scholarly journals Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa

GigaScience ◽  
2019 ◽  
Vol 8 (12) ◽  
Author(s):  
Miriam Payá-Milans ◽  
Laura Poza-Viejo ◽  
Patxi San Martín-Uriz ◽  
David Lara-Astiaso ◽  
Mark D Wilkinson ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Chromatin Immunoprecipitation ◽  
High Throughput Sequencing ◽  
Model Systems ◽  
Epigenetic Mark ◽  
Protein Coding ◽  
Brassica Crops ◽  
Genome Wide ◽  
Floral Regulatory Genes ◽  
Complex Genome

Abstract Background Genome-wide maps of histone modifications have been obtained for several plant species. However, most studies focus on model systems and do not enforce FAIR data management principles. Here we study the H3K27me3 epigenome and associated transcriptome of Brassica rapa, an important vegetable cultivated worldwide. Findings We performed H3K27me3 chromatin immunoprecipitation followed by high-throughput sequencing and transcriptomic analysis by 3′-end RNA sequencing from B. rapa leaves and inflorescences. To analyze these data we developed a Reproducible Epigenomic Analysis pipeline using Galaxy and Jupyter, packaged into Docker images to facilitate transparency and reuse. We found that H3K27me3 covers roughly one-third of all B. rapa protein-coding genes and its presence correlates with low transcript levels. The comparative analysis between leaves and inflorescences suggested that the expression of various floral regulatory genes during development depends on H3K27me3. To demonstrate the importance of H3K27me3 for B. rapa development, we characterized a mutant line deficient in the H3K27 methyltransferase activity. We found that braA.clf mutant plants presented pleiotropic alterations, e.g., curly leaves due to increased expression and reduced H3K27me3 levels at AGAMOUS-like loci. Conclusions We characterized the epigenetic mark H3K27me3 at genome-wide levels and provide genetic evidence for its relevance in B. rapa development. Our work reveals the epigenomic landscape of H3K27me3 in B. rapa and provides novel genomics datasets and bioinformatics analytical resources. We anticipate that this work will lead the way to further epigenomic studies in the complex genome of Brassica crops.

scholarly journals Genome-wide identification of accessible chromatin regions in bumblebee (Bombus terrestris) by ATAC-seq

2019 ◽  
Author(s):  
Xiaomeng Zhao ◽  
Weilin Xu ◽  
Sarah Schaack ◽  
Cheng Sun
Keyword(s):  
Crop Production ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Bombus Terrestris ◽  
Regulatory Elements ◽  
Natural Ecosystem ◽  
Protein Coding ◽  
Genome Wide ◽  
Pollinating Insects ◽  
Accessible Chromatin

AbstractBumblebees (Hymenoptera: Apidae) are important pollinating insects that play pivotal roles in crop production and natural ecosystem services. To date, while the protein-coding sequences of bumblebees have been extensively annotated, regulatory elements, such as promoters and enhancers, have been poorly annotated in the bumblebee genome. To achieve a comprehensive profile of accessible chromatin regions and provide clues for all possible regulatory elements in the bumblebee genome, we did ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) for B. terrestris samples derived from its four developmental stages: egg, larva, pupa, and adult, respectively. The sequencing reads of ATAC-seq were mapped to B. terrestris reference genome, and the accessible chromatin regions of bumblebee were identified and characterized by using bioinformatic methods. Our study will provide important resources not only for uncovering regulatory elements in the bumblebee genome, but also for expanding our understanding of bumblebee biology. The ATAC-seq data generated in this study has been deposited in NCBI GEO (accession#: GSE131063).

scholarly journals Osmotic stress induces phosphorylation of histone H3 at threonine 3 in pericentromeric regions of Arabidopsis thaliana

2015 ◽  
Vol 112 (27) ◽  
pp. 8487-8492 ◽  
Author(s):  
Zhen Wang ◽  
Juan Armando Casas-Mollano ◽  
Jianping Xu ◽  
Jean-Jack M. Riethoven ◽  
Chi Zhang ◽  
...  
Keyword(s):  
Osmotic Stress ◽  
Protein Kinases ◽  
Double Mutant ◽  
Histone H3 ◽  
Epigenetic Mark ◽  
Wild Type ◽  
Protein Coding ◽  
Transcriptional Reprogramming ◽  
Genome Wide ◽  
In The Wild

Histone phosphorylation plays key roles in stress-induced transcriptional reprogramming in metazoans but its function(s) in land plants has remained relatively unexplored. Here we report that an Arabidopsis mutant defective in At3g03940 and At5g18190, encoding closely related Ser/Thr protein kinases, shows pleiotropic phenotypes including dwarfism and hypersensitivity to osmotic/salt stress. The double mutant has reduced global levels of phosphorylated histone H3 threonine 3 (H3T3ph), which are not enhanced, unlike the response in the wild type, by drought-like treatments. Genome-wide analyses revealed increased H3T3ph, slight enhancement in trimethylated histone H3 lysine 4 (H3K4me3), and a modest decrease in histone H3 occupancy in pericentromeric/knob regions of wild-type plants under osmotic stress. However, despite these changes in heterochromatin, transposons and repeats remained transcriptionally repressed. In contrast, this reorganization of heterochromatin was mostly absent in the double mutant, which exhibited lower H3T3ph levels in pericentromeric regions even under normal environmental conditions. Interestingly, within actively transcribed protein-coding genes, H3T3ph density was minimal in 5′ genic regions, coincidental with a peak of H3K4me3 accumulation. This pattern was not affected in the double mutant, implying the existence of additional H3T3 protein kinases in Arabidopsis. Our results suggest that At3g03940 and At5g18190 are involved in the phosphorylation of H3T3 in pericentromeric/knob regions and that this repressive epigenetic mark may be important for maintaining proper heterochromatic organization and, possibly, chromosome function(s).

scholarly journals Genome-wide identification of long non-coding RNAs in the gravid ectoparasite Varroa destructor

2020 ◽  
Author(s):  
Zheguang Lin ◽  
Yibing Liu ◽  
Xiaomei Chen ◽  
Cong Han ◽  
Wei Wang ◽  
...  
Keyword(s):  
Varroa Destructor ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Protein Coding ◽  
Genome Wide ◽  
Genomic Studies ◽  
Genetic Information Processing ◽  
Non Coding Rnas ◽  
Environmental Responses ◽  
Living Organisms

AbstractLong non-coding RNAs (lncRNAs) emerge as critical regulators with various biological functions in living organisms. However, to date, no systematic characterization of lncRNAs has been investigated in the ectoparasitic mite Varroa destructor, the most severe biotic threat to honey bees worldwide. Here, we performed an initial genome-wide identification of lncRNAs in V. destructor via high-throughput sequencing technology and reported, for the first time, the transcriptomic landscape of lncRNAs in the devastating parasite. By means of a lncRNA identification pipeline, 6,645 novel lncRNA transcripts, encoded by 3,897 gene loci, were identified, including 2,066 sense lncRNAs, 2,772 lincRNAs, and 1,807 lncNATs. Compared with protein-coding mRNAs, V. destructor lncRNAs are shorter in terms of full length, as well as of the ORF length, contain less exons, and express at lower level. GO term and KEGG pathway enrichment analyses of the lncRNA target genes demonstrated that these predicted lncRNAs are likely to play key roles in cellular processes, genetic information processing and environmental responses. To our knowledge, this is the first catalog of lncRNA profile in the parasitiformes species, providing a valuable resource for genetic and genomic studies. Understanding the characteristics and features of lncRNAs in V. destructor would promote sustainable pest control.

Genome-wide mapping of endogenous G-quadruplex DNA structures by chromatin immunoprecipitation and high-throughput sequencing

2018 ◽  
Vol 13 (3) ◽  
pp. 551-564 ◽  
Author(s):  
Robert Hänsel-Hertsch ◽  
Jochen Spiegel ◽  
Giovanni Marsico ◽  
David Tannahill ◽  
Shankar Balasubramanian
Keyword(s):  
High Throughput ◽  
Chromatin Immunoprecipitation ◽  
High Throughput Sequencing ◽  
Quadruplex Dna ◽  
Dna Structures ◽  
Genome Wide ◽  
G Quadruplex

scholarly journals Genome-wide identification and functional analysis of circRNAs in Zea mays

2018 ◽  
Author(s):  
Baihua Tang ◽  
Zhiqiang Hao ◽  
Yanfeng Zhu ◽  
Hua Zhang ◽  
Guanglin Li
Keyword(s):  
Gene Expression ◽  
Zea Mays ◽  
High Throughput Sequencing ◽  
Circular Rnas ◽  
Biological Functions ◽  
Molecular Processes ◽  
Oxidoreductase Activity ◽  
Protein Coding ◽  
Genome Wide ◽  
And Function

AbstractCircular RNAs (circRNAs) are a class of endogenous noncoding RNAs, which increasingly drawn researchers’ attention in recent years as their importance in regulating gene expression at the transcriptional and post-transcriptional levels. With the development of high-throughput sequencing and bioinformatics, circRNAs have been widely analysed in animals, but the understanding of characteristics and function of circRNAs is limited in plants, especially in maize. Here, 3715 unique circRNAs were predicted in Zea mays systematically, and 8 of 12 circRNAs were validated by experiments. By analysing circRNA sequence, the events of alternative circularization phenomenon were found prevailed in maize. By comparing circRNAs in different species, it showed that part circRNAs are conserved across species, for example, there are 273 circRNAs conserved between maize and rice. Although most of the circRNAs have low expression levels, we found 213 differential expressed circRNAs responding to heat, cold, or drought, and 1782 tissue-specific expressed circRNAs. The results showed that those circRNAs may have potential biological functions in specific situations. Finally, two different methods were used to search circRNA functions, which were based on circRNAs originated from protein-coding genes and circRNAs as miRNA decoys. 346 circRNAs could act as miRNA decoys, which might modulate the effects of multiple molecular functions, including binding, catalytic activity, oxidoreductase activity, and transmembrane transporter activity. Maize circRNAs were identified, classified and characterized systematically. We also explored circRNA functions, suggesting that circRNAs are involved in multiple molecular processes and play important roles in regulating of gene expression. Our results provide a rich resource for further study of maize circRNAs.

scholarly journals Epigenetic regulation and epigenomic landscape in rice

2016 ◽  
Vol 3 (3) ◽  
pp. 309-327 ◽  
Author(s):  
Xian Deng ◽  
Xianwei Song ◽  
Liya Wei ◽  
Chunyan Liu ◽  
Xiaofeng Cao
Keyword(s):  
Epigenetic Regulation ◽  
High Throughput Sequencing ◽  
Agronomic Traits ◽  
Food Crop ◽  
Recent Advances ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Epigenetic Regulators ◽  
Complex Genome

Abstract Epigenetic regulation has been implicated in the control of complex agronomic traits in rice (Oryza sativa), a staple food crop and model monocot plant. Recent advances in high-throughput sequencing and the moderately complex genome of rice have made it possible to study epigenetic regulation in rice on a genome-wide scale. This review discusses recent advances in our understanding of epigenetic regulation in rice, with an emphasis on the roles of key epigenetic regulators, the epigenomic landscape, epigenetic variation, transposon repression, and plant development.

scholarly journals Genome-Wide Mapping Reveals Complex Regulatory Activities of BfmR in Pseudomonas aeruginosa

2021 ◽  
Vol 9 (3) ◽  
pp. 485
Author(s):  
Ke Fan ◽  
Qiao Cao ◽  
Lefu Lan
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Chromatin Immunoprecipitation ◽  
Biofilm Formation ◽  
High Throughput Sequencing ◽  
Response Regulator ◽  
Cellular Functions ◽  
Genome Wide ◽  
Component Systems ◽  
Genes Encoding ◽  
Two Component Systems

BfmR is a response regulator that modulates diverse pathogenic phenotypes and induces an acute-to-chronic virulence switch in Pseudomonas aeruginosa, an important human pathogen causing serious nosocomial infections. However, the mechanisms of action of BfmR remain largely unknown. Here, using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq), we showed that 174 chromosomal regions of P. aeruginosa MPAO1 genome were highly enriched by coimmunoprecipitation with a C-terminal Flag-tagged BfmR. Integration of these data with global transcriptome analyses revealed that 172 genes in 106 predicted transcription units are potential targets for BfmR. We determined that BfmR binds to and modulates the promoter activity of genes encoding transcriptional regulators CzcR, ExsA, and PhoB. Intriguingly, BfmR bound to the promoters of a number of genes belong to either CzcR or PhoB regulon, or both, indicating that CzcRS and PhoBR two-component systems (TCSs) deeply feed into the BfmR-mediated regulatory network. In addition, we demonstrated that phoB is required for BfmR to promote the biofilm formation by P. aeruginosa. These results delineate the direct BfmR regulon and exemplify the complexity of BfmR-mediated regulation of cellular functions in P. aeruginosa.

scholarly journals Gene by environment interaction mouse model reveals a functional role for 5-hydroxymethylcytosine in neurodevelopmental disorders

2021 ◽  
pp. gr.276137.121
Author(s):  
Ligia A Papale ◽  
Andy Madrid ◽  
Qi Zhang ◽  
Kailei Chen ◽  
Lara Sak ◽  
...  
Keyword(s):  
Neurodevelopmental Disorders ◽  
Chromatin Immunoprecipitation ◽  
High Throughput Sequencing ◽  
Repetitive Behaviors ◽  
Environment Interaction ◽  
Genome Wide ◽  
A Genome ◽  
Number Of Genes ◽  
Prenatally Stressed ◽  
Environmentally Sensitive

Mouse knockouts of Cntnap2 exhibit altered neurodevelopmental behavior, deficits in striatal GABAergic signaling and a genome-wide disruption of an environmentally sensitive DNA methylation modification (5-hydroxymethylcytosine, 5hmC) in the orthologs of a significant number of genes implicated in human neurodevelopmental disorders. We tested adult Cntnap2 heterozygous mice (Cntnap2+/-, lacking behavioral or neuropathological abnormalities) subjected to a prenatal stress and found that prenatally stressed Cntnap2+/- female mice showed repetitive behaviors and altered sociability, similar to the homozygote phenotype. Genomic profiling revealed disruptions in hippocampal and striatal 5hmC levels that were correlated to altered transcript levels of genes linked to these phenotypes (e.g., Reln, Dst, Trio, and Epha5). Chromatin-immunoprecipitation coupled with high-throughput sequencing and hippocampal nuclear lysate pull-down data indicated that 5hmC abundance alters the binding of the transcription factor CLOCK in the promoters of these genes (e.g., Palld, Gigyf1, and Fry), providing a mechanistic role for 5hmC in gene regulation. Together, these data support gene by environment hypotheses for the origins of mental illness and provide a means to identify the elusive factors contributing to complex human diseases.

scholarly journals Comparative ChIP-seq (Comp-ChIP-seq): a practical guideline for experimental design and a novel computational methodology

2019 ◽  
Author(s):  
Enrique Blanco ◽  
Luciano Di Croce ◽  
Sergi Aranda
Keyword(s):  
Chromatin Immunoprecipitation ◽  
High Throughput Sequencing ◽  
Confounding Factor ◽  
Decision Making Process ◽  
Local Regression ◽  
Binary Decision ◽  
Genome Wide ◽  
A Genome ◽  
Standard Chip ◽  
Multiple Conditions

ABSTRACTChromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is a pivotal technique for understanding the functionality of the chromatin-bound factors and for mapping the functional elements of the genome. In order to evaluate cell- and disease-specific changes in the interacting strength of chromatin targets, ChIP-seq signal across multiple conditions must undergo robust normalization. However, this is not possible using the standard ChIP-seq scheme, which lacks a reference for the control of biological and experimental variabilities. While several studies have recently proposed different solutions to circumvent this problem, substantial technical and analytical differences among methodologies could hamper the experimental reproducibility. Here we provide a practical binary decision-making process to experimentally implement a normalizing method for comparative ChIP-seq across different samples. In addition, we evaluate side-by-side the current computational approaches for normalizing using a reference internal genome. Finally, we propose a local regression strategy to accurately normalize ChIP-seq data in a genome-wide manner. Overall, our proposed experimental and computational standard for comparative ChIP-seq (Comp-ChIP-seq) will increase experimental reproducibility, thereby reducing this major confounding factor in interpreting ChIP-seq results.

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