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Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha (Mouse ChIP-seq, RNA-seq, and DNase-seq)

ABSTRACT: We profiled transcriptome and chromatin landscapes in jejunal mouse intestinal epithelial cells (IECs) from mice reared in the absence (Germ Free or GF) or presence (Conventionalized or CV) of microbiota. We show that microbiota colonization results in changes in histone modifications at hundreds of enhancers that are associated with microbiota-regulated genes. Furthermore, we show that microbiota colonization is associated with a drastic genome-wide reduction in Hnf4a and Hnf4g binding.

ORGANISM(S): Mus musculus

PROVIDER: GSE90461 | GEO | 2017/03/27

SECONDARY ACCESSION(S): PRJNA354705

REPOSITORIES: GEO

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Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha (zebrafish RNA-seq)

Project description:We performed RNA-seq from 6 days post fertilization hnf4a-/- and hnf4a+/+ zebrafish larval digestive tracts raised in the absence (Germ Free, GF) or presence (Conventionalized, CV) of microbiota. We found that zebrafish hnf4a activates almost half of the microbiota-suppressed genes, indicating that the microbiota supress Hnf4a trans-activity. We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis.

2017-03-27 | GSE90446 | GEO

Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape

Project description:We profiled transcriptome and accessible chromatin landscapes in intestinal epithelial cells (IECs) from mice reared in the presence or absence of microbiota. We show that regional differences in gene transcription along the intestinal tract were accompanied by major alterations in chromatin organization. Surprisingly, we discovered that microbiota modify host gene transcription in IECs without significantly impacting the accessible chromatin landscape. Instead, microbiota regulation of host gene transcription might be achieved by differential expression of specific TFs and enrichment of their binding sites in nucleosome depleted CRRs near target genes. Our results suggest that the chromatin landscape in IECs is pre-programmed by the host in a region-specific manner to permit responses to microbiota through binding of open CRRs by specific TFs. mRNA and accessible chromatin (DNase-seq) profiles from colonic and ileal IECs were compared between conventionally-raised (CR), germ-free (GF), and conventionalized (CV) C57BL/6 mice.

2014-06-07 | E-GEOD-57919 | biostudies-arrayexpress

Transcriptional integration of separated and simultaneous microbial and nutritional signals by the intestinal epithelium

Project description:We performed RNA-seq, H3K27ac ChIP-seq, and HNF4a ChIP-seq on jejunal intestinal epithelial cells, which are primarily responsible for the absorption of fatty acids, in four conditions: Germ-free (GF), Germ-free plus high fat meal (GF+HFM), ex-GF colonized with a conventional microbiota for 2 weeks (Colonized, CV), and Colonized plus high fat meal (CV+HFM). We, for the first time, map genomewide HFM responsive regulatory regions in the intestine. We identify that in the absence of microbes the HNF4a transcriptional program supports a FAO program in enterocytes while suppressing a proliferation program.

2022-02-22 | GSE185835 | GEO

Interaction between microbiota and development of the olfactory system in Zebrafish

Project description:Olfactory systems are one of the most conserved and ancient sensory systems in vertebrates. The vertebrate olfactory epithelium is colonized by complex communities of commensal microorganisms, but their impact on olfactory epithelial development and function remains unknown. Using germ-free zebrafish model, we aim to understand the transcriptional responses that colonization with a microbiota induces in olfactory organs. This study was aimed to understand the changes in gene expression in the olfactory organ of Germ Free (GF) zebrafish compared to conventionalized (ConvD) zebrafish. This experiment is related to E-MTAB-5046 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5046)

2021-02-04 | E-MTAB-5045 | biostudies-arrayexpress

Interaction between microbiota and development of the olfactory system in mouse

Project description:Olfactory systems are one of the most conserved and ancient sensory systems in vertebrates. The vertebrate olfactory epithelium is colonized by complex communities of commensal microorganisms, but their impact on olfactory epithelial development and function remains unknown. Using germ-free mouse model, we aim to understand the transcriptional responses that colonization with a microbiota induces in olfactory organs. This study was aimed to understand the changes in gene expression in the nose of Germ Free (GF) mice compared to conventionalized (ConvD) mice. This experiment is related to E-MTAB-5045 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5045)

2021-02-04 | E-MTAB-5046 | biostudies-arrayexpress

Zebrafish response to microbiota

Project description:Vertebrates are colonized at birth by complex microbial communities (microbiota) that influence diverse aspects of host biology. We have used a functional genomics approach to identify zebrafish genes that are differentially expressed in response to the microbiota. We assessed RNA expression profiles from zebrafish larvae at 6 days post-fertilization (dpf) that were either raised continuously in the absence of any microorganism (germ-free or GF), or raised GF through 3dpf then colonized with a normal zebrafish microbiota (conventionalized or CONVD).

2010-01-01 | GSE16857 | GEO

Muc2-dependent microbial colonization of the jejunal mucus layer is diet sensitive and confers resistance to enteric pathogen infection

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2023-05-12 | PXD028613 | Pride

Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response

Project description:The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA-sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g-/- zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type, hnf4g-/-, and hnf4a-/-;hnf4g-/- zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10-15 pooled gastrointestinal tracts, and 4 biological replicates per treatment group were sequenced.

2022-09-01 | GSE183799 | GEO

Transcription profiling of mouse myocardium from gnotobiotic wild-type and Ppara-/- animals

Project description:Germ free (GF) and conventionalized (CONV-D) wild-type C57Bl/6 male mice in the CARB-fed, 24h fasted, and 30d trained states; plus GF and CONV-D CARB-fed Ppara-/- mice. CARB-fed indicates a standard polysaccharide-rich mouse chow diet. CONV-D mice are those that received a microbiota transplant from conventionally raised mice 2-3 weeks before experiment was initiated Experiment Overall Design: Hearts from six to ten week-old GF and CONV-D mice, from the following eight treatment groups (GF, CONV-D) X (CARB-fed [wild-type], 24h fast [wild-type], 30d trained [wild-type], Ppara-/- [CARB-fed])

2009-07-01 | E-GEOD-14929 | biostudies-arrayexpress

Myocardial expression data from gnotobiotic wild-type and Ppara-/- mice

2009-06-23 | GSE14929 | GEO

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