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

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Chao Yan ◽  
Yupeng Wang ◽  
Tao Lyu ◽  
Zhikang Hu ◽  
Ning Ye ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Populus Trichocarpa ◽  
Alternative Polyadenylation ◽  
Open Reading Frames ◽  
Polya Tail ◽  
Frequent Change ◽  
Heat Condition ◽  
Woody Perennials ◽  
Genome Wide ◽  
A Genome

Abstract 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.

scholarly journals Alternative Polyadenylation in Response to Temperature Stress Contributes to Gene Regulation in Populus trichocarpa

2020 ◽  
Author(s):  
Chao Yan ◽  
Yupeng Wang ◽  
Tao Lyu ◽  
Zhikang Hu ◽  
Ning Ye ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Populus Trichocarpa ◽  
Alternative Polyadenylation ◽  
Open Reading Frames ◽  
Polya Tail ◽  
Frequent Change ◽  
Heat Condition ◽  
Woody Perennials ◽  
Genome Wide ◽  
A Genome

Abstract 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.

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

2020 ◽  
Author(s):  
Chao Yan ◽  
Yupeng Wang ◽  
Tao Lyu ◽  
Zhikang Hu ◽  
Ning Ye ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Populus Trichocarpa ◽  
Alternative Polyadenylation ◽  
Open Reading Frames ◽  
Polya Tail ◽  
Frequent Change ◽  
Heat Condition ◽  
Woody Perennials ◽  
Genome Wide ◽  
A Genome

Abstract 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.

scholarly journals Common genetic risk variants identified in the SPARK cohort implicate DDHD2 as a novel autism risk gene

2020 ◽  
Author(s):  
Nana Matoba ◽  
Dan Liang ◽  
Huaigu Sun ◽  
Nil Aygün ◽  
Jessica C. McAfee ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Association Study ◽  
Genetic Risk ◽  
Molecular Mechanisms ◽  
Autism Spectrum ◽  
Risk Variants ◽  
Genome Wide ◽  
Common Genetic Variants ◽  
A Genome ◽  
Gene Regulatory

AbstractBackgroundAutism spectrum disorder (ASD) is a highly heritable neurodevelopmental disorder. Large genetically informative cohorts of individuals with ASD have led to the identification of three common genome-wide significant (GWS) risk loci to date. However, many more common genetic variants are expected to contribute to ASD risk given the high heritability. Here, we performed a genome-wide association study (GWAS) using the Simons Foundation Powering Autism Research for Knowledge (SPARK) dataset to identify additional common genetic risk factors and molecular mechanisms underlying risk for ASD.MethodsWe performed an association study on 6,222 case-pseudocontrol pairs from SPARK and meta-analyzed with a previous GWAS. We integrated gene regulatory annotations to map non-coding risk variants to their regulated genes. Further, we performed a massively parallel reporter assay (MPRA) to identify causal variant(s) within a novel risk locus.ResultsWe identified one novel GWS locus from the SPARK GWAS. The meta-analysis identified four significant loci, including an additional novel locus. We observed significant enrichment of ASD heritability within regulatory regions of the developing cortex, indicating that disruption of gene regulation during neurodevelopment is critical for ASD risk. The MPRA identified one variant at the novel locus with strong impacts on gene regulation (rs7001340), and expression quantitative trait loci data demonstrated an association between the risk allele and decreased expression of DDHD2 (DDHD domain containing 2) in both adult and pre-natal brains.ConclusionsBy integrating genetic association data with multi-omic gene regulatory annotations and experimental validation, we fine-mapped a causal risk variant and demonstrated that DDHD2 is a novel gene associated with ASD risk.

scholarly journals Genome-Wide Analysis of the Stationary-Phase Sigma Factor (Sigma-H) Regulon of Bacillus subtilis

2002 ◽  
Vol 184 (17) ◽  
pp. 4881-4890 ◽  
Author(s):  
Robert A. Britton ◽  
Patrick Eichenberger ◽  
Jose Eduardo Gonzalez-Pastor ◽  
Paul Fawcett ◽  
Rita Monson ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Rna Polymerase ◽  
Stationary Phase ◽  
Sigma Factor ◽  
Transcriptional Profiling ◽  
Open Reading Frames ◽  
Nutrient Sources ◽  
Genome Wide ◽  
A Genome ◽  
Sigma H

ABSTRACT Sigma-H is an alternative RNA polymerase sigma factor that directs the transcription of many genes that function at the transition from exponential growth to stationary phase in Bacillus subtilis. Twenty-three promoters, which drive transcription of 33 genes, are known to be recognized by sigma-H-containing RNA polymerase. To identify additional genes under the control of sigma-H on a genome-wide basis, we carried out transcriptional profiling experiments using a DNA microarray containing >99% of the annotated B. subtilis open reading frames. In addition, we used a bioinformatics-based approach aimed at the identification of promoters recognized by RNA polymerase containing sigma-H. This combination of approaches was successful in confirming most of the previously described sigma-H-controlled genes. In addition, we identified 26 putative promoters that drive expression of 54 genes not previously known to be under the direct control of sigma-H. Based on the known or inferred function of most of these genes, we conclude that, in addition to its previously known roles in sporulation and competence, sigma-H controls genes involved in many physiological processes associated with the transition to stationary phase, including cytochrome biogenesis, generation of potential nutrient sources, transport, and cell wall metabolism.

scholarly journals Genome-Wide Identification and Characterization of Small Peptides in Maize

2021 ◽  
Vol 12 ◽  
Author(s):  
Yan Liang ◽  
Wanchao Zhu ◽  
Sijia Chen ◽  
Jia Qian ◽  
Lin Li
Keyword(s):  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Translational Efficiency ◽  
Small Peptides ◽  
Bioinformatics Pipeline ◽  
Protein Coding ◽  
Genome Wide ◽  
A Genome ◽  
Intergenic Regions ◽  
New Perspective

Small peptides (sPeptides), <100 amino acids (aa) long, are encoded by small open reading frames (sORFs) often found in the 5′ and 3′ untranslated regions (or other parts) of mRNAs, in long non-coding RNAs, or transcripts from introns and intergenic regions; various sPeptides play important roles in multiple biological processes. In this study, we conducted a comprehensive study of maize (Zea mays) sPeptides using mRNA sequencing, ribosome profiling (Ribo-seq), and mass spectrometry (MS) on six tissues (each with at least two replicates). To identify maize sORFs and sPeptides from these data, we set up a robust bioinformatics pipeline and performed a genome-wide scan. This scan uncovered 9,388 sORFs encoding peptides of 2–100 aa. These sORFs showed distinct genomic features, such as different Kozak region sequences, higher specificity of translation, and high translational efficiency, compared with the canonical protein-coding genes. Furthermore, the MS data verified 2,695 sPeptides. These sPeptides perfectly discriminated all the tissues and were highly associated with their parental genes. Interestingly, the parental genes of sPeptides were significantly enriched in multiple functional gene ontology terms related to abiotic stress and development, suggesting the potential roles of sPeptides in the regulation of their parental genes. Overall, this study lays out the guidelines for genome-wide scans of sORFs and sPeptides in plants by integrating Ribo-seq and MS data and provides a more comprehensive resource of functional sPeptides in maize and gives a new perspective on the complex biological systems of plants.

scholarly journals Genome-wide investigation and expression profiling of polyphenol oxidase (PPO) family genes uncover likely functions in organ development and stress responses in Populus trichocarpa

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Fang He ◽  
Yu-Jie Shi ◽  
Qian Zhao ◽  
Kuang-Ji Zhao ◽  
Xing-Lei Cui ◽  
...  
Keyword(s):  
Polyphenol Oxidase ◽  
Stress Responses ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Mechanical Damage ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Element Analysis ◽  
Genome Wide ◽  
A Genome

Abstract Background Trees such as Populus are planted extensively for reforestation and afforestation. However, their successful establishment greatly depends upon ambient environmental conditions and their relative resistance to abiotic and biotic stresses. Polyphenol oxidase (PPO) is a ubiquitous metalloproteinase in plants, which plays crucial roles in mediating plant resistance against biotic and abiotic stresses. Although the whole genome sequence of Populus trichocarpa has long been published, little is known about the PPO genes in Populus, especially those related to drought stress, mechanical damage, and insect feeding. Additionally, there is a paucity of information regarding hormonal responses at the whole genome level. Results A genome-wide analysis of the poplar PPO family was performed in the present study, and 18 PtrPPO genes were identified. Bioinformatics and qRT-PCR were then used to analyze the gene structure, phylogeny, chromosomal localization, gene replication, cis-elements, and expression patterns of PtrPPOs. Sequence analysis revealed that two-thirds of the PtrPPO genes lacked intronic sequences. Phylogenetic analysis showed that all PPO genes were categorized into 11 groups, and woody plants harbored many PPO genes. Eighteen PtrPPO genes were disproportionally localized on 19 chromosomes, and 3 pairs of segmented replication genes and 4 tandem repeat genomes were detected in poplars. Cis-acting element analysis identified numerous growth and developmental elements, secondary metabolism processes, and stress-related elements in the promoters of different PPO members. Furthermore, PtrPPO genes were expressed preferentially in the tissues and fruits of young plants. In addition, the expression of some PtrPPOs could be significantly induced by polyethylene glycol, abscisic acid, and methyl jasmonate, thereby revealing their potential role in regulating the stress response. Currently, we identified potential upstream TFs of PtrPPOs using bioinformatics. Conclusions Comprehensive analysis is helpful for selecting candidate PPO genes for follow-up studies on biological function, and progress in understanding the molecular genetic basis of stress resistance in forest trees might lead to the development of genetic resources.

scholarly journals Genome-wide investigation and expression profiling of polyphenol oxidase (PPO) family genes uncover likely functions in organ development and stress responses in populus trichocarpa

2021 ◽  
Author(s):  
Fang He ◽  
Yu-Jie Shi ◽  
Qian Zhao ◽  
Kuang-Ji Zhao ◽  
Xing-Lei Cui ◽  
...  
Keyword(s):  
Polyphenol Oxidase ◽  
Stress Responses ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genetic Progress ◽  
Element Analysis ◽  
Genome Wide ◽  
A Genome

Abstract Background: Trees such as Populus are planted extensively for reforestation and afforestation. However, their successful establishment greatly depends upon ambient environmental conditions and their relative resistance to abiotic as well as biotic stress. Polyphenol oxidase (PPO) is a ubiquitous metalloproteinase in plants, which plays crucial roles in plant resistance against biotic and abiotic stresses. Although the whole genome sequence of populus trichocarpa has long been published, little is known about the PPO genes in Populus, especially those related to drought stress, mechanical damage, insect feeding and hormone response at the whole genome level. Results: In the recent research, a genome-wide analysis of the Poplar PPOs family was finished and 18 PtrPPOs gene were identified. Then, bioinformatics and qRT-PCR were applied to analyze the gene structure, phylogeny, chromosomal localization, gene replication, Cis-elements, expression patterns of PtrPPOs. Sequence analysis revealed that 2/3 of the PtrPPO genes not contained introns. Phylogenetic analysis revealed that all PPOs gene were split into 11 subfamilies, and woody plants differentiated a large number of PPO genes. 18 PtrPPOs gene were disproportionally apportioned on 19 chromosomes, and the number of three pairs of segmented replication genes and four tandem repeat genomes were detected in poplars. Cis-acting element analysis identified a large number elements of growth and development, secondary metabolism process, and stress-related elements on the promoters of different PPO members. Furthermore, PtrPPO genes were expressed preferably in young plant tissues and fruits. In addition, some PtrPPOs could be significantly induced by PEG, ABA and JA, thus revealing their potential role in regulating stress response. Conclusions: Comprehensive analysis is helpful to select candidate PPO genes for the follow-up study of the biological function, and molecular genetic progress of stress resistance in forest trees provides genetic resources.

scholarly journals Selective Coregulator Function and Restriction of Steroid Receptor Chromatin Occupancy by Hic-5

2015 ◽  
Vol 29 (5) ◽  
pp. 716-729 ◽  
Author(s):  
Rajas Chodankar ◽  
Dai-Ying Wu ◽  
Daniel S. Gerke ◽  
Michael R. Stallcup
Keyword(s):  
Gene Regulation ◽  
Hormonal Regulation ◽  
Steroid Receptors ◽  
Estrogen Receptor Α ◽  
Regulatory Sequences ◽  
Specific Expression ◽  
Tissue Specific ◽  
Genome Wide ◽  
A Genome ◽  
Dna Regulatory Sequences

Abstract Steroid receptors (SRs) bind specific DNA regulatory sequences, thereby activating and repressing gene expression. We previously showed that transcriptional coregulator Hic-5 facilitates glucocorticoid regulation of some genes but blocks glucocorticoid regulation of others. Here, in a genome-wide analysis, Hic-5 depletion dramatically increased the global number of sites occupied by glucocorticoid receptor (GR) α (the major GR isoform), and many binding sites blocked by Hic-5 were associated with genes for which Hic-5 also blocked glucocorticoid-regulated expression. Hic-5 had similar effects on GRγ (a splice variant of GRα) and estrogen receptor α (ERα), facilitating hormonal regulation of some genes and blocking hormonal regulation of others. As with GRα, Hic-5 blocking of hormonal gene regulation mediated by GRγ and ERα was associated with blocking of GRγ and ERα occupancy at nearby sites. Hic-5 supported hormonal regulation of many more genes for GRα than for GRγ or ERα and thus exhibited selective coregulator functions for different SRs. In contrast, the number of Hic-5–blocked genes was similar for all 3 SRs. In addition to classic coregulator activity, Hic-5 influences the genomic occupancy of multiple SRs and thereby blocks some aspects of hormonal regulation. Thus, Hic-5, because of its tissue-specific expression, could contribute to tissue-specific genomic occupancy and gene regulation by SRs.

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