INTS8 mutations cause severe neurodevelopmental syndrome
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Zheng Xia
PROVIDER: E-GEOD-76878 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Integrator (INT) is an RNA polymerase II (RNAPII)-associated complex that was recently identified to have a broad role in both RNA processing and transcription regulation. INT has at least 14 subunits, but INT germline mutations causing human disease have not been reported. We identified mutations in the Integrator Complex Subunit 8 gene (INTS8) causing a rare neurodevelopmental syndrome. In patient cells we identified significant disturbance of gene expression and RNA processing. Also, we show that injection of ints8 oligonucleotide morpholinos into zebrafish embryos leads to prominent underdevelopment of the head demonstrating the evolutionary conserved requirement of INTS8 in brain development.
2017-05-17 | GSE76878 | GEO
Project description:Integrator (INT) is a multi-subunit modular RNA processing complex, which exhibits both RNA endonuclease and protein phosphatase activity. It is responsible for transcription termination at the 3’ ends of a diverse array of RNA polymerase II (RNAP2) transcribed non-coding RNAs, as well as transcription regulation at a large number of protein coding genes. There, it terminates RNAP2 at promoter proximal pausing sites, cleaves the nascent transcript and competes with elongation factors.This INT-mediated tapering of gene expression attenuates stimulus responsive genes and is essential for cell differentiation. Although INT affects transcription at varying classes of RNAs in diverse biological contexts, how it achieves specificity in a gene- and context-dependent manner has remained elusive. Using a combination of proteomics, interaction studies and structural characterization, we identified a diverse set of transcription factors (TFs) that associate directly with defined surfaces on INT. Stress conditions lead to changes in the types of TFs bound by INT, and quantitative binding studies suggest that TF affinities can be modulated by altering the phosphorylation states of specific residues in their INT-binding motifs. Integrated multi-omics data show that INT and its TF interactors regulate significantly overlapping sets of genes and indicate that these TFs recruit INT to specific genomic loci. Consistently, we find that starvation induced formation of primary cilia, which is a cellular stress response reliant on INT-mediated transcription regulation, depends on intact TF-INT binding. Taken together, our data suggest that TFs lend INT specificity to elicit targeted gene regulation as a transcriptional response in defined biological contexts.
2024-06-20 | GSE260520 | GEO
Project description:Integrator (INT) is a multi-subunit modular RNA processing complex, which exhibits both RNA endonuclease and protein phosphatase activity. It is responsible for transcription termination at the 3’ ends of a diverse array of RNA polymerase II (RNAP2) transcribed non-coding RNAs, as well as transcription regulation at a large number of protein coding genes. There, it terminates RNAP2 at promoter proximal pausing sites, cleaves the nascent transcript and competes with elongation factors.This INT-mediated tapering of gene expression attenuates stimulus responsive genes and is essential for cell differentiation. Although INT affects transcription at varying classes of RNAs in diverse biological contexts, how it achieves specificity in a gene- and context-dependent manner has remained elusive. Using a combination of proteomics, interaction studies and structural characterization, we identified a diverse set of transcription factors (TFs) that associate directly with defined surfaces on INT. Stress conditions lead to changes in the types of TFs bound by INT, and quantitative binding studies suggest that TF affinities can be modulated by altering the phosphorylation states of specific residues in their INT-binding motifs. Integrated multi-omics data show that INT and its TF interactors regulate significantly overlapping sets of genes and indicate that these TFs recruit INT to specific genomic loci. Consistently, we find that starvation induced formation of primary cilia, which is a cellular stress response reliant on INT-mediated transcription regulation, depends on intact TF-INT binding. Taken together, our data suggest that TFs lend INT specificity to elicit targeted gene regulation as a transcriptional response in defined biological contexts.
2024-06-20 | GSE233957 | GEO
Project description:Integrator (INT) is a multi-subunit modular RNA processing complex, which exhibits both RNA endonuclease and protein phosphatase activity. It is responsible for transcription termination at the 3’ ends of a diverse array of RNA polymerase II (RNAP2) transcribed non-coding RNAs, as well as transcription regulation at a large number of protein coding genes. There, it terminates RNAP2 at promoter proximal pausing sites, cleaves the nascent transcript and competes with elongation factors.This INT-mediated tapering of gene expression attenuates stimulus responsive genes and is essential for cell differentiation. Although INT affects transcription at varying classes of RNAs in diverse biological contexts, how it achieves specificity in a gene- and context-dependent manner has remained elusive. Using a combination of proteomics, interaction studies and structural characterization, we identified a diverse set of transcription factors (TFs) that associate directly with defined surfaces on INT. Stress conditions lead to changes in the types of TFs bound by INT, and quantitative binding studies suggest that TF affinities can be modulated by altering the phosphorylation states of specific residues in their INT-binding motifs. Integrated multi-omics data show that INT and its TF interactors regulate significantly overlapping sets of genes and indicate that these TFs recruit INT to specific genomic loci. Consistently, we find that starvation induced formation of primary cilia, which is a cellular stress response reliant on INT-mediated transcription regulation, depends on intact TF-INT binding. Taken together, our data suggest that TFs lend INT specificity to elicit targeted gene regulation as a transcriptional response in defined biological contexts.
2024-06-20 | GSE233956 | GEO
Project description:Mutations in BRAT1, encoding BRCA1-associated ATM activator 1, have been associated with neurodevelopmental and neurodegenerative disorders characterized by heterogeneous phenotypes with varying levels of clinical severity. However, the underlying molecular mechanisms of disease pathology remain poorly understood. Here, we show that BRAT1 is a functional component of the RNA processing protein complex, Integrator. BRAT1 interacts with the INTS9/INTS11 heterodimer, the core Integrator cleavage complex that processes the 3’ ends of various non-coding RNAs and pre-mRNAs, and we find that Integrator integrity and function are disrupted by BRAT1 deletion. In particular, defects in BRAT1 impede proper 3’ end processing of UsnRNAs, snoRNAs, and replication-dependent histone mRNAs, and alter expression of protein-coding genes. Importantly, defects in Integrator integrity and function are also evident in patient-derived cells from BRAT1 related neurological disease. Collectively, these data identify BRAT1 as a functional component of Integrator and link defects in this critical endonuclease complex with hereditary neurodegenerative disease.
2022-08-30 | PXD028591 | Pride
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.
2021-07-11 | GSE154197 | GEO
Project description:INTS13 Mutations Causing a Developmental Ciliopathy Disrupt Integrator Complex Assembly
| PRJNA645398 | ENA
Project description:Termination of RNA polymerase II (RNAPII) transcription in metazoans relies largely on the Cleavage and Polyadenylation (CPA) and Integrator (INT) complexes originally found to act at the ends of protein-coding and snRNA genes, respectively. Here we monitor CPA- and INT-dependent termination activities genome-wide, including at thousands of previously unannotated transcription units (TUs), producing unstable RNA. We verify the global activity of CPA, occurring at pA sites indiscriminately of their positioning relative to the TU promoter. We also identify a global activity of INT, which is, however, largely sequence-independent and restricted to a ~3 kb promoter-proximal region. Our analyses suggest two functions of genome-wide INT activity; it dampens transcriptional output from weak promoters and it provides quality-control of RNAPII complexes that are unfavorably configured for transcriptional elongation. We suggest that the function of INT in stable snRNA production is an exception from its general cellular role, the attenuation of non-productive transcription.
2021-01-03 | GSE151919 | GEO
Project description:Alternative 3’-end RNA processing provides an important source of transcriptome diversification, which impacts various biological processes and the etiology of diseases, including cancer. Here, we focused on a transcript isoform switch that leads to the readthrough expression of the long noncoding RNA NEAT1_2, at the expense of the shorter polyadenylated transcript NEAT1_1. Expression of NEAT1_2 is required for the formation of paraspeckles (PS), nuclear bodies that protect cancer cells from oncogene-induced replication stress and chemotherapy. Searching for proteins that interact with endogenous NEAT1 by RNA Affinity Purification coupled to mass spectrometry (RAP-MS), we identified factors involved in the 3’-end processing of polyadenylated (pA+) RNA as well as several components of the Integrator complex, known to process the 3’-ends of RNAs lacking polyadenylation sites. Unexpectedly, genetic perturbation experiments established that Integrator restraints NEAT1_2 expression, and thereby PS assembly, by promoting the 3’-end processing of pA+ NEAT1_1. Consistently, low expression levels of several Integrator subunits correlated with poorer prognosis of cancer patients exposed to chemotherapeutics. Our study identifies Integrator as a key regulator of PS biogenesis and highlights a previously unrecognized ability of the complex to process pA+ RNA. The data also establish a link between Integrator, cancer biology and chemosensitivity, which may be exploited therapeutically.
2020-10-14 | PXD015158 | Pride
Project description:The Integrator Complex (IC) is responsible for the 3'-end processing of the U1/U2 major spliceosome snRNAs. Maturation of these snRNAs is essential for the proper function of the major spliceosome. Also, there is accumulating evidence that the IC is necessary for normal vertebrate development, however no association with human disease has been reported yet. Three siblings presented with severe intellectual disability, cerebellar hypoplasia and periventricular nodular heterotopia (PNH) of unknown cause. Using whole genome sequencing (Complete Genomics), and filtering for recessive inheritance, we discovered co-segregating compound heterozygous mutations in Integrator Complex Subunit 8 (INTS8) in the three sibs. QRT-PCR showed 2-fold decreased INTS8 RNA levels and in patients’ fibroblasts lower levels of the catalytic subunits INTS4, INTS9 and INTS11 were observed on western blots, indicating that the integrity of the complex is disrupted. Northern blots showed significantly misprocessed levels of U1, U2 and U4. Pathway analysis (DAVID) of expression data (Affymetrix Gene Chip 1.0 ST exon arrays) of RNA extracted from patient fibroblasts showed enrichment of deregulated genes involved in mRNA splicing and posttranscriptional modification. Expression data of (developing) human brain structures (Allen Brain Atlas) show that expression of INTS8 peaks prenatally, especially in the ganglionic eminences, (sub)ventricular zone and hindbrain, similar to the developmental expression in mouse embryo (Emage databse). Interestingly, neuronal precursors from these areas migrate to the cortex and are compatible to affected regions in PNH and cerebellar hypoplasia in the patients. We propose that dysfunction of the Integrator Complex, through snRNA misprocessing and spliceosomal defects, leads to severely disrupted brain development in humans. We used RNA isolated from human cultured fibroblasts, cell-lines were obtained from 3 individuals with INTS8 mutations and from 3 unaffected individuals. R,Oegema Six Affymetrix Gene Chip 1.0 ST exon arrays (patients: 04RD83, 83RD247, 04RD84 ; controls: 81RD193, GMO2037C, 86RD677) were rma normalized on transcript level using the R package oligo (http://www.r-project.org). Top down regulated (n=402) or up regulated (n=281) genes with p values <0.02 were analyzed for enriched gene ontology terms (goterms_BP_all) using DAVID (medium stringency)(down: 329 DAVID IDs, up: 225 DAVID IDs).
2013-09-01 | E-GEOD-48849 | biostudies-arrayexpress