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

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

PROVIDER: PRJNA853272 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19866068_1.fastq.gz	Fastqsanger.gz
	SRR19866068_2.fastq.gz	Fastqsanger.gz
	SRR19866069_1.fastq.gz	Fastqsanger.gz
	SRR19866069_2.fastq.gz	Fastqsanger.gz
	SRR19866070_1.fastq.gz	Fastqsanger.gz

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Chromatin Accessibility-Based Characterization of the Gene Regulatory Networks Underpinning Phenotypic Plasticity in the Honey Bee

Project description:Chromatin Accessibility-Based Characterization of the Gene Regulatory Networks Underpinning Phenotypic Plasticity in the Honey Bee

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

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

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

2022-11-09 | GSE206991 | GEO

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

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

| PRJNA853271 | ENA

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

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

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The IRE1 Pathway Regulates Honey Bee Unfolded Protein Response Gene Expression

Project description:Our molecular understanding of honey bee cellular stress responses is incomplete. Previously, we sought to identify and began functional characterization of the components of the UPR in honey bees. We observed that UPR stimulation resulted in induction of target genes upon and IRE1 pathway activation, as assessed by splicing of Xbp1 mRNA. However, were not able to determine the relative role of the various UPR pathways in gene activation. Our understanding of honey bee signal transduction and transcriptional regulation has been hampered by a lack of tools. After using RNAseq to expand the known UPR targets in the bee, we use the Drosophila melanogaster S2 cell line and honey bee trans and cis elements to investigate the role of the IRE-1 pathway in the transcriptional activation of one of these targets, the honey bee Hsc70-3 gene. Using a luciferase reporter, we show that honey bee hsc70 promoter activity is inducible by UPR activation. In addition, we show that this activation is IRE1-dependent and relies on specific cis regulatory elements. Experiments using exogenous honey bee or fruit fly XBP1S proteins demonstrate that both factors can activate the Hsc70-3 promoter and further support a role for the IRE-1 pathway in control of its expression in the honey bee. By providing foundational knowledge about the UPR in the honey bee and demonstrating the usefulness of a heterologous cell line for molecular characterization of honey bee pathways, this work stands to improve our understanding of this critical species.

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Recipe for a busy bee: MicroRNAs in honey bee caste determination (microRNA array)

Project description:Social caste determination in the honey bee is assumed to be determined by the dietary status of the young larvae and translated into physiological and epigenetic changes through nutrient-sensing pathways. We have employed microRNA gene-microarray, and observed that both worker jelly and royal jelly showed dynamic changes in miRNA content during the 4th to 6th day of larval development . Adding specific miRNAs to royal jelly elicited significant changes in queen larval mRNA expression and in morphological characters of the emerging adult queen bee. We propose that miRNAs in the nurse bee secretions constitute an additional element in the regulatory control of caste determination in the honey bee.

2013-12-31 | GSE50457 | GEO

Recipe for a busy bee: MicroRNAs in honey bee caste determination

Project description:Social caste determination in the honey bee is assumed to be determined by the dietary status of the young larvae and translated into physiological and epigenetic changes through nutrient-sensing pathways. We have employed Illumina/Solexa sequencing to examine the small RNA content in the bee larval food source, and show that worker jelly is enriched in miRNA complexity and abundance relative to royal jelly. The miRNA levels in worker jelly were 7-215 fold higher than in royal jelly, and both jellies showed dynamic changes in miRNA content during the 4th to 6th day of larval development. Adding specific miRNAs to royal jelly elicited significant changes in queen larval mRNA expression and in morphological characters of the emerging adult queen bee. We propose that miRNAs in the nurse bee secretions constitute an additional element in the regulatory control of caste determination in the honey bee.

2014-01-06 | GSE44853 | GEO

Transcriptome of honey bee larvae

Project description:Honey bee drones, queens and workers have vastly different phenotypes. Here we profile the the expression level of mRNAs and microRNAs of honeybee, drones, queens and workers at the L5 larval stage (91 hours +/- 1).

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