Wide‐ranging transcriptome remodelling mediated by alternative polyadenylation in response to abiotic stresses in <i>Sorghum</i>

Chakrabarti, Manohar; Lorenzo, Laura de; Abdel‐Ghany, Salah E.; Reddy, Anireddy S. N.; Hunt, Arthur G.

doi:10.1111/tpj.14671

Cited by 30 publications

(32 citation statements)

References 91 publications

(117 reference statements)

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“…First, our interest was to investigate rapid changes in gene expression in response to drought stress. Second, we and others have previously shown that drought marker genes are induced within 1 to 6 h [32,37] Two biological replicates were analyzed for each condition resulting in 32 samples (4 genotypes × 2 conditions × 2 time points × 2 replicates). The correlation coefficient between biological replicates was high (R 2 = 0.87-0.99) supporting the reproducibility of the results.…”

Section: Transcriptome Analysis Of Two Drought-resistant and Two Droumentioning

confidence: 99%

Transcriptome Analysis of Drought-Resistant and Drought-Sensitive Sorghum (Sorghum bicolor) Genotypes in Response to PEG-Induced Drought Stress

Abdel‐Ghany

Ullah

Ben-Hur

et al. 2020

IJMS

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Drought is a major limiting factor of crop yields. In response to drought, plants reprogram their gene expression, which ultimately regulates a multitude of biochemical and physiological processes. The timing of this reprogramming and the nature of the drought-regulated genes in different genotypes are thought to confer differential tolerance to drought stress. Sorghum is a highly drought-tolerant crop and has been increasingly used as a model cereal to identify genes that confer tolerance. Also, there is considerable natural variation in resistance to drought in different sorghum genotypes. Here, we evaluated drought resistance in four genotypes to polyethylene glycol (PEG)-induced drought stress at the seedling stage and performed transcriptome analysis in seedlings of sorghum genotypes that are either drought-resistant or drought-sensitive to identify drought-regulated changes in gene expression that are unique to drought-resistant genotypes of sorghum. Our analysis revealed that about 180 genes are differentially regulated in response to drought stress only in drought-resistant genotypes and most of these (over 70%) are up-regulated in response to drought. Among these, about 70 genes are novel with no known function and the remaining are transcription factors, signaling and stress-related proteins implicated in drought tolerance in other crops. This study revealed a set of drought-regulated genes, including many genes encoding uncharacterized proteins that are associated with drought tolerance at the seedling stage.

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Section: Transcriptome Analysis Of Two Drought-resistant and Two Droumentioning

confidence: 99%

Transcriptome Analysis of Drought-Resistant and Drought-Sensitive Sorghum (Sorghum bicolor) Genotypes in Response to PEG-Induced Drought Stress

Abdel‐Ghany

Ullah

Ben-Hur

et al. 2020

IJMS

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“…In Arabidopsis, the "AAAAAA" is not identified from the comparable region, and CE is usually rich in Ts [28]. Interestingly, in a recent study of sorghum, the hexamer "AAAAAA" has been revealed prominently in PACs from both 3'UTR and intron at the same region; and heat, salt and drought stresses do not affect the enrichment [17]. These results indicate that the heat stress could induce the usage of specific sequence signals to confer unique APA-mediated transcripts.…”

Section: Discussionmentioning

confidence: 97%

“…5'UTR and protein-coding) polyA sites, which suggested a negative role of gene regulation [15]. In addition, genomewide profiling of APA in sorghum has shown that some stress-induced isoforms were associated with a unique intronic polyA signal [17]. These results indicate that global shift of polyA site in response of stress is a strategy of survival which affect a wide-range of gene functions.…”

Section: Introductionmentioning

confidence: 95%

Alternative Polyadenylation in response to temperature stress contributes to gene regulation in Populus trichocarpa

et al. 2021

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Background Genome-wide change of polyadenylation (polyA) sites (also known as alternative polyadenylation, APA) is emerging as an important strategy of gene regulation in response to stress in plants. But little is known in woody perennials that are persistently dealing with multiple abiotic stresses. Results Here, we performed a genome-wide profiling of polyadenylation sites under heat and cold treatments in Populus trichocarpa. Through a comprehensive analysis of polyA tail sequences, we identified 25,919 polyA-site clusters (PACs), and revealed 3429 and 3139 genes shifted polyA sites under heat and cold stresses respectively. We found that a small proportion of genes possessed APA that affected the open reading frames; and some shifts were commonly identified. Functional analysis of genes displaying shifted polyA tails suggested that pathways related to RNA metabolism were linked to regulate the APA events under both heat and cold stresses. Interestingly, we found that the heat stress induced a significantly more antisense PACs comparing to cold and control conditions. Furthermore, we showed that a unique cis-element (AAAAAA) was predominately enriched downstream of PACs in P. trichocarpa genes; and this sequence signal was only absent in shifted PACs under the heat condition, indicating a distinct APA mechanism responsive to heat tolerance. Conclusions This work provides a comprehensive picture of global polyadenylation patterns in response to temperatures stresses in trees. We show that the frequent change of polyA tail is a potential mechanism of gene regulation responsive to stress, which are associated with distinctive sequence signatures.

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“…In Arabidopsis, the "AAAAAA" is not identi ed from the comparable region, and CE is usually rich in Ts [28]. Interestingly, in a recent study of sorghum, the hexamer "AAAAAA" has been revealed prominently in PACs from both 3'UTR and intron at the same region; and heat, salt and drought stresses do not affect the enrichment [17]. These results indicate that the heat stress could induce the usage of speci c sequence signals to confer unique APA-mediated transcripts.…”

Section: Discussionmentioning

confidence: 99%

“…5'UTR and protein-coding) polyA sites, which suggested a negative role of gene regulation [15]. In addition, genome-wide pro ling of APA in sorghum has shown that some stress-induced isoforms were associated with a unique intronic polyA signal [17]. These results indicate that global shift of polyA site in response of stress is a strategy of survival which affect a wide-range of gene functions.…”

Section: Introductionmentioning

confidence: 94%

Alternative Polyadenylation in Response to Temperature Stress Contributes to Gene Regulation in Trees

Yan

Wang

Lyu

et al. 2020

Preprint

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Background Genome-wide change of polyadenylation (polyA) sites (also known as alternative polyadenylation, APA) is emerging as an important strategy of gene regulation in response to stress in plants. But little is known in woody perennials that are persistently dealing with multiple abiotic stresses.Results Here, we performed a genome-wide profiling of polyadenylation sites under heat and cold treatments in Populus trichocarpa. Through a comprehensive analysis of polyA tail sequences, we identified 25,919 polyA-site clusters (PACs), and revealed 3429 and 3139 genes shifted polyA sites under heat and cold stresses respectively. We found that a small proportion of genes possessed APA that affected the open reading frames; and some shifts were commonly identified. Functional analysis of genes displaying shifted polyA tails suggested that pathways related to RNA metabolism were linked to regulate the APA events under both heat and cold stresses. Interestingly, we found that the heat stress induced a significantly more antisense PACs comparing to cold and control conditions. Furthermore, we showed that a unique cis-element (AAAAAA) was predominately enriched downstream of PACs in P. trichocarpa genes; and this sequence signal was only absent in shifted PACs under the heat condition, indicating a distinct APA mechanism responsive to heat tolerance. Conclusions This work provides a comprehensive picture of global polyadenylation patterns in response to temperatures stresses in trees. We show that the frequent change of polyA tail is a potential mechanism of gene regulation responsive to stress, which are associated with distinctive sequence signatures.

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Wide‐ranging transcriptome remodelling mediated by alternative polyadenylation in response to abiotic stresses in Sorghum

Cited by 30 publications

References 91 publications

Transcriptome Analysis of Drought-Resistant and Drought-Sensitive Sorghum (Sorghum bicolor) Genotypes in Response to PEG-Induced Drought Stress

Transcriptome Analysis of Drought-Resistant and Drought-Sensitive Sorghum (Sorghum bicolor) Genotypes in Response to PEG-Induced Drought Stress

Alternative Polyadenylation in response to temperature stress contributes to gene regulation in Populus trichocarpa

Alternative Polyadenylation in Response to Temperature Stress Contributes to Gene Regulation in Trees

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