Structural basis of Integrator-mediated transcription regulation

Description How Integrator ends transcription early Transcription is the central process that activates the genetic information in cells, but our understanding of how gene transcription is regulated is incomplete. The so-called Integrator can stop the transcribing enzyme RNA polymerase II at the beginning of genes, but how such downregulation of transcription occurs is unclear. Fianu et al. present the three-dimensional structure of Integrator bound to the transcribing polymerase complex, providing molecular and mechanistic insights into how Integrator mediates transcription regulation. —DJ Structural analysis suggests how Integrator-PP2A counteracts Pol II elongation and mediates nascent RNA cleavage and transcription termination. Integrator and protein phosphatase 2A (PP2A) form a complex that dephosphorylates paused RNA polymerase II (Pol II), cleaves the nascent RNA, and terminates transcription. We report the structure of the pretermination complex containing the human Integrator-PP2A complex bound to paused Pol II. Integrator binds Pol II and the pausing factors DSIF and NELF to exclude binding of the elongation factors SPT6 and PAF1 complex. Integrator also binds the C-terminal domain of Pol II and positions PP2A to counteract Pol II phosphorylation and elongation. The Integrator endonuclease docks to the RNA exit site and opens to cleave nascent RNA about 20 nucleotides from the Pol II active site. Integrator does not bind the DNA clamps formed by Pol II and DSIF, enabling release of DNA and transcription termination.

• Publication year

  2021

• Venue

  Science

• Publication date

  2021-11-12

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1126/science.abk0154PMID 34762484
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Crystal structure of the INTS3/INTS6 complex reveals the functional importance of INTS3 dimerization in DSB repair

  2021cited by this paper
• Cryo-EM structure of mammalian RNA polymerase II in complex with human RPAP2

  2021cited by this paper
• Structures of the human Mediator and Mediator-bound preinitiation complex

  2021cited by this paper
• Structure of the catalytic core of the Integrator complex

  2021cited by this paper
• The PP2A-Integrator-CDK9 axis fine-tunes transcription and can be targeted therapeutically in cancer.

  2021cited by this paper
• The Human Integrator Complex Facilitates Transcriptional Elongation by Endonucleolytic Cleavage of Nascent Transcripts

  2020cited by this paper
• Structure of an active human histone pre-mRNA 3′-end processing machinery

  2020cited by this paper
• UCSF ChimeraX: Structure visualization for researchers, educators, and developers

  2020cited by this paper
• Integrator restrains paraspeckles assembly by promoting isoform switching of the lncRNA NEAT1.

  2020cited by this paper
• Integrator Recruits Protein Phosphatase 2A to Prevent Pause Release and Facilitate Transcription Termination.

  2020cited by this paper
• Identification of Integrator-PP2A complex (INTAC), an RNA polymerase II phosphatase

  2020cited by this paper
• Structural basis for multifunctional roles of human Ints3 C-terminal domain

  2020cited by this paper
• Integrator is a genome-wide attenuator of non-productive transcription

  2020cited by this paper
• Integrator restrains paraspeckles assembly by promoting isoform switching of the lncRNA NEAT1

  2020cited by this paper
• Reconstitution and atomic structure of an active human histone pre-mRNA 3'-end processing machinery

  2020cited by this paper
• INTS10–INTS13–INTS14 form a functional module of Integrator that binds nucleic acids and the cleavage module

  2020cited by this paper
• Improved protein structure prediction using predicted interresidue orientations

  2019cited by this paper
• Transcriptional Control by Premature Termination: A Forgotten Mechanism

  2019cited by this paper
• Integrator is a key component of human telomerase RNA biogenesis

  2019cited by this paper
• The Integrator Complex Attenuates Promoter-Proximal Transcription at Protein-Coding Genes.

  2019cited by this paper
• New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink “waters,” and NGL Viewer to recapture online 3D graphics

  2019cited by this paper
• The Integrator complex cleaves nascent mRNAs to attenuate transcription

  2019cited by this paper
• A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides

  2019cited by this paper
• Structure of activated transcription complex Pol II–DSIF–PAF–SPT6

  2018cited by this paper
• Tyrosine-1 of RNA Polymerase II CTD Controls Global Termination of Gene Transcription in Mammals.

  2018cited by this paper
• Real-space refinement in PHENIX for cryo-EM and crystallography

  2018cited by this paper
• Targeted Enhancer Activation by a Subunit of the Integrator Complex.

  2018cited by this paper
• Structure of paused transcription complex Pol II-DSIF-NELF

  2018cited by this paper
• Namdinator – automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps

  2018cited by this paper
• Real-time cryo–EM data pre-processing with Warp

  2018cited by this paper
• New tools for automated high-resolution cryo-EM structure determination in RELION-3

  2018cited by this paper
• MacroBac: New Technologies for Robust and Efficient Large-Scale Production of Recombinant Multiprotein Complexes.

  2017cited by this paper
• CDK9-dependent RNA polymerase II pausing controls transcription initiation

  2017cited by this paper
• Improvements to the APBS biomolecular solvation software suite

  2017cited by this paper
• Structure of a transcribing RNA polymerase II–DSIF complex reveals a multidentate DNA–RNA clamp

  2017cited by this paper
• Integrator subunit 4 is a ‘Symplekin-like’ scaffold that associates with INTS9/11 to form the Integrator cleavage module

  2017cited by this paper
• Architecture and RNA binding of the human negative elongation factor

  2016cited by this paper
• Structure of transcribing mammalian RNA polymerase II

  2016cited by this paper
• Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

  2016cited by this paper
• xiNET: Cross-link Network Maps With Residue Resolution

  2015cited by this paper
• Integrator mediates the biogenesis of enhancer RNAs

  2015cited by this paper
• The Integrator complex controls the termination of transcription at diverse classes of gene targets

  2015cited by this paper
• EMRinger: Side-chain-directed model and map validation for 3D Electron Cryomicroscopy

  2015cited by this paper
• Xlink Analyzer: Software for analysis and visualization of cross-linking data in the context of three-dimensional structures

  2015cited by this paper
• Integrator regulates transcriptional initiation and pause release following activation.

  2014cited by this paper
• Deciphering key features in protein structures with the new ENDscript server

  2014cited by this paper
• DSIF and NELF interact with Integrator to specify the correct post-transcriptional fate of snRNA genes

  2014cited by this paper
• Integrator complex regulates NELF-mediated RNA polymerase II pause/release and processivity at coding genes

  2014cited by this paper
• Functional Analysis of the Integrator Subunit 12 Identifies a Microdomain That Mediates Activation of the Drosophila Integrator Complex*

  2013cited by this paper
• Identification of cross-linked peptides from complex samples

  2012cited by this paper
• An RNAi screen identifies additional members of the Drosophila Integrator complex and a requirement for cyclin C/Cdk8 in snRNA 3'-end formation.

  2012cited by this paper
• RELION: Implementation of a Bayesian approach to cryo-EM structure determination

  2012cited by this paper
• NIH Image to ImageJ: 25 years of image analysis

  2012cited by this paper
• Ser7 Phosphorylation of the CTD Recruits the RPAP2 Ser5 Phosphatase to snRNA Genes

  2012cited by this paper
• snRNA 3' end formation: the dawn of the Integrator complex.

  2010cited by this paper
• Features and development of Coot

  2010cited by this paper
• The Integrator Complex Recognizes a New Double Mark on the RNA Polymerase II Carboxyl-terminal Domain*

  2010cited by this paper
• Jalview Version 2—a multiple sequence alignment editor and analysis workbench

  2009cited by this paper
• DNA Cloning and Engineering by Uracil Excision

  2009cited by this paper
• Circular Polymerase Extension Cloning of Complex Gene Libraries and Pathways

  2009cited by this paper
• rtracklayer: an R package for interfacing with genome browsers

  2009cited by this paper
• An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol

  2008cited by this paper
• A construct with fluorescent indicators for conditional expression of miRNA

  2008cited by this paper
• Structure of a protein phosphatase 2A holoenzyme: insights into B55-mediated Tau dephosphorylation.

  2008cited by this paper
• Serine-7 of the RNA Polymerase II CTD Is Specifically Required for snRNA Gene Expression

  2007cited by this paper
• Crystal structure of a protein phosphatase 2A heterotrimeric holoenzyme

  2007cited by this paper
• Automated electron microscope tomography using robust prediction of specimen movements.

  2005cited by this paper
• Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II.

  2005cited by this paper
• The polyadenylation factor CPSF-73 is involved in histone-pre-mRNA processing.

  2005cited by this paper
• UCSF Chimera—A visualization system for exploratory research and analysis

  2004cited by this paper
• Baculovirus expression system for heterologous multiprotein complexes

  2004cited by this paper
• The 3′ ends of human pre‐snRNAs are produced by RNA polymerase II CTD‐dependent RNA processing

  2003cited by this paper
• Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution

  2001cited by this paper
• Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution

  2001cited by this paper
• Formation of the 3′ end of U1 snRNA is directed by a conserved sequence located downstream of the coding region.

  1985cited by this paper

• Integrator subunit INTS12 links ribotoxic stress to transcription-coupled nucleotide excision repair.

  2026cites this paper
• A sequence‑encoded promoter proximal super pause stabilizes an offline RNA polymerase II state

  2026cites this paper
• Scaling perturbations: beyond genome-scale CRISPR screens

  2026cites this paper
• Sequence-specific RNA recognition drives Restrictor-mediated termination of extragenic transcription.

  2026cites this paper
• ATM promotes reversed fork processing during DNA interstrand cross-link repair

  2025cites this paper
• The Integrator-PP2A complex integrates promoter-proximal premature termination with chromatin context and genome maintenance.

  2025cites this paper
• Integrator 20th anniversary: a molecular machine indispensable in development and disease.

  2025cites this paper
• Transcription quality control at the promoter-proximal checkpoint

  2025influential citation
• Novel Biallelic INTS1 Variants May Expand the Phenotypic Spectrum of INTS1-Related Disorders—Case Report and Literature Review

  2025cites this paper
• A CDK11-dependent RNA polymerase II pause-checkpoint precedes CDK9-mediated transition to transcriptional elongation.

  2025cites this paper
• Integrator promotes the association of TFIID and RNA polymerase II to maintain pluripotency during development.

  2025cites this paper
• Toward structural understanding of eukaryotic transcription elongation

  2025cites this paper
• DSS1 is required for proper Integrator–PP2A function

  2025cites this paper
• Restrictor slows RNAPII elongation to promote termination at noncoding RNA loci

  2025cites this paper
• Integrator loss leads to dsRNA formation that triggers the integrated stress response.

  2025cites this paper
• Integrator complex subunit 12 knockout overcomes a transcriptional block to HIV latency reversal

  2025cites this paper
• Defining the roles of the Integrator, NEXT, and nuclear exosome complexes in Drosophila oogenesis

  2025cites this paper
• Structural insights into promoter-proximal pausing of RNA polymerase II at +1 nucleosome

  2025cites this paper
• Combining cryo-electron microscopy (cryo-EM) with orthogonal solution state methods to define the molecular basis of the phosphoprotein phosphatase family regulation and substrate specificity.

  2025cites this paper
• Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition

  2025cites this paper
• Catalytic-independent functions of the Integrator–PP2A complex (INTAC) confer sensitivity to BET inhibition

  2025cites this paper
• DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts

  2025cites this paper
• Restrictor slows early transcription elongation to render RNA polymerase II susceptible to termination at non-coding RNA loci

  2025cites this paper
• INTS1 is required for maintaining accurate transcriptional integrity and behavior in zebrafish

  2025cites this paper
• Structure of cytoplasmic RNA polymerase II

  2025cites this paper
• Transcription-replication conflict resolution by nuclear RNA interference

  2025influential citation
• Enhancer-promoter communication in Drosophila developmental gene transcription.

  2024cites this paper
• Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9

  2024influential citation
• RNA polymerase II elongation factors use conserved regulatory mechanisms.

  2024cites this paper
• Comparative analysis of retroviral Gag-host cell interactions: focus on the nuclear interactome

  2024cites this paper
• Collaborators or competitors: the communication between RNA polymerase II and the nucleosome during eukaryotic transcription

  2024cites this paper
• Structural basis of the Integrator complex assembly and association with transcription factors

  2024influential citation
• Catalytic-independent functions of INTAC in conferring sensitivity to BET inhibition

  2024cites this paper
• Tetrameric INTS6-SOSS1 complex facilitates DNA:RNA hybrid autoregulation at double-strand breaks

  2024cites this paper
• Distinct negative elongation factor conformations regulate RNA polymerase II promoter-proximal pausing.

  2024cites this paper
• Stabilization of Integrator/INTAC by the small but versatile DSS1 protein

  2024cites this paper
• Structural basis of exoribonuclease-mediated mRNA transcription termination

  2024cites this paper
• Global control of RNA polymerase II.

  2024cites this paper
• Structural basis of Integrator-dependent RNA polymerase II termination

  2024influential citation
• Changing structures, changing paradigms: NELF helps regulate paused or elongating RNA polymerase II.

  2024cites this paper
• The cell biology of HIV-1 latency and rebound

  2024cites this paper
• Transcription directionality is licensed by Integrator at active human promoters

  2024influential citation
• Integrator Complex Subunit 3 Knockdown Has Minimal Effect on Lytic Herpes Simplex Virus Type-1 Infection in Fibroblast Cells

  2024cites this paper
• DNA-directed termination of mammalian RNA polymerase II

  2024cites this paper
• Comparative analysis of retroviral Gag-host cell interactions: focus on the nuclear interactome

  2024cites this paper
• Basis of gene-specific transcription regulation by the Integrator complex.

  2024cites this paper
• Defining a chromatin architecture that supports transcription at RNA polymerase II promoters

  2024cites this paper
• ZC3H4/Restrictor exerts a stranglehold on pervasive transcription.

  2024cites this paper
• Assembly mechanism of Integrator's RNA cleavage module.

  2024cites this paper
• Cytoplasmic binding partners of the Integrator endonuclease INTS11 and its paralog CPSF73 are required for their nuclear function.

  2024cites this paper
• Mechanisms of RNA Polymerase II termination at the 3'-end of genes.

  2024cites this paper
• Multiple forms and functions of premature termination by RNA polymerase II.

  2024cites this paper
• A deleterious variant of INTS1 leads to disrupted sleep–wake cycles

  2024cites this paper
• Integrator complex subunit 12 knockout overcomes a transcriptional block to HIV latency reversal

  2024cites this paper
• Pause Patrol: Negative Elongation Factor's role in Promoter-Proximal Pausing and beyond.

  2024cites this paper
• Resolution of transcription-induced hexasome-nucleosome complexes by Chd1 and FACT.

  2024cites this paper
• Structural basis of archaeal FttA-dependent transcription termination

  2024influential citation
• Nuclear sorting of short RNA polymerase II transcripts.

  2024cites this paper
• Mechanism of polyadenylation-independent RNA polymerase II termination

  2024cites this paper
• Redundant pathways for removal of defective RNA polymerase II complexes at a promoter-proximal pause checkpoint.

  2024cites this paper
• The enhancer module of Integrator controls cell identity and early neural fate commitment

  2024cites this paper
• The PNUTS phosphatase complex controls transcription pause release.

  2024cites this paper
• Defining gene ends: RNA polymerase II CTD threonine 4 phosphorylation marks transcription termination regions genome-wide

  2024cites this paper
• Structural basis of the human negative elongation factor NELF-B/C/E ternary complex.

  2023cites this paper
• The Integrator complex desensitizes cellular response to TGF-β/BMP signaling.

  2023cites this paper
• Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity

  2023cites this paper
• Dopey2 and Pcdh7 orchestrate the development of embryonic neural stem cells/ progenitors in zebrafish

  2023cites this paper
• Cytoplasmic mRNA levels are regulated by a combination of chromatin retention and RNA stability

  2023cites this paper
• IntS6 and the Integrator phosphatase module tune the efficiency of select premature transcription termination events

  2023influential citation
• A combinatorial approach to uncover an additional Integrator subunit

  2023cites this paper
• 3′‐end mRNA processing within apicomplexan parasites, a patchwork of classic, and unexpected players

  2023cites this paper
• 3′-End Processing of Eukaryotic mRNA: Machinery, Regulation, and Impact on Gene Expression

  2023influential citation
• Bi-allelic variants in INTS11 are associated with a complex neurological disorder.

  2023cites this paper
• INTAC endonuclease and phosphatase modules differentially regulate transcription by RNA polymerase II.

  2023cites this paper
• Molecular details of the CPSF73-CPSF100 C-terminal heterodimer and interaction with Symplekin

  2023cites this paper
• CDK12 and Integrator-PP2A complex modulates LEO1 phosphorylation for processive transcription elongation

  2023cites this paper
• A restrictor complex of ZC3H4, WDR82, and ARS2 integrates with PNUTS to control unproductive transcription.

  2023cites this paper
• Beyond gene expression: how MYC relieves transcription stress.

  2023cites this paper
• ARS2 instructs early transcription termination-coupled RNA decay by recruiting ZC3H4 to nascent transcripts.

  2023cites this paper
• DNA-dependent RNA polymerases in plants

  2023cites this paper
• hnRNPUL1 ensures efficient Integrator-mediated cleavage of snRNAs and is mutated in amyotrophic lateral sclerosis

  2023cites this paper
• BurstDECONV: a signal deconvolution method to uncover mechanisms of transcriptional bursting in live cells

  2023cites this paper
• Structural basis of archaeal FttA-dependent transcription termination

  2023cites this paper
• Structures of co-transcriptional RNA capping enzymes on paused transcription complex

  2023cites this paper
• Protein Phosphatase 2A as a Therapeutic Target in Pulmonary Diseases

  2023cites this paper
• Structural basis of INTAC-regulated transcription

  2023cites this paper
• Integrator-mediated clustering of poised RNA polymerase II synchronizes histone transcription

  2023cites this paper
• Small-Molecule Activation of Protein Phosphatase 2A Counters Bleomycin-Induced Fibrosis in Mice.

  2023cites this paper
• SOSS-INTAC: a new gatekeeper of genomic integrity at the interface of transcription and R-loops.

  2023cites this paper
• Transcriptional elongation control in developmental gene expression, aging, and disease.

  2023cites this paper
• Structure of the transcribing RNA polymerase II–Elongin complex

  2023cites this paper
• Coevolution combined with molecular dynamics simulations provides structural and mechanistic insights into the interactions between the integrator complex subunits

  2023cites this paper
• Pathogen protein modularity enables elaborate mimicry of a host phosphatase

  2023cites this paper
• Mechanisms of eukaryotic transcription termination at a glance.

  2023cites this paper
• Integrator is a global promoter-proximal termination complex.

  2023cites this paper
• Control of non-productive RNA polymerase II transcription via its early termination in metazoans.

  2022cites this paper
• Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics

  2022cites this paper
• Role of RNA Biogenesis Factors in the Processing and Transport of Human Telomerase RNA

  2022cites this paper
• Structural insights into nuclear transcription by eukaryotic DNA-dependent RNA polymerases

  2022cites this paper
• The PAF1 complex promotes 3' processing of pervasive transcripts.

  2022cites this paper