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A new model for long-range chromatin reorganisation linked to enhancer activation [ChIP-chip]

ABSTRACT: A new model for long-range chromatin reorganisation linked to enhancer activation [ChIP-chip]

PROVIDER: PRJNA475629 | ENA |

REPOSITORIES: ENA

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A new model for long-range chromatin reorganisation linked to enhancer activation [ChIP-chip]

Project description:The most prominent model for long-range enhancer regulation involves direct enhancer-promoter interaction by looping out the intervening chromatin. Using a synthetic biology approach, we have determined that a chromatin unfolding between Shh and its enhancers is regulated specifically by the Shh-Brain-Enhancers and is mediated by the recruitment of Poly (ADP-Ribose) Polymerase 1. This ‘chromatin unfolding’ model represents a new mechanism of long-range enhancer-promoter communication in addition to the looping and tracking models. ChIP-on-chip for H3K27me3 and H3K27ac on the Shh regulatory region on ESCs and transfected ESCs showed a gain of H3k27ac specifically on active enhancers and no loss of Polycomb marks upon Shh activation.

2018-12-01 | GSE115642 | GEO

A new model for long-range chromatin reorganization linked to enhancer activation [Agilent_ChIP]

Project description:The most prominent model for long-range enhancer regulation involves direct enhancer-promoter interaction by looping out the intervening chromatin. Using a synthetic biology approach, we have determined that a chromatin unfolding bteween Shh and its enhancers is regulated specifically by the Shh-Brain-Enhancers and is mediated by the recruitment of Poly (ADP-Ribose) Polymerase 1. This ‘chromatin unfolding’ model represents a new mechanism of long-range enhancer-promoter communication in addition to the looping and tracking models. ChIP-on-chip for H3K27me3 on the Shh regulatory region on ESCs and transfected ESCs and NPC showed no loss of Polycomb marks upon Shh activation.

2016-11-04 | GSE89550 | GEO

A new model for long-range chromatin reorganization linked to enhancer activation

Project description:A new model for long-range chromatin reorganization linked to enhancer activation

| PRJNA352538 | ENA

A new model for long-range chromatin reorganization linked to enhancer activation [Agilent_RNA]

Project description:The most prominent model for long-range enhancer regulation involves direct enhancer-promoter interaction by looping out the intervening chromatin. Using a synthetic biology approach, we have determined that a chromatin unfolding bteween Shh and its enhancers is regulated specifically by the Shh-Brain-Enhancers and is mediated by the recruitment of Poly (ADP-Ribose) Polymerase 1. This ‘chromatin unfolding’ model represents a new mechanism of long-range enhancer-promoter communication in addition to the looping and tracking models. RNA-on-chip for probing nuclear RNA on the Shh regulatory region on ESCs and NPC showed no spreading of nuclear RNA in the regulatory region upon Shh activation.

2016-11-04 | GSE89515 | GEO

A new model for long-range chromatin reorganization linked to enhancer activation [5C]

Project description:The most prominent model for long-range enhancer regulation involves direct enhancer-promoter interaction by looping out the intervening chromatin. Using a synthetic biology approach, we have determined that a chromatin unfolding bteween Shh and its enhancers is regulated specifically by the Shh-Brain-Enhancers and is mediated by the recruitment of Poly (ADP-Ribose) Polymerase 1. This ‘chromatin unfolding’ model represents a new mechanism of long-range enhancer-promoter communication in addition to the looping and tracking models. Using 5C study the enhancer-driven activation of the Sonic hedgehog gene (Shh)

2016-11-02 | GSE89388 | GEO

Nucleosome reorganisation in breast cancer tissues

Project description:Nucleosome reorganisation in breast cancer tissues

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A new model for long-range chromatin reorganization linked to enhancer activation

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-11-04 | GSE89557 | GEO

3D genome structures of single differentiating mouse ES cells reveal a unique reorganisation of chromatin in the formative state

Project description:Pluripotency is the ability of an embryonic stem (ES) cell to differentiate into all the different cell lineages of a mature organism. Naïve and primed pluripotent ES cells in vitro correspond to the pre- and post-implantation populations in the embryo, and they are developmentally linked to each other via progression through a ‘formative’ transition state where naïve ES cells mature in response to inductive cues prior to becoming specified towards certain cell fates. Studying the formative state is thus crucial for understanding the mechanisms of multi-lineage decision-making. Here we show that in the formative state there is a profound reorganisation of 3D genome structure, where genes whose expression levels are changing become located in multi-way chromatin hubs and highly intermingled regions of the genome. Our results suggest that the reorganisation of 3D genome structure is driven by changes in DNA methylation and Polycomb-mediated heterochromatin formation, which is accompanied by a global increase in transcriptional bursting, leading to a reconfiguration of enhancer-promoter interactions – consistent with changes in the epigenome priming promoters for lineage specific gene expression.

2024-01-19 | GSE214264 | GEO

Long-range Pitx2c Enhancer Promoter Interactions Prevent Predisposition to Atrial Fibrillation [ChIP-seq]

Project description:Long-range Pitx2c Enhancer Promoter Interactions Prevent Predisposition to Atrial Fibrillation [ChIP-seq]

| PRJNA576256 | ENA

Long-range Pitx2c Enhancer Promoter Interactions Prevent Predisposition to Atrial Fibrillation [ChIP-seq]

Project description:Genome-wide association studies (GWAS) have found that increased risk for atrial fibrillation (AF), the most common type of arrhythmia in humans, is associated with non-coding sequence variants located in proximity to the PITX2 homeobox gene. Using cardiomyocyte-specific epigenomic and comparative genomic analyses, we identified two AF-associated enhancers neighboring PITX2 with varying degrees of conservation in mice. Pitx2c promoter directly contacted the AF-associated enhancer regions. CRISPR/Cas9 mediated deletion of a 20 kb long topologically engaged enhancer lead to reduced Pitx2c transcription and AF predisposition. Allele-specific ChIP-seq and CUT&RUN experiments showed that long-range interaction of this AF-associated region with the Pitx2c promoter was required for maintenance of the Pitx2c promoter chromatin state. Moreover, long-range looping was mediated by CTCF, as the genetic disruption of an intronic CTCF binding site caused decreased Pitx2c cardiac expression, AF predisposition, and reduced active chromatin marks on Pitx2. Our findings reveal that AF risk variants located at 4q25 reside in genomic regions possessing long-range transcriptional regulatory functions directed at PITX2

2019-10-08 | GSE138528 | GEO

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