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Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation [III]

ABSTRACT: Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation [III]

PROVIDER: PRJNA903167 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22334317_1.fastq.gz	Fastqsanger.gz
	SRR22334317_2.fastq.gz	Fastqsanger.gz
	SRR22334318_1.fastq.gz	Fastqsanger.gz
	SRR22334318_2.fastq.gz	Fastqsanger.gz
	SRR22334319_1.fastq.gz	Fastqsanger.gz

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Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation [III]

Project description:During intestinal organogenesis, equipotent epithelial progenitors mature into phenotypically distinct stem cells that are responsible for life-long maintenance of the tissue. While the morphological changes associated with the transition are well-characterized, the molecular mechanisms underpinning the maturation process are not fully understood. Here, we leverage intestinal organoid cultures to profile transcriptional, chromatin accessibility, DNA methylation and 3D chromatin conformation landscapes defining fetal and adult epithelial cells. We observed prominent differences in gene expression and enhancer activity, accompanied by changes in 3D organization and local changes in DNA accessibility and methylation, between the two cellular states. Using integrative analyses, we identified sustained YAP transcriptional activity as a major gatekeeper of the immature fetal state. We found the YAP-associated transcriptional network to be regulated at various levels of chromatin organization, and likely to be coordinated by changes in extracellular matrix composition. Altogether, our work highlights the value of unbiased profiling of regulatory landscapes for the identification of key mechanisms underlying tissue maturation.

2023-07-13 | GSE218333 | GEO

Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation

Project description:Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation

| PRJNA950090 | ENA

Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation [IV]

Project description:Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation [IV]

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Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation [I]

Project description:Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation [I]

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Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation [II]

Project description:Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation [II]

| PRJNA685170 | ENA

Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation

Project description:During intestinal organogenesis, equipotent epithelial progenitors mature into phenotypically distinct stem cells that are responsible for life-long maintenance of the tissue. While the morphological changes associated with the transition are well-characterized, the molecular mechanisms underpinning the maturation process are not fully understood. Here, we leverage intestinal organoid cultures to profile transcriptional, chromatin accessibility, DNA methylation and 3D chromatin conformation landscapes in fetal and adult epithelial cells. We observed prominent differences in gene expression and enhancer activity, which are accompanied by local changes in 3D organization, DNA accessibility and methylation, between the two cellular states. Using integrative analyses, we identified sustained YAP transcriptional activity as a major gatekeeper of the immature fetal state. We found the YAP-associated transcriptional network to be regulated at various levels of chromatin organization, and likely to be coordinated by changes in extracellular matrix composition. Altogether, our work highlights the value of unbiased profiling of regulatory landscapes for the identification of key mechanisms underlying tissue maturation.

2023-07-13 | GSE228519 | GEO

Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation [II]

Project description:During intestinal organogenesis, equipotent epithelial progenitors mature into phenotypically distinct stem cells that are responsible for life-long maintenance of the tissue. While the morphological changes associated with the transition are well-characterized, the molecular mechanisms underpinning the maturation process are not fully understood. Here, we leverage intestinal organoid cultures to profile transcriptional, chromatin accessibility, DNA methylation and 3D chromatin conformation landscapes in fetal and adult epithelial cells. We observed prominent differences in gene expression and enhancer activity, which are accompanied by local changes in 3D organization, DNA accessibility and methylation, between the two cellular states. Using integrative analyses, we identified sustained YAP transcriptional activity as a major gatekeeper of the immature fetal state. We found the YAP-associated transcriptional network to be regulated at various levels of chromatin organization, and likely to be coordinated by changes in extracellular matrix composition. Altogether, our work highlights the value of unbiased profiling of regulatory landscapes for the identification of key mechanisms underlying tissue maturation.

2023-07-13 | GSE163191 | GEO

Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation [I]

Project description:During intestinal organogenesis, equipotent epithelial progenitors mature into phenotypically distinct stem cells that are responsible for life-long maintenance of the tissue. While the morphological changes associated with the transition are well-characterized, the molecular mechanisms underpinning the maturation process are not fully understood. Here, we leverage intestinal organoid cultures to profile transcriptional, chromatin accessibility, DNA methylation and 3D chromatin conformation landscapes in fetal and adult epithelial cells. We observed prominent differences in gene expression and enhancer activity, which are accompanied by local changes in 3D organization, DNA accessibility and methylation, between the two cellular states. Using integrative analyses, we identified sustained YAP transcriptional activity as a major gatekeeper of the immature fetal state. We found the YAP-associated transcriptional network to be regulated at various levels of chromatin organization, and likely to be coordinated by changes in extracellular matrix composition. Altogether, our work highlights the value of unbiased profiling of regulatory landscapes for the identification of key mechanisms underlying tissue maturation.

2023-07-13 | GSE160449 | GEO

Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation [IV]

Project description:During intestinal organogenesis, equipotent epithelial progenitors mature into phenotypically distinct stem cells that are responsible for life-long maintenance of the tissue. While the morphological changes associated with the transition are well-characterized, the molecular mechanisms underpinning the maturation process are not fully understood. Here, we leverage intestinal organoid cultures to profile transcriptional, chromatin accessibility, DNA methylation and 3D chromatin conformation landscapes in fetal and adult epithelial cells. We observed prominent differences in gene expression and enhancer activity, which are accompanied by local changes in 3D organization, DNA accessibility and methylation, between the two cellular states. Using integrative analyses, we identified sustained YAP transcriptional activity as a major gatekeeper of the immature fetal state. We found the YAP-associated transcriptional network to be regulated at various levels of chromatin organization, and likely to be coordinated by changes in extracellular matrix composition. Altogether, our work highlights the value of unbiased profiling of regulatory landscapes for the identification of key mechanisms underlying tissue maturation.

2023-07-13 | GSE230581 | GEO

The effect of YAP/TAZ knockdown on the intestinal epithelium

Project description:The Hippo pathway plays a crucial in organ size control during development and tissue homeostasis in adult life. To examine a role for Hippo signaling in the intestinal epithelium, we analyzed gene expression patterns in the mouse intestinal epithelilum transfected with siRNAs or expression plasmids for shRNAs targeting the Hippo pathway effectors, YAP and TAZ. We performed two independent series of experiments (siGFP (n=3) vs siYAP/siTAZ (n=3), and shLacZ (n=1) vs shYAP/shTAZ (n=1)). Control siRNA (siGFP), YAP/TAZ siRNAs, or expression plasmids for control shRNA (shLacZ) or YAP/TAZ shRNAs were introduced into the mouse intestinal epithelium by the newly-developed in vivo transfection method. Four days after transfection, intestinal epithelial cells were isolated from the tissues and total RNA was extracted.

2014-07-18 | E-GEOD-45155 | biostudies-arrayexpress

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