scholarly journals Chromatin Accessibility Is Associated with Artemisinin Biosynthesis Regulation in Artemisia annua

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 1194
Author(s):  
Limeng Zhou ◽  
Yingzhang Huang ◽  
Qi Wang ◽  
Dianjing Guo
Keyword(s):  
Gene Expression ◽  
Artemisia Annua ◽  
Glandular Trichomes ◽  
Regulation Of Gene Expression ◽  
Glandular Trichome ◽  
Chromatin Accessibility ◽  
Biosynthetic Genes ◽  
Nuclear Molecules ◽  
Accessible Chromatin ◽  
Artemisinin Biosynthesis

Glandular trichome (GT) is the dominant site for artemisinin production in Artemisia annua. Several critical genes involved in artemisinin biosynthesis are specifically expressed in GT. However, the molecular mechanism of differential gene expression between GT and other tissue types remains elusive. Chromatin accessibility, defined as the degree to which nuclear molecules are able to interact with chromatin DNA, reflects gene expression capacity to a certain extent. Here, we investigated and compared the landscape of chromatin accessibility in Artemisia annua leaf and GT using the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) technique. We identified 5413 GT high accessible and 4045 GT low accessible regions, and these GT high accessible regions may contribute to GT-specific biological functions. Several GT-specific artemisinin biosynthetic genes, such as DBR2 and CYP71AV1, showed higher accessible regions in GT compared to that in leaf, implying that they might be regulated by chromatin accessibility. In addition, transcription factor binding motifs for MYB, bZIP, C2H2, and AP2 were overrepresented in the highly accessible chromatin regions associated with artemisinin biosynthetic genes in glandular trichomes. Finally, we proposed a working model illustrating the chromatin accessibility dynamics in regulating artemisinin biosynthetic gene expression. This work provided new insights into epigenetic regulation of gene expression in GT.

scholarly journals 32 Functional annotation of livestock genomes: chromatin structure and regulation of gene expression

2019 ◽  
Vol 97 (Supplement_2) ◽  
pp. 15-16
Author(s):  
Sylvain Foissac ◽  
Sarah Djebali ◽  
Kylie Munyard ◽  
Nathalie Vialaneix ◽  
Andrea Rau ◽  
...  
Keyword(s):  
Gene Expression ◽  
Functional Annotation ◽  
Regulation Of Gene Expression ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Rna Seq ◽  
Chromosome Conformation ◽  
Accessible Chromatin ◽  
Animal Genomes

Abstract Improving the functional annotation of animal genomes is a key challenge in bridging the gap between genotype and phenotype, thus enabling predictive biology. Regarding livestock production, major outcomes are expected from a better understanding of the genetic architecture underlying quantitative traits. As part of the Functional Annotation of ANimal Genomes action (FAANG: www.faang.org), the FR-AgENCODE project generated omics data to improve the reference annotation of the cattle, pig, goat and chicken genome. High-throughput molecular assays have been performed on tissues/cells relevant to immune and metabolic traits. From two males and two females per species (pig, cattle, goat, chicken), strand-oriented RNA-seq gene expression and ATAC-seq chromatin accessibility assays were performed on liver and two PBMC-sorted T-cell types (CD4+ and CD8+). Chromosome Conformation Capture (in situ Hi-C) was also carried out on liver samples. About 4,000 samples have been collected at the INRA biorepository and registered at the EBI BioSamples registry. More than 80% of the planned experiments could be completed, generating ~11.5 billions of sequencing reads over the 3 assays. While most (50–80%) RNA-seq reads mapped to annotated exons, thousands of novel transcripts were found, with ~60K mRNAs and ~22K lncRNAs in cattle. Differentially expressed genes between cell types were enriched for immunity- or metabolism-related terms, and differentially accessible chromatin regions were identified as potential regulatory sites. Interestingly, correlations between gene expression and promoter accessibility across samples were skewed towards both positive and negative values, suggesting distinct regulatory mechanisms of gene expression. These patterns have been further investigated using human data from the Epigenome Roadmap Mapping Consortium. Altogether, this study illustrates the interest of a coordinated effort to tackle the genome-to-phenome challenge and provides a useful resource to the community. Availability: www.fragencode.org.

Chromatin-Modifying Enzymes in T Cell Development

2020 ◽  
Vol 38 (1) ◽  
pp. 397-419
Author(s):  
Michael J. Shapiro ◽  
Virginia Smith Shapiro
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
Biological Effects ◽  
Critical Role ◽  
T Cell Development ◽  
Regulation Of Gene Expression ◽  
Chromatin Accessibility ◽  
Cell Development ◽  
Specific Gene ◽  
Dynamic Regulation

T cell development involves stepwise progression through defined stages that give rise to multiple T cell subtypes, and this is accompanied by the establishment of stage-specific gene expression. Changes in chromatin accessibility and chromatin modifications accompany changes in gene expression during T cell development. Chromatin-modifying enzymes that add or reverse covalent modifications to DNA and histones have a critical role in the dynamic regulation of gene expression throughout T cell development. As each chromatin-modifying enzyme has multiple family members that are typically all coexpressed during T cell development, their function is sometimes revealed only when two related enzymes are concurrently deleted. This work has also revealed that the biological effects of these enzymes often involve regulation of a limited set of targets. The growing diversity in the types and sites of modification, as well as the potential for a single enzyme to catalyze multiple modifications, is also highlighted.

RNAi-mediated modulation of squalene synthase gene expression in Artemisia annua L. and its impact on artemisinin biosynthesis

2017 ◽  
Vol 28 (4) ◽  
pp. 731-741 ◽  
Author(s):  
Athar Ali ◽  
Malik Mobeen Ahmad ◽  
Mather Ali Khan ◽  
Parul Saxena ◽  
Shazia Khan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Artemisia Annua ◽  
Squalene Synthase ◽  
Artemisia Annua L ◽  
Artemisinin Biosynthesis

GLANDULAR TRICHOME-SPECIFIC WRKY 1 promotes artemisinin biosynthesis in Artemisia annua

2016 ◽  
Vol 214 (1) ◽  
pp. 304-316 ◽  
Author(s):  
Minghui Chen ◽  
Tingxiang Yan ◽  
Qian Shen ◽  
Xu Lu ◽  
Qifang Pan ◽  
...  
Keyword(s):  
Artemisia Annua ◽  
Glandular Trichome ◽  
Artemisinin Biosynthesis

scholarly journals Low-input ATAC&mRNA-Seq: a simple and robust method for simultaneous dual-omics profiling with low cell number

2021 ◽  
Author(s):  
Ruifang Li ◽  
Sara A Grimm ◽  
Paul A Wade
Keyword(s):  
Gene Expression ◽  
Strong Association ◽  
Regulation Of Gene Expression ◽  
Cell Number ◽  
Chromatin Accessibility ◽  
Robust Method ◽  
Data Types ◽  
Single Experiment ◽  
Low Input ◽  
Input Material

AbstractDeciphering epigenetic regulation of gene expression requires measuring the epigenome and transcriptome jointly. Single-cell multi-omics technologies have been developed for concurrent profiling of chromatin accessibility and gene expression. However, multi-omics profiling of low-input bulk samples remains challenging. Therefore, we developed low-input ATAC&mRNA-seq, a simple and robust method for studying the role of chromatin structure in gene regulation in a single experiment with thousands of cells, to maximize insights from limited input material by obtaining ATAC-seq and mRNA-seq data simultaneously from the same cells with data quality comparable to conventional mono-omics assays. Integrative data analysis revealed similar strong association between promoter accessibility and gene expression using the data of low-input ATAC&mRNA-seq as using single-assay data, underscoring the accuracy and reliability of our dual-omics assay to generate both data types simultaneously with just thousands of cells. We envision our method to be widely applied in many biological disciplines with limited materials.

Genomic and epigenomic active vitamin Dresponses in human colonic organoids

2021 ◽  
Author(s):  
Jinchao Li ◽  
David Witonsky ◽  
Emily Sprague ◽  
Dereck Alleyne ◽  
Margaret C Bielski ◽  
...  
Keyword(s):  
Gene Expression ◽  
Vitamin D ◽  
Differentially Expressed Genes ◽  
Chromatin Accessibility ◽  
Differentially Expressed ◽  
Active Vitamin ◽  
Host Environment ◽  
Genome Wide ◽  
Ideal System ◽  
Accessible Chromatin

Background & Aims: Active vitamin D, 1α,25(OH)2D3, is a nuclear hormone with roles in colonic homeostasis and carcinogenesis; yet, mechanisms underlying these effects are incompletely understood. Organoids are an ideal system to study genomic and epigenomic host-environment interactions. We utilize colonic organoids to measure 1α,25(OH)2D3 responses on genome-wide gene expression and chromatin accessibility over time. Methods: Human colonic organoids were treated in triplicate with 100nM 1α,25(OH)2D3 or vehicle control for 4 and 18 hours (h) for chromatin accessibility, and 6 and 24h for gene expression. ATAC- and RNA-sequencing were performed. Differentially accessible peaks were analyzed using DiffBind and EdgeR; differentially expressed genes were analyzed using DESeq2. Motif enrichment was determined using HOMER. Results: At 6h and 24h, 2870 and 2721 differentially expressed genes, respectively (false discovery rate, FDR<5%) were identified with overall stronger responses with 1α,25(OH)2D3. Vitamin D treatment led to stronger chromatin accessibility especially at 4h. The vitamin D receptor (VDR) motif was strongly enriched among accessible chromatin peaks with 1α,25(OH)2D3 treatment accounting for 30.5% and 11% of target sequences at 4h and 18h, respectively (FDR<1%). Genes such as CYP24A1, FGF19, MYC, FOS and TGFBR2 showed significant transcriptional and chromatin accessibility responses to 1α,25(OH)2D3 treatment with accessible chromatin located distant from promoters for some gene regions. Conclusions: Assessment of chromatin accessibility and transcriptional responses to 1α,25(OH)2D3 yielded new observations about vitamin D genome-wide effects in the colon facilitated by application of human colonic organoids. This framework can be applied to study host-environment interactions between individuals and populations in future.

SNARE-seq2 v2

2021 ◽  
Author(s):  
Nongluk Plongthongkum ◽  
Dinh H Diep ◽  
Song Chen ◽  
Blue Lake ◽  
Kun Zhang
Keyword(s):  
Gene Expression ◽  
High Throughput ◽  
Chromatin Accessibility ◽  
Single Experiment ◽  
Data Set ◽  
Whole Cells ◽  
High Throughput Method ◽  
Single Nucleus ◽  
Accessible Chromatin ◽  
Entire Procedure

To study the heterogeneity of complex tissues by joint profiling of gene expression and its regulation, we require an accurate and high-throughput method. Here we described improved high-throughput combinatorial indexing-based single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-Seq2) co-assay. This protocol involves fixing and permeabilizing the nucleus followed by tagmentation, chromatin barcode ligation, reverse transcription, pooling and splitting for the next rounds of cell barcode ligation into cDNA and accessible chromatin (AC) on the same nucleus. The captured cDNA and AC are co-amplified before splitting and enrichment into single-nucleus RNA and single-nucleus AC sequencing libraries. The protocol can also be applied to both nuclei and whole cells to capture mRNA in the cytoplasm. This improvement allows us to generate hundreds of thousands of data set of each assay and can be scaled up to half a million cells from a single experiment. The entire procedure can be complete in 3.5 d for generating joint single-nucleus RNA and single-nucleus ATAC sequencing libraries.

scholarly journals ATAC-Seq Identifies Chromatin Landscapes Linked to the Regulation of Oxidative Stress in the Human Fungal Pathogen Candida albicans

2020 ◽  
Vol 6 (3) ◽  
pp. 182
Author(s):  
Sabrina Jenull ◽  
Michael Tscherner ◽  
Theresia Mair ◽  
Karl Kuchler
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Candida Albicans ◽  
Stress Responses ◽  
De Novo ◽  
Fungal Infections ◽  
Chromatin Accessibility ◽  
Robust Detection ◽  
Genomic Regions ◽  
Accessible Chromatin

Human fungal pathogens often encounter fungicidal stress upon host invasion, but they can swiftly adapt by transcriptional reprogramming that enables pathogen survival. Fungal immune evasion is tightly connected to chromatin regulation. Hence, fungal chromatin modifiers pose alternative treatment options to combat fungal infections. Here, we present an assay for transposase-accessible chromatin using sequencing (ATAC-seq) protocol adapted for the opportunistic pathogen Candida albicans to gain further insight into the interplay of chromatin accessibility and gene expression mounted during fungal adaptation to oxidative stress. The ATAC-seq workflow not only facilitates the robust detection of genomic regions with accessible chromatin but also allows for the precise modeling of nucleosome positions in C. albicans. Importantly, the data reveal genes with altered chromatin accessibility in upstream regulatory regions, which correlate with transcriptional regulation during oxidative stress. Interestingly, many genes show increased chromatin accessibility without change in gene expression upon stress exposure. Such chromatin signatures could predict yet unknown regulatory factors under highly dynamic transcriptional control. Additionally, de novo motif analysis in genomic regions with increased chromatin accessibility upon H2O2 treatment shows significant enrichment for Cap1 binding sites, a major factor of oxidative stress responses in C. albicans. Taken together, the ATAC-seq workflow enables the identification of chromatin signatures and highlights the dynamics of regulatory mechanisms mediating environmental adaptation of C. albicans.

scholarly journals Integration of ATAC-seq and RNA-seq Unravels Chromatin Accessibility during Sex Reversal in Orange-Spotted Grouper (Epinephelus coioides)

2020 ◽  
Vol 21 (8) ◽  
pp. 2800 ◽  
Author(s):  
Xi Wu ◽  
Yang Yang ◽  
Chaoyue Zhong ◽  
Yin Guo ◽  
Tengyu Wei ◽  
...  
Keyword(s):  
Gene Expression ◽  
Binding Sites ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Sex Reversal ◽  
Open Chromatin ◽  
Specific Marker ◽  
Epinephelus Coioides ◽  
Rna Seq ◽  
Accessible Chromatin

Chromatin structure plays a pivotal role in maintaining the precise regulation of gene expression. Accessible chromatin regions act as the binding sites of transcription factors (TFs) and cis-elements. Therefore, information from these open regions will enhance our understanding of the relationship between TF binding, chromatin status and the regulation of gene expression. We employed an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and RNA-seq analyses in the gonads of protogynous hermaphroditic orange-spotted groupers during sex reversal to profile open chromatin regions and TF binding sites. We focused on several crucial TFs, including ZNF263, SPIB, and KLF9, and analyzed the networks of TF-target genes. We identified numerous transcripts exhibiting sex-preferred expression among their target genes, along with their associated open chromatin regions. We then investigated the expression patterns of sex-related genes as well as the mRNA localization of certain genes during sex reversal. We found a set of sex-related genes that—upon further study—might be identified as the sex-specific or cell-specific marker genes that trigger sex reversal. Moreover, we discovered the core genes (gnas, ccnb2, and cyp21a) of several pathways related to sex reversal that provide the guideposts for future study.

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