the Wxb allele in japonica rice by affecting the splicing efficiency of the Wxb pre‐mRNA. Here, we uncover dual roles for a novel Dull gene in pre‐mRNA splicing and microRNA processing. We isolated the dull mutant, du13, with a dull endosperm and low amylose content. Map‐based cloning showed that Du13 encodes a C2H2 zinc‐finger protein. Du13 coordinates with the nuclear cap‐binding complex to regulate the splicing of Wxb transcripts in rice endosperm. Moreover, Du13 also regulates alternative splicing of other protein‐coding transcripts and affects the biogenesis of a subset of microRNAs. Our results reveal an evolutionarily conserved link between pre‐mRNA splicing and microRNA biogenesis in rice endosperm. Our findings also provide new insights into the functions of Dull genes in rice and expand our knowledge of microRNA biogenesis in monocots.
... However, our results are opposite to the effect of drought stress and overexpression of 35S:HIN1 on the location of IR in the intron-containing genes . Whether SKIP and SDG725 are related with the 5 ′ cap-binding complex to affect splicing at first introns is unclear (Raczynska et al. 2010). The asterisks indicate a significant difference from the control by using two-tailed unpaired t test with Welch's correction (*P < 0.05; **P < 0.01). ...
Abscisic acid (ABA) plays key roles in plant development and responses to abiotic stresses. A wide number of transcriptional and post-translational regulatory mechanisms on ABA signaling are known; however, less to know about the regulatory roles of alternative splicing. In this work, we found that SKIP, a splicing factor, positively regulates ABA signaling. SKIP binds to the pre-mRNA of ABA signaling related genes, such as PYL7, PYL8, ABI1, HAB1, and ABI5, to regulate their splicing. The precursor mRNA alternative splicing of several PYL receptors, PP2C phosphatases, and ABF transcriptional factors is disrupted by skip-1 mutation. The abnormal alternative splicing in skip-1 represses the expression of ABA positive regulators, including PYLs and ABFs, and activates the expression of ABA negative regulators, such as PP2Cs, which confers ABA hyposensitive phenotype of skip-1. We also found that ABA-mediated genome-wide alternative splicing and differential gene expression are changed by skip-1 mutation. The number of the differential splicing events is increased by skip-1; however, the number of differential expressed genes in response to ABA is reduced by skip-1. Our results reveal a principle on how a splicing factor regulates ABA signaling and ABA-mediated genome-wide alternative splicing.
... The CAP-BINDING PROTEIN 20 (CBP20) and CAP-BINDING PROTEIN 80/ABSCISIC ACID HYPERSENSITIVE1 (CBP80/ABH1) genes were found to affect plant sensitivity to ABA and the ABA signaling pathway (Hugouvieux et al. 2001;Hugouvieux et al. 2002;Pieczynski et al. 2013). CBP20 and CBP80 form a nuclear cap-binding complex (CBC) that binds to the cap structure and affects pre-mRNA splicing, mRNA stability and microRNA biogenesis (Flaherty et al. 1997;Izaurralde et al. 1994;Kmieciak and Jarmolowski 2002;Lewis et al. 1996;Pieczynski et al. 2013;Raczynska et al. 2010;Szarzynska et al. 2009). Arabidopsis cbp20 and cbp80/abh1 mutants were found to be hypersensitive to ABA during germination (Hugouvieux et al. 2001;Reyes and Chua 2007). ...
Aims
Drought is a climate threat limiting crop production. Potato is one of the four most important food crops worldwide and is sensitive to water shortage. The CBP80 gene was shown to affect plant response to drought by regulating the level of microRNA159, and, consequently, the levels of the MYB33 and MYB101 transcription factors. (TF) Our studies aimed to show whether indeed the level of MYB33, MYB65, and MYB101 TFs affects plant response to water shortage.
Methods
Arabidopsis transgenic plants exhibiting downregulation and Arabidopsis and potato transgenic plants exhibiting overexpression of selected MYB TFs were obtained. Plants response to drought was mainly measured using relative water content (RWC) and stomata closure upon exogenous ABA.
Results
Three MYB TFs studied are involved in plant response to drought. When downregulated in Arabidopsis, the MYB33, MYB65 and MYB101 genes cause stomatal hyposensitivity to ABA, leading to reduced tolerance to drought. Transgenic Arabidopsis and potato plants overexpressing a mutated version of these genes with changed miR159 recognition site, show hypersensitivity to ABA and relatively high tolerance to drought conditions.
Conclusions
The MYB33, MYB65, and MYB101 genes are good be potential targets for innovative breeding to obtain crops with relatively high tolerance to drought.
... For example, in turn the ratio of IDD14a and IDD14b are affected to mediate the downstream targets (QQS, etc.). could regulate the spliceosome formation efficiency, splicing precision and pre-mRNA efficiency (Raczynska et al., 2010). It was previously shown that the cbp20 mutant and cbp20 9 cbp80 double mutant are hypersensitive to salt stress, and many salt-related genes are also affected in these mutants (Kong et al., 2014). ...
Alternative splicing (AS) is emerging as a critical co‐transcriptional regulation for plants in response to environmental stresses. Although multiple splicing factors have been linked to the salt‐sensitive signaling network, the molecular mechanism remains unclear.
We discovered that a conserved serine/arginine‐rich (SR)‐like protein, SR45a, as a component of the spliceosome, was involved in post‐transcriptional regulation of salinity tolerance in Arabidopsis thaliana. Furthermore, SR45a was required for the AS and messenger RNA (mRNA) maturation of several salt‐tolerance genes. Two alternatively spliced variants of SR45a were induced by salt stress, full‐length SR45a‐1a and the truncated isoform SR45a‐1b, respectively. Lines with overexpression of SR45a‐1a and SR45a‐1b exhibited hypersensitive to salt stress.
Our data indicated that SR45a directly interacted with the cap‐binding complex (CBC) subunit cap‐binding protein 20 (CBP20) which mediated salt‐stress responses. Instead of binding to other spliceosome components, SR45a‐1b promoted the association of SR45a‐1a with CBP20, therefore mediating salt‐stress signal transduction pathways. Additionally, the mutations in SR45a and CBP20 led to different salt‐stress phenotypes.
Together, these results provide the evidence that SR45a‐CBP20 acts as a regulatory complex to regulate the plant response to salt stress, through a regulatory mechanism to fine‐tune the splicing factors, especially in stressful conditions.
... Zhan et al., 2015). The two mRNA cap-binding proteins CBP20 and CBP80 function as negative regulators of ABA responses by influencing alternative splicing of the first intron in most genes, particularly at the 5' SS in Arabidopsis (Hugouvieux et al., 2001;Papp et al., 2004;Raczynska et al., 2010). Additionally, two ABA-responsive genes, ABI5 and CIPK3, also undergo alternative pre-RNA splicing by which these two genes function to affect ABA signaling (Zou et al., 2007;Sanyal et al., 2017a;Xiong et al., 2019). ...
Signaling by the phytohormone abscisic acid (ABA) involves pre-mRNA splicing, a key process of post-transcriptional regulation of gene expression. However, the regulatory mechanism of alternative pre-mRNA splicing in ABA signaling remains largely unknown. We previously identified a pentatricopeptide repeat protein SOAR1 (suppressor of the ABAR-overexpressor 1) as a crucial player downstream of ABAR (putative ABA receptor) in ABA signaling. In this study, we identified a SOAR1 interaction partner USB1, which is an exoribonuclease catalyzing U6 production for spliceosome assembly. We reveal that together USB1 and SOAR1 negatively regulate ABA signaling in early seedling development. USB1 and SOAR1 are both required for the splicing of transcripts of numerous genes, including those involved in ABA signaling pathways, suggesting that USB1 and SOAR1 collaborate to regulate ABA signaling by affecting spliceosome assembly. These findings provide important new insights into the mechanistic control of alternative pre-mRNA splicing in the regulation of ABA-mediated plant responses to environmental cues.
... In addition to facilitating constitutive splicing of first introns, the CBC regulates hundreds of alternative splicing events in human cells (Lenasi et al. 2011) and plants (Raczynska et al. 2010(Raczynska et al. , 2014Kanno et al. 2020). In humans, one proposed mechanism involves CBC-dependent recruitment of P-TEFb, phosphorylation of RNAPII S2, followed by the recruitment of the SR splicing factor 2/alternative splicing factor (SF2/ASF, now renamed SRSF1) on a splicing enhancer so as to promote exon inclusion (Lenasi et al. 2011). ...
... The possible involvement of sequence-specific RNA-binding proteins such as SRSF1 (Anczuków et al. 2015) or structure-specific RNA-binding protein such as hnRNPF suggests that RNA features influence the CBC-dependent control of alternative pre-mRNA splicing. RNA-seq analyses of 5-wk-old A. thaliana leaves knocked out for CBP80 or CBP20 (Raczynska et al. 2010) or expressing SE harboring a point mutation (Raczynska et al. 2014) indicate that the three proteins cooperate to regulate an overlapping set of alternative splicing events, primarily selecting alternative 5 ′ splice sites of first introns. In contrast, 2-wk-old A. thaliana seedlings expressing a CBP80 harboring a point mutation predominantly manifest intron retention (Kanno et al. 2020). ...
The largely nuclear cap-binding complex (CBC) binds to the 5' caps of RNA polymerase II (RNAPII)-synthesized transcripts and serves as a dynamic interaction platform for a myriad of RNA processing factors that regulate gene expression. While influence of the CBC can extend into the cytoplasm, here we review the roles of the CBC in the nucleus, with a focus on protein-coding genes. We discuss differences between CBC function in yeast and mammals, covering the steps of transcription initiation, release of RNAPII from pausing, transcription elongation, cotranscriptional pre-mRNA splicing, transcription termination, and consequences of spurious transcription. We describe parameters known to control the binding of generic or gene-specific cofactors that regulate CBC activities depending on the process(es) targeted, illustrating how the CBC is an ever-changing choreographer of gene expression.
