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Chromatin Accessibility-Based Characterization of the Gene Regulatory Networks Underpinning Phenotypic Plasticity in the Honey Bee (RNA-Seq).

ABSTRACT: Using the assay for transposase-accessible chromatin by sequencing (ATAC-seq), we produce the first genome- wide maps of chromatin accessibility across all three adult honey bee phenotypes. We identify ~ 3000 regulatory regions in queen, ~ 4500 in worker and ~ 4000 in drone, with the vast majority of these sites located within intronic regions. Integrating ATAC-seq, RNA-seq and ChIP-seq data, we show a positive correlation between chromatin accessibility at introns, flanking H3K27ac modified nucleosomes and abundance of the respective mRNA transcript. Importantly, we find that these regulatory regions are enriched in transcription factor binding motifs and using ATAC-seq footprinting we identify queen, worker and drone - specific occupancy and uncover novel transcription factor networks.

ORGANISM(S): Apis mellifera

PROVIDER: GSE206993 | GEO | 2022/11/09

REPOSITORIES: GEO

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Chromatin Accessibility-Based Characterization of the Gene Regulatory Networks Underpinning Phenotypic Plasticity in the Honey Bee (ATAC-Seq).

Project description:Using the assay for transposase-accessible chromatin by sequencing (ATAC-seq), we produce the first genome- wide maps of chromatin accessibility across all three adult honey bee phenotypes. We identify ~ 3000 regulatory regions in queen, ~ 4500 in worker and ~ 4000 in drone, with the vast majority of these sites located within intronic regions. Integrating ATAC-seq, RNA-seq and ChIP-seq data, we show a positive correlation between chromatin accessibility at introns, flanking H3K27ac modified nucleosomes and abundance of the respective mRNA transcript. Importantly, we find that these regulatory regions are enriched in transcription factor binding motifs and using ATAC-seq footprinting we identify queen, worker and drone - specific occupancy and uncover novel transcription factor networks.

2022-11-09 | GSE206991 | GEO

Chromatin Accessibility-Based Characterization of the Gene Regulatory Networks Underpinning Phenotypic Plasticity in the Honey Bee (ChIP-Seq).

2022-11-09 | GSE206992 | GEO

Phenotypic plasticity shapes genome architecture in the honeybee Apis mellifera (RNA-seq)

Project description:Female honeybees are specified as workers or queens based on diet during early development. Workers are essentially sterile with a reduced number of ovarioles and no spermatheca. In the presence of the queen (queen mandibular pheromone) and her brood, worker ovaries are kept in an inactive quiescent state. If the queen is removed, or lost, worker bees are able to sense this change in their environment and their ovaries undergo complete remodeling producing unfertilized haploid eggs that will produce male (drone bees). In this study we analyze gene expression in queen, worker, and laying worker ovaries using RNA-seq and explore differences in the chromatin landscape (focusing on H3K27me3).

2019-09-17 | GSE120561 | GEO

Phenotypic plasticity shapes genome architecture in the honeybee Apis mellifera (ChIP-seq)

Project description:Female honeybees are specified as workers or queens based on diet during early development. Workers are essentially sterile with a reduced number of ovarioles and no spermatheca. In the presence of the queen (queen mandibular pheromone) and her brood, worker ovaries are kept in an inactive quiescent state. If the queen is removed, or lost, worker bees are able to sense this change in their environment and their ovaries undergo complete remodelling producing unfertilised haploid eggs that will produce male (drone bees). In this study we analyse gene expression in queen, worker, and laying worker ovaries using RNA-seq and explore differences in the chromatin landscape (focussing on H3K27me3).

2019-09-17 | GSE120560 | GEO

mRNA-Seq of brain tissue from honeybee (Apis mellifera) drones (male), workers (female) and queens (female).

Project description:Transcriptional profiling of brain tissue of was performed by RNA-SEQ in workers, queens and males. The sex and caste specific expressed and spliced genes were examined comparing drone, worker and queen honeybees.

2013-03-27 | GSE45408 | GEO

Sex-specific development in haplodiploid honeybee is controlled by the female-embryo-specific activation of thousands of intronic lncRNAs

Project description:Sex determination in the honeybee (Apis mellifera) is governed by the queen-controlled unfertilization or fertilization of embryo, though the mechanisms of determination are poorly understood. Here, we obtained the transcriptomes from individual worker and drone embryo during the embryonic development (day 1 to day 3). We show that transcriptional difference between worker and drone embryo is very small during the first day of hatching, during which sex-determinant gene csd expresses similarly. Differential transcription between worker and drone embryo bursts at day 2, among which csd is induced in worker embryo at day 2 and sex-lethal gene sxl is repressed in male embryo. An unexpected global regulation of alternative splicing accompanies the honeybee embryonic development, and male and worker embryo show distinct regulatory patterns and mechanisms. This study suggests the honeybee sex determination is more globally controlled at both the transcriptional and alternative splicing levels.

2021-07-27 | GSE101741 | GEO

Small RNA expression and caste differentiation in the honeybee

Project description:Honeybees are very important eusocial insects and are involved in the pollination of many plants. Queen bees and worker bees develop from the same fertilized eggs, and are thus genetically identical despite their substantial behavioural and physiological differences. The mechanism governing developmental differences between worker and queen bees has always attracted much interest. While there are several reports on mRNA expression related to caste differentiation, no systematic investigation of small RNAs has thus far been carried out. Results: Using deep sequencing we systematically profiled small RNA expression in 4th-6th day worker larvae and queen larvae (the critical stages at which the fates of workers and queens are determined), and found that 38 miRNAs were differentially expressed between worker and queen larvae. In addition, 639 mature miRNA candidates were identified in our work for the first time, of which, 526 were expressed only in workers (318) or queens (208). Conclusion: We present the first profile of honeybee small RNAs and explore the mechanism of caste differentiation between worker and queen bees. Caste-specific expression patterns and large discrepancies in small RNA profiles between worker and queen bees indicate that small RNAs may be related to the differential development of worker and queen bee larvae. Results presented here will make a valuable contribution to understanding the caste switch between worker and queen bees.

2014-07-28 | GSE52630 | GEO

Multi-omics Analyses Reveal Sex Differences in Mouse Renal Proximal Tubules

Project description:Sex-dependent differences in kidney function have been recognized. However, the molecular mechanisms underlying these differences remain largely unexplored. Advances in genomics and proteomic technologies now allow for an extensive characterization of sex differences. In this study, the authors apply multi-omics approaches integrating RNA-seq, ATAC-seq, and proteomics to investigate gene expression, chromatin accessibility, and protein expression between male and female mouse proximal tubules. This study identifies a large number of sex-biased genes and proteins associated with various kidney functions, including metabolism and transport processes. The authors demonstrate that sex differences may also arise from differences in interaction between transcription factors and accessible chromatin regions. A comprehensive web resource is provided to the research community to advance understanding of sex differences.

2023-05-05 | PXD037098 | Pride

Reduced polymerase pausing compensates for increased chromatin accessibility in the aging liver

Project description:Regulation of gene expression is linked to the organization of the genome. With age, chromatin alterations occur on all levels of genome organization, accompanied by changes in the gene expression profile. However, little is known about the changes on the level of transcriptional regulation. Here, we used a multi-omics approach and integrated ATAC-, RNA- and NET-seq to identify age-related changes in the chromatin landscape of murine liver and to investigate how these are linked to transcriptional regulation. We provide the first systematic inventory of the connection between aging, chromatin accessibility and transcriptional regulation in a whole tissue. Aging in murine liver is characterized by an increase in chromatin accessibility at promoter regions, but not in an increase of transcriptional output. Instead, aging is accompanied by a decrease of promoter-proximal pausing of RNA polymerase II (Pol II). We propose that these changes in transcriptional regulation are due to a reduced stability of the pausing complex and may represent a mechanism to compensate for the age-related increase in chromatin accessibility in order to prevent aberrant transcription.

2022-09-15 | PXD034564 | Pride

The molecular basis of socially-mediated phenotypic plasticity in a eusocial paper wasp

Project description:We report analyses the individual-level brain gene expression profiles of Polistes dominula paper wasps following the loss of a queen, a perturbation that induces some individuals to undergo a significant phenotypic shift and become queens while others maintain an apparently unchanged worker phenotype. We use a machine learning approach to map individual transcriptomes on a continuum between worker and queen states and then match these scores to detailed phenotypic data. We find a strong response of caste-associated gene expression to queen loss, with individuals’ expression profiles becoming intermediate between queen and worker states.

2020-12-23 | GSE153532 | GEO

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