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Progressing enhancer landscape during mammary differentiation controls gene regulation [ChIP-seq]

ABSTRACT: The mammary luminal lineage relies on the common cytokine-sensing transcription factor STAT5 to establish super-enhancers during pregnancy and activate mammary genes required for the nutrition of the offspring. Exploiting progressive differentiation during lactation, we investigated how hormonal cues shape an evolving enhancer landscape and impact the biology of mammary cells. Employing ChIP-seq, we uncover a changing transcription factor occupancy at mammary enhancers. Using mouse genetics, we demonstrate changing biological properties of enhancers as lactation progresses, with individual enhancers gaining strength and an abolished need for the Wap seed enhancer. We further investigated whether permissive chromatin facilitates cell-specific transcription factor binding. Wap enhancers translocated into the widely expressed neighboring Ramp3 gene retained their mammary-specificity and failed to activate the receptive Ramp3 gene in non-mammary tissues. Our studies unveil a previously unrecognized progressive enhancer landscape, in which structurally equivalent components serve unique and differentiation-specific functions. While enhancer redundancy has been suggested and demonstrated for many genes, components of the cytokine-responsive mammary tripartite Wap super-enhancer display a remarkable specificity.

ORGANISM(S): Mus musculus

PROVIDER: GSE115368 | GEO | 2018/09/18

REPOSITORIES: GEO

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Progressing enhancer landscape during mammary differentiation controls gene regulation [RNA-seq]

Project description:The mammary luminal lineage relies on the common cytokine-sensing transcription factor STAT5 to establish super-enhancers during pregnancy and activate mammary genes required for the nutrition of the offspring. Exploiting progressive differentiation during lactation, we investigated how hormonal cues shape an evolving enhancer landscape and impact the biology of mammary cells. Employing ChIP-seq, we uncover a changing transcription factor occupancy at mammary enhancers. Using mouse genetics, we demonstrate changing biological properties of enhancers as lactation progresses, with individual enhancers gaining strength and an abolished need for the Wap seed enhancer. We further investigated whether permissive chromatin facilitates cell-specific transcription factor binding. Wap enhancers translocated into the widely expressed neighboring Ramp3 gene retained their mammary-specificity and failed to activate the receptive Ramp3 gene in non-mammary tissues. Our studies unveil a previously unrecognized progressive enhancer landscape, in which structurally equivalent components serve unique and differentiation-specific functions. While enhancer redundancy has been suggested and demonstrated for many genes, components of the cytokine-responsive mammary tripartite Wap super-enhancer display a remarkable specificity.

2018-09-18 | GSE115369 | GEO

Facultative CTCF sites moderate mammary super-enhancer activity and regulate juxtaposed gene in non-mammary cells [RNA-seq]

Project description:Precise spatiotemporal regulation of genetic programs, driven by cellspecific super-enhancers, is paramount for the function of cell lineages. Studies have suggested that insulated neighborhoods, formed by the zincfinger protein CTCF, sequester genes and their associated enhancers thus preventing them from trespassing on off-target genes. Although this could explain the enhancer-gene-specificity conundrum, there is limited genetic evidence that the search space of cell-specific super-enhancers is constrained by CTCF. We have addressed this question in the Wap locus with its exceptional mammary-specific super-enhancer, which is separated by five CTCF sites from neighboring genes. Three of these sites are positioned between the Wap super-enhancer and the widely expressed Ramp3. Enhancer deletions demonstrated that the Wap super-enhancer controls Ramp3 expression despite the presence of three parting CTCF sites. Individual and combinatorial deletions of these CTCF sites revealed cell-specific functions of the conserved anchor site. Although unable to block super-enhancer activity, it muffled its impact on Ramp3 in mammary tissue. Unexpectedly, this CTCF site was obligatory for Ramp3 expression in cerebellum, suggesting the coinciding presence of regulatory elements. While our results suggest a surprisingly limited in vivo role for a CTCF anchor in blocking a mammary-specific super-enhancer, they also implicate this site in cerebellum-specific gene activation. Our study illustrates additional complexities of CTCF sites supporting tissue-specific functions.

2017-05-25 | GSE92931 | GEO

Facultative CTCF sites moderate mammary super-enhancer activity and regulate juxtaposed gene in non-mammary cells [ChIP-seq]

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Facultative CTCF sites moderate mammary super-enhancer activity and regulate juxtaposed gene in non-mammary cells [4C-seq]

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Interdependence of a mammary-specific super-enhancer and its native promoter facilitates gene activation during pregnancy

Project description:Lineage-specific genetic programs rely on cell-restricted super-enhancers, platforms for high-density occupation by transcription factors. It is not known whether super-enhancers synergize specifically with their native promoters or provide autonomous regulatory platforms. Here we investigate the ability of the mammary Wap super-enhancer to activate the promoter of the juxtaposed and ubiquitously expressed Tbrg4 gene in the mouse mammary gland. The Wap super-enhancer was fused, by itself or in combination with its promoter, with the Tbrg4 gene. While the Wap super-enhancer activated the Tbrg4 promoter five-fold, the combination of Wap super-enhancer and promoter resulted in an 80-fold gene activation, demonstrating lineage-specific promoter-enhancer synergy. Employing ChIP-seq profiling, we uncover a chromatin platform permissive for high level expression that develops in the native promoter-enhancer context but not with a heterologous promoter. Post-transcriptional mechanisms through the Wap 3’UTR have been proposed to account for the exceptional high mRNA levels during lactation, but our mouse genetic experiments failed to support this. Lastly, we discovered that the CREB transcription factor is an integral part of the Tbrg4 promoter but not essential for its function. Taken together, our data reveal that lineage-specific enhancer-promoter synergy is critical for mammary gene regulation during pregnancy and lactation.

2020-03-24 | GSE145193 | GEO

Hierarchy within the mammary STAT5-driven Wap super-enhancer

Project description:Super-enhancers comprise of dense transcription factor platforms highly enriched for active chromatin marks. A paucity of functional data led us to investigate their role in the mammary gland, an organ characterized by exceptional gene regulatory dynamics during pregnancy. ChIP-Seq for the master regulator STAT5, the glucocorticoid receptor, H3K27ac and MED1, identified 440 mammary-specific super-enhancers, half of which were associated with genes activated during pregnancy. We interrogated the Wap super-enhancer, generating mice carrying mutations in STAT5 binding sites within its three constituent enhancers. Individually, only the most distal site displayed significant enhancer activity. However, combinatorial mutations showed that the 1,000-fold gene induction relied on all enhancers. Disabling the binding sites of STAT5, NFIB and ELF5 in the proximal enhancer incapacitated the entire super-enhancer, suggesting an enhancer hierarchy. The identification of mammary-specific super-enhancers and the mechanistic exploration of the Wap locus provide insight into the complexity of cell-specific and hormone-regulated genes. ChIP-Seq for STAT5A, GR, H3K27ac, MED1, NFIB, ELF5, RNA Pol II, and H3K4me3 in wild type (WT) mammary tissues at day one of lactation (L1), and ChIP-Seq for STAT5A, GR, H3K27ac, MED1, NFIB, ELF5, and H3K4me3 in WT mammary tissues at day 13 of pregnancy (p13). ChIP-Seq for STAT5A, GR, H3K27a in Wap-delE1a, -delE1b, -delE1c, -delE2 and -delE3 mutant mammary tissues at L1, and ChIP-Seq for NFIB and ELF5 in Wap-delE1b and -delE1c mutant mammary tissues at L1. ChIP-Seq for H3K4me3 in mammary-epthelial cells at p13 and L1. DNase-seq in WT mammary tissues at L1 and DNase-seq in Wap-delE1a, -delE1c, and -delE3 mutant mammary tissues at L1.

2016-05-31 | E-GEOD-74826 | biostudies-arrayexpress

Lineage-specific super-enhancer activates genes in a promoter-selective manner

Project description:Lineage-specific genetic programs rely on cell-restricted super-enhancers but it is not clear whether they selectively engage with their associated promoters to attain maximum activity. Exploiting the highly expressed Wap gene, we investigate the relative contributions of the super-enhancer and promoter in mammary tissue during lactation. Employing ChIP-seq profiling and mouse genetics, we uncover a selective lineage-specific promoter-enhancer synergy. Mechanistically, a chromatin platform permissive for high level expression develops in the native promoter-enhancer configuration but not with a heterologous promoter. While this promoter-enhancer synergy permits the induction of gene expression during pregnancy, post-transcriptional mechanisms need to be invoked to account for the high levels of Wap mRNA during lactation. Taken together, our data reveal that lineage-specific enhancer-promoter synergy and post-transcriptional regulation are critical for mammary gene regulation during pregnancy and lactation.

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Hierarchy within the mammary STAT5-driven Wap super-enhancer

2016-05-31 | GSE74826 | GEO

Functional dissection of the Csn1s2b locus identifies complex redundant and non-redundant cytokine-activated enhancers in mouse mammary gland tissue

Project description:Enhancers are transcription factor platforms that synergize with promoters to activate gene expression. While genome-wide chromatin studies can predict enhancers, only experimental genetics can reveal their in vivo significance and the respective contribution of individual transcription factors. Here we investigate the regulation of the Csn1s2b gene whose expression in the mouse mammary gland is induced several thousand-fold during pregnancy and lactation. Using ChIP-seq for activating histone marks and transcription factors, we identified candidate enhancers distal to the promoter and within an intron and one super-enhancer separated from the Csn1s2b gene by the Prr27 gene. Using experimental mouse genetics, we dissected the complex lactation-specific distal enhancer bound by the prolactin-activated transcription factor STAT5 and the mammary-enriched NFIB and the glucocorticoid receptor. Deletion of the canonical binding motifs for NFIB and STAT5, individually and combined, had a limited biological impact. Additional deletions revealed the importance of a non-canonical STAT5 binding site for enhancer activity throughout lactation. In contrast, the intronic enhancer activated gene expression only in late pregnancy and early lactation, likely by interacting with the distal enhancer. A downstream super-enhancer, which physically interacts with the distal enhancer, was required for the functional establishment of the Csn1s2b promoter and gene activation. Lastly, NFIB binding in the promoter region fine-tuned Csn1s2b expression. Our study provides comprehensive insight into the anatomy and biology of regulatory elements spanning 70 bp that employ the JAK/STAT signaling pathway and activate gene expression several hundred-fold during lactation.

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Expression profiling on lactation day 2 mammary epithelial cells from constitutive miR-150 expressing mice compared to controls.

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