An eRNA Transcription Checkpoint For Diverse Signal-dependent Enhancer Activation Programs [ATAC-Seq]
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE277381 | GEO | 2024/09/18
REPOSITORIES: GEO
Similar Datasets
Project description:The evidence that several signal and ligand-dependent pathways function by activating regulatory enhancer programs suggests that a “checkpoint” strategy may underline activation of some or even many diversely-regulated enhancers. Here, we report a molecular mechanism common to several acute signal- and ligand-dependent enhancer activation programs based on release of a shared eRNA transcription checkpoint. This requires recruitment of a DNA-PKcs-phosphorylated RING finger repressor, KAP1, functioning as a modulator, inhibiting its association with 7SK and E3 SUMO ligase activity on the CDK9 subunit of P-TEFb, facilitating formation of an activated P-TEFb complex, licensing eRNA elongation. Overcoming this checkpoint for signal-dependent enhancer activation occurs in diverse pathways including estrogen receptor α, NF-κB-regulated proinflammatory, androgen receptor and neuronal depolarization. Therefore, a specific strategy required to convert a basal state enhancer P-TEFb complex to an active state to release a conserved checkpoint is apparently employed by several functionally-important signal/ligand-regulated regulatory enhancers to implement the instructions of endocrine/paracrine system.
2024-09-18 | GSE277391 | GEO
Project description:The evidence that several signal and ligand-dependent pathways function by activating regulatory enhancer programs suggests that a “checkpoint” strategy may underline activation of some or even many diversely-regulated enhancers. Here, we report a molecular mechanism common to several acute signal- and ligand-dependent enhancer activation programs based on release of a shared eRNA transcription checkpoint. This requires recruitment of a DNA-PKcs-phosphorylated RING finger repressor, KAP1, functioning as a modulator, inhibiting its association with 7SK and E3 SUMO ligase activity on the CDK9 subunit of P-TEFb, facilitating formation of an activated P-TEFb complex, licensing eRNA elongation. Overcoming this checkpoint for signal-dependent enhancer activation occurs in diverse pathways including estrogen receptor α, NF-κB-regulated proinflammatory, androgen receptor and neuronal depolarization. Therefore, a specific strategy required to convert a basal state enhancer P-TEFb complex to an active state to release a conserved checkpoint is apparently employed by several functionally-important signal/ligand-regulated regulatory enhancers to implement the instructions of endocrine/paracrine system.
2024-09-18 | GSE277380 | GEO
Project description:While many or most signal and ligand-dependent pathways function by directing binding of specific transcription factors to large cohorts of regulatory enhancers, the possible “universal” strategies underling activation of these lorge enhancer programs by diverse signals remains poorly understood. Here, we report that ligands, exemplified by estrogen-17-b (E2), cause the recruitment of DNA-PKcs-phosphorylated KAP1 to estrogen receptor a (ERa)-bound enhancers, inhibiting its E3 SUMO ligase activity for the CDK9 subunit of P-TEFb, which permits formation of active P-TEFb required for eRNA elongation overcoming this checkpoint and permitting enhancer activation. We find that most, or all, signal and ligand enhancer activation programs similarly require the loss of SUMOligase function by phoshorylation of KAP1 to prevent Pol II pausing at regulated enhancers. This is based on activation of P-TEFb consequent to deSUMOylation of CDK9, permitting eRNA synthesis. Overcoming this checkpoint appears to be a widely, if not universally, used strategy for signal-dependent enhancer activation because similar events occur on AR and NF-kB-regulated enhancers and even following depolarization acutely-activated neuronal enhancers. This study reveals an unexpected strategy required to overcome a checkpoint common to most or all signal/ligand-regulated enhancers critical to activate broad programs of biologically-important regulatory enhancers that implement the instructions of the endocrine system.
2024-09-17 | GSE240598 | GEO
Project description:While many or most signal and ligand-dependent pathways function by directing binding of specific transcription factors to large cohorts of regulatory enhancers, the possible “universal” strategies underling activation of these lorge enhancer programs by diverse signals remains poorly understood. Here, we report that ligands, exemplified by estrogen-17-b (E2), cause the recruitment of DNA-PKcs-phosphorylated KAP1 to estrogen receptor a (ERa)-bound enhancers, inhibiting its E3 SUMO ligase activity for the CDK9 subunit of P-TEFb, which permits formation of active P-TEFb required for eRNA elongation overcoming this checkpoint and permitting enhancer activation. We find that most, or all, signal and ligand enhancer activation programs similarly require the loss of SUMOligase function by phoshorylation of KAP1 to prevent Pol II pausing at regulated enhancers. This is based on activation of P-TEFb consequent to deSUMOylation of CDK9, permitting eRNA synthesis. Overcoming this checkpoint appears to be a widely, if not universally, used strategy for signal-dependent enhancer activation because similar events occur on AR and NF-kB-regulated enhancers and even following depolarization acutely-activated neuronal enhancers. This study reveals an unexpected strategy required to overcome a checkpoint common to most or all signal/ligand-regulated enhancers critical to activate broad programs of biologically-important regulatory enhancers that implement the instructions of the endocrine system.
2024-09-17 | GSE240601 | GEO
Project description:While many or most signal and ligand-dependent pathways function by directing binding of specific transcription factors to large cohorts of regulatory enhancers, the possible “universal” strategies underling activation of these lorge enhancer programs by diverse signals remains poorly understood. Here, we report that ligands, exemplified by estrogen-17-b (E2), cause the recruitment of DNA-PKcs-phosphorylated KAP1 to estrogen receptor a (ERa)-bound enhancers, inhibiting its E3 SUMO ligase activity for the CDK9 subunit of P-TEFb, which permits formation of active P-TEFb required for eRNA elongation overcoming this checkpoint and permitting enhancer activation. We find that most, or all, signal and ligand enhancer activation programs similarly require the loss of SUMOligase function by phoshorylation of KAP1 to prevent Pol II pausing at regulated enhancers. This is based on activation of P-TEFb consequent to deSUMOylation of CDK9, permitting eRNA synthesis. Overcoming this checkpoint appears to be a widely, if not universally, used strategy for signal-dependent enhancer activation because similar events occur on AR and NF-kB-regulated enhancers and even following depolarization acutely-activated neuronal enhancers. This study reveals an unexpected strategy required to overcome a checkpoint common to most or all signal/ligand-regulated enhancers critical to activate broad programs of biologically-important regulatory enhancers that implement the instructions of the endocrine system.
2024-09-17 | GSE240599 | GEO
Project description:The discovery that enhancers are regulated transcription units, encoding eRNAs, has raised new questions about the mechanisms of their activation. Here, we report an unexpected molecular mechanism that underlies ligand-dependent enhancer activation, based on DNA nicking to relieve torsional stress from eRNA synthesis. Using dihydrotestosterone (DHT)-induced binding of androgen receptor (AR) to prostate cancer cell enhancers as a model, we show rapid recruitment, within minutes, of DNA topoisomerase I (TOP1) to a large cohort of AR-regulated enhancers. Furthermore, we show that the DNA nicking activity of TOP1 is a prerequisite for robust eRNA synthesis and enhancer activation and is kinetically accompanied by the recruitment of ATR and the MRN complex, followed by additional components of DNA damage repair machinery to the AR-regulated enhancers. Together, our studies reveal a linkage between eRNA synthesis and ligand-dependent TOP1-mediated nicking - a strategy exerting quantitative effects on eRNA expression in regulating AR-bound enhancer-dependent transcriptional programs. Genome-wide binding analysis of AR, TOP1, MRE11 in prostate cancer cell line LNCaP with or without 5alpha-dihydrotestosterone (DHT) treatment. Nascent RNA analysis by global nuclear run-on (GRO-seq) in LNCaP cells transfected with siRNA with or without DHT treatment. Distribution of transcriptionally engaged RNA Pol II in LNCaP cells with or without DHT treatment by precision nuclear run-on and sequencing (PRO-seq).
2015-01-22 | E-GEOD-63202 | biostudies-arrayexpress
Project description:The discovery that enhancers are regulated transcription units, encoding eRNAs, has raised new questions about the mechanisms of their activation. Here, we report an unexpected molecular mechanism that underlies ligand-dependent enhancer activation, based on DNA nicking to relieve torsional stress from eRNA synthesis. Using dihydrotestosterone (DHT)-induced binding of androgen receptor (AR) to prostate cancer cell enhancers as a model, we show rapid recruitment, within minutes, of DNA topoisomerase I (TOP1) to a large cohort of AR-regulated enhancers. Furthermore, we show that the DNA nicking activity of TOP1 is a prerequisite for robust eRNA synthesis and enhancer activation and is kinetically accompanied by the recruitment of ATR and the MRN complex, followed by additional components of DNA damage repair machinery to the AR-regulated enhancers. Together, our studies reveal a linkage between eRNA synthesis and ligand-dependent TOP1-mediated nicking - a strategy exerting quantitative effects on eRNA expression in regulating AR-bound enhancer-dependent transcriptional programs.
2015-01-22 | GSE63202 | GEO
Project description:The functional importance of gene enhancers in regulated gene expression is well established. In addition to widespread transcription of long non-coding RNA (ncRNA) transcripts in mammalian cells, bidirectional ncRNAs referred to as eRNAs are present on enhancers. However, it has remained unclear whether these eRNAs are functional, or merely a reflection of enhancer activation. Here, we report that 17 ?-estradiol (E2)-bound estrogen receptor alpha (ER?) on enhancers causes a global increase in eRNA transcription on enhancers adjacent to E2 upregulated coding genes. These induced eRNAs, as functional transcripts, appear to exert important roles for the observed ligand-dependent induction of target coding genes, causing an increased strength of specific enhancer:promoter looping initiated by ER? binding. Cohesin, present on many ER?-regulated enhancers even prior to ligand treatment, apparently contributes to E2-dependent gene activation by stabilizing E2/ER?/eRNA-induced enhancer:promoter looping. Our data indicate that eRNAs are likely to exert important functions in many regulated programs of gene transcription. The ChIP-seqs in this study measure the binding landscape of master transcription regulator of estrogen signaling - ER?, together with common histone marks including H3K27ac and H3K4me1 in MCF7 cells. These data serve as the basis to understand the enhancer map and subsequent analysis of eRNA expression using GRO-seq. The GRO-seq measures the trancription of nascent RNAs in the genome. From MCF7 cells treated with veichle or estrodial, we could identify estrogen-regulated eRNAs and subsequently could study their functions.
2013-06-04 | E-GEOD-45822 | biostudies-arrayexpress
Project description:Pathologic activation of c-Myc plays a central role in pathogenesis of several neoplasias, including multiple myeloma. However, therapeutic targeting of c-Myc has remained elusive due to its lack of a clear ligand-binding domain. We therefore targeted c-Myc transcriptional function by another means, namely the disruption of chromatin-dependent signal transduction. Members of the bromodomain and extra-terminal (BET) subfamily of human bromodomain proteins (BRD2, BRD3 and BRD4) associate with acetylated chromatin and facilitate transcriptional activation by increasing the effective molarity of recruited transcriptional activators. Notably, BRD4 marks select M/G1 genes in mitotic chromatin for transcriptional memory and direct post-mitotic transcription, via direct interaction with the positive transcription elongation factor complex b (P-TEFb). Because c-Myc is known to regulate promoter-proximal pause release of Pol II, also through the recruitment of P-TEFb, we evaluated the selective small-molecule inhibitor of BET bromodomains, JQ1, as a chemical probe to interrogate the role of BET bromodomains in Myc-dependent transcription and to explore their role as therapeutic targets in c-Myc-driven neoplasias. Duplicate cultures of MM.1S, OPM1 and KMS11 human myeloma cells were treated with either DMSO alone or with JQ1 (500 nM), for 24 hours. Total RNA was extracted and hybridized to Affymetrix human Gene 1.0 ST microarrays (two arrays per treatment per cell line for a total of 12 arrays).
2011-09-01 | E-GEOD-31365 | biostudies-arrayexpress
Project description:Pathologic activation of c-Myc plays a central role in pathogenesis of several neoplasias, including multiple myeloma. However, therapeutic targeting of c-Myc has remained elusive due to its lack of a clear ligand-binding domain. We therefore targeted c-Myc transcriptional function by another means, namely the disruption of chromatin-dependent signal transduction. Members of the bromodomain and extra-terminal (BET) subfamily of human bromodomain proteins (BRD2, BRD3 and BRD4) associate with acetylated chromatin and facilitate transcriptional activation by increasing the effective molarity of recruited transcriptional activators. Notably, BRD4 marks select M/G1 genes in mitotic chromatin for transcriptional memory and direct post-mitotic transcription, via direct interaction with the positive transcription elongation factor complex b (P-TEFb). Because c-Myc is known to regulate promoter-proximal pause release of Pol II, also through the recruitment of P-TEFb, we evaluated the selective small-molecule inhibitor of BET bromodomains, JQ1, as a chemical probe to interrogate the role of BET bromodomains in Myc-dependent transcription and to explore their role as therapeutic targets in c-Myc-driven neoplasias.
2011-09-02 | GSE31365 | GEO