A combinatorial approach to uncover a novel Integrator subunit [ChIP-seq II]
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE223296 | GEO | 2023/01/25
REPOSITORIES: GEO
Similar Datasets
Project description:The Integrator complex is one of the most elusive transcriptional regulators in metazoans, deemed to be recruited after initiation to help establish and modulate paused RNAPII. Recent structural, biochemical, and functional evidence suggest that Integrator is composed of 14 subunits, assembling, and operating in a modular fashion. We employed proteomics and machine-learning (alphafold2) approaches to discover a novel Integrator subunit, INTS15. We report that INTS15 assembles primarily with the INTS10-INTS13-INTS14 module and interfaces with the Int-PP2A phosphatase module. Functional genomics analysis further reveals a role for INTS15 in modulating RNAPII pausing at a subset of genes in human cell lines.
2023-01-25 | GSE204905 | GEO
Project description:The Integrator complex is one of the most elusive transcriptional regulators in metazoans, deemed to be recruited after initiation to help establish and modulate paused RNAPII. Recent structural, biochemical, and functional evidence suggest that Integrator is composed of 14 subunits, assembling, and operating in a modular fashion. We employed proteomics and machine-learning (alphafold2) approaches to discover a novel Integrator subunit, INTS15. We report that INTS15 assembles primarily with the INTS10-INTS13-INTS14 module and interfaces with the Int-PP2A phosphatase module. Functional genomics analysis further reveals a role for INTS15 in modulating RNAPII pausing at a subset of genes in human cell lines.
2023-01-25 | GSE204932 | GEO
Project description:RNA Polymerase II (RNAPII) controls expression of all protein coding genes and most noncoding loci in higher eukaryotes. Calibrating RNAPII activity requires an assortment of polymerase-associated factors that are recruited at sites of active transcription. The Integrator complex is one of the most elusive transcriptional regulators in metazoans, deemed to be recruited after initiation to help establish and modulate paused RNAPII. Integrator is known to be composed of 14 subunits that assemble and operate in a modular fashion. We employed proteomics and machine-learning structure prediction (AlphaFold2) to identify an additional Integrator subunit, INTS15. We report that INTS15 assembles primarily with the INTS13/INTS14/INTS10 module and interfaces with the Int-PP2A module. Functional genomics analysis further reveals a role for INTS15 in modulating RNAPII pausing at a subset of genes. Our study shows that omics approaches combined with AlphaFold2-based predictions provide additional insights into the molecular architecture of large and dynamic multiprotein complexes.
2023-02-10 | PXD039995 | Pride
Project description:RNA polymerase II (RNAPII) controls the expression of all protein coding genes and most noncoding loci in higher eukaryotes. The ultimate rate of transcription is regulated at the level of multiple checkpoints during the transcription cycle (initiation, pausing, termination). Calibrating the activity of RNAPII is fundamental to all cellular processes and requires an assortment of polymerase-associated factors that are recruited at sites of active transcription. The Integrator complex is one of the most elusive transcriptional regulators in metazoans, deemed to be recruited after initiation to help establish and modulate paused RNAPII. Recent structural, biochemical, and functional evidence suggest that Integrator is composed of 14 subunits that assemble and operate in a modular fashion. We employed proteomics and machine-learning structure prediction (AlphaFold2) approaches to identify a novel Integrator subunit, INTS15. We report that INTS15 assembles primarily with the INTS13/INTS14/INTS10 module and interfaces with the core of the Int-PP2A complex. Functional genomics analysis further reveals a role for INTS15 in modulating RNAPII pausing at a subset of genes in human cell lines. Our study shows that omics approaches combined with AlphaFold2-based predictions provide novel insights into the molecular architecture of large and flexible multiprotein complexes.
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Project description:Oral-facial-digital syndromes (OFD) are a heterogeneous group of congenital disorders characterized by malformations of the face and oral cavity, and digit anomalies. To date, mutations in 12 ciliary-related genes have been identified to cause several OFD types suggesting OFDs constitute a subgroup of developmental ciliopathies. Through homozygosity mapping and exome sequencing performed on two families with variable OFD type 2, we identified distinct germline mutations in INTS13, a subunit of the Integrator Complex. This 14-component complex associates with RNAPII and can cleave nascent RNA to modulate gene expression. We determined that INTS13 utilizes a discrete domain within its C-terminus to bind the Integrator cleavage module, which is disrupted by the identified germline INTS13 mutations. Depletion of INTS13 disrupts ciliogenesis in human cultured cells and causes dysregulation of a broad collection of ciliary genes. Accordingly, its knockdown in Xenopus embryos lead to motile cilia anomalies. Altogether, we show that mutations in INTS13 cause an autosomal recessive ciliopathy, which reveal key interactions within Integrator components.
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Project description:Lineage-specific transcription factors (TFs) operate as master orchestrators of developmental processes by activating select cis-regulatory enhancers and proximal promoters. Direct DNA binding of TFs ultimately drives context-specific recruitment of the basal transcriptional machinery that comprises RNA Polymerase II (RNAPII) and a host of polymerase-associated multiprotein complexes, including the metazoan-specific Integrator complex. Integrator is primarily known to modulate RNAPII processivity and to surveil RNA integrity across coding genes. Here we show an enhancer module of Integrator that directs cell fate specification by promoting epigenetic changes and TF binding at neural enhancers. Depletion of Integrator’s INTS10 upends neural traits and derails cells towards mesenchymal identity. Commissioning of neural enhancers relies on Integrator’s enhancer module, which stabilizes SOX2 binding at chromatin upon exit from pluripotency. We propose Integrator as a functional bridge between enhancers and promoters and a main driver of early development, providing new insight into a growing family of neurodevelopmental syndromes.
2024-08-15 | PXD054928 | Pride
Project description:Cell fate specification occurs via coordinated transcriptional changes in pluripotent cells, resulting in progressive commitment towards distinct lineages. Lineage-specific transcription factors (TFs), through their intrinsic DNA-binding ability, operate as master orchestrators of early and late developmental processes by turning on select cis-regulatory enhancers and proximal promoter elements. TF binding ultimately drives recruitment of the basal transcriptional machinery that comprises RNA Polymerase II (RNAPII) and a host of polymerase-associated multiprotein complexes, including the metazoan-specific Integrator complex. Integrator is primarily known to modulate RNAPII processivity and to surveil RNA integrity. Here we show that a set of Integrator subunits (enhancer module) plays a direct role in cell fate specification by promoting epigenetic changes and TF binding at enhancer elements that drive neurogenesis and maintain neuronal cell identity. Depletion of a single Integrator subunit (INTS10) results in loss of molecular and morphological neuronal features, while diverting progenitor cells towards mesenchymal identity. Commissioning of developmental enhancers rely on Integrator’s enhancer module, which stabilizes SOX2 binding at chromatin upon exit from pluripotency. Integrator therefore operates as a functional bridge between enhancers and target promoters and is a driver of early developmental processes, providing new insight into a growing family of neurodevelopmental syndromes.
2023-05-02 | GSE230894 | GEO
Project description:Cell fate specification occurs via coordinated transcriptional changes in pluripotent cells, resulting in progressive commitment towards distinct lineages. Lineage-specific transcription factors (TFs), through their intrinsic DNA-binding ability, operate as master orchestrators of early and late developmental processes by turning on select cis-regulatory enhancers and proximal promoter elements. TF binding ultimately drives recruitment of the basal transcriptional machinery that comprises RNA Polymerase II (RNAPII) and a host of polymerase-associated multiprotein complexes, including the metazoan-specific Integrator complex. Integrator is primarily known to modulate RNAPII processivity and to surveil RNA integrity. Here we show that a set of Integrator subunits (enhancer module) plays a direct role in cell fate specification by promoting epigenetic changes and TF binding at enhancer elements that drive neurogenesis and maintain neuronal cell identity. Depletion of a single Integrator subunit (INTS10) results in loss of molecular and morphological neuronal features, while diverting progenitor cells towards mesenchymal identity. Commissioning of developmental enhancers rely on Integrator’s enhancer module, which stabilizes SOX2 binding at chromatin upon exit from pluripotency. Integrator therefore operates as a functional bridge between enhancers and target promoters and is a driver of early developmental processes, providing new insight into a growing family of neurodevelopmental syndromes.
2023-05-02 | GSE230893 | GEO
Project description:Cell fate specification occurs via coordinated transcriptional changes in pluripotent cells, resulting in progressive commitment towards distinct lineages. Lineage-specific transcription factors (TFs), through their intrinsic DNA-binding ability, operate as master orchestrators of early and late developmental processes by turning on select cis-regulatory enhancers and proximal promoter elements. TF binding ultimately drives recruitment of the basal transcriptional machinery that comprises RNA Polymerase II (RNAPII) and a host of polymerase-associated multiprotein complexes, including the metazoan-specific Integrator complex. Integrator is primarily known to modulate RNAPII processivity and to surveil RNA integrity. Here we show that a set of Integrator subunits (enhancer module) plays a direct role in cell fate specification by promoting epigenetic changes and TF binding at enhancer elements that drive neurogenesis and maintain neuronal cell identity. Depletion of a single Integrator subunit (INTS10) results in loss of molecular and morphological neuronal features, while diverting progenitor cells towards mesenchymal identity. Commissioning of developmental enhancers rely on Integrator’s enhancer module, which stabilizes SOX2 binding at chromatin upon exit from pluripotency. Integrator therefore operates as a functional bridge between enhancers and target promoters and is a driver of early developmental processes, providing new insight into a growing family of neurodevelopmental syndromes.
2023-05-02 | GSE230889 | GEO
Project description:Cell fate specification occurs via coordinated transcriptional changes in pluripotent cells, resulting in progressive commitment towards distinct lineages. Lineage-specific transcription factors (TFs), through their intrinsic DNA-binding ability, operate as master orchestrators of early and late developmental processes by turning on select cis-regulatory enhancers and proximal promoter elements. TF binding ultimately drives recruitment of the basal transcriptional machinery that comprises RNA Polymerase II (RNAPII) and a host of polymerase-associated multiprotein complexes, including the metazoan-specific Integrator complex. Integrator is primarily known to modulate RNAPII processivity and to surveil RNA integrity. Here we show that a set of Integrator subunits (enhancer module) plays a direct role in cell fate specification by promoting epigenetic changes and TF binding at enhancer elements that drive neurogenesis and maintain neuronal cell identity. Depletion of a single Integrator subunit (INTS10) results in loss of molecular and morphological neuronal features, while diverting progenitor cells towards mesenchymal identity. Commissioning of developmental enhancers rely on Integrator’s enhancer module, which stabilizes SOX2 binding at chromatin upon exit from pluripotency. Integrator therefore operates as a functional bridge between enhancers and target promoters and is a driver of early developmental processes, providing new insight into a growing family of neurodevelopmental syndromes.
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