INTS13 variants causing a recessive developmental ciliopathy disrupt assembly of the Integrator complex

Abstract

Oral-facial-digital (OFD) syndromes are a heterogeneous group of congenital disorders characterized by malformations of the face and oral cavity, and digit anomalies. Mutations within 12 cilia-related genes have been identified that cause several types of OFD, suggesting that OFDs constitute a subgroup of developmental ciliopathies. Through homozygosity mapping and exome sequencing of two families with variable OFD type 2, we identified distinct germline variants in INTS13, a subunit of the Integrator complex. This multiprotein complex associates with RNA Polymerase II and cleaves nascent RNA to modulate gene expression. We determined that INTS13 utilizes its C-terminus to bind the Integrator cleavage module, which is disrupted by the identified germline variants p.S652L and p.K668Nfs*9. 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 leads to motile cilia anomalies. Altogether, we show that mutations in INTS13 cause an autosomal recessive ciliopathy, which reveals key interactions between components of the Integrator complex.

Catalytic-independent functions of INTAC in conferring sensitivity to BET inhibition

“…Meanwhile, the loss of the INTAC auxiliary module had a minimal effect on snRNA processing, corroborating prior studies. [71][72][73][74] Furthermore, our data showed that the INTAC auxiliary module did not influence the phosphatase activity of INTAC, aligning with structural analyses showing the auxiliary and phosphatase modules are located on opposite ends of the complex. 88,89 These observations imply that while the auxiliary module can integrate with INTAC and support the functioning of other modules in specific developmental contexts, [71][72][73][74] it likely holds independent roles beyond the two catalytic activities of the complex.…”

A role for theC. elegansArgonaute protein CSR-1b isoform in small nuclear RNA 3’ processing

“…Beyond csr-1 , the genome-wide RNAi screen presented in this study has also identified several yet to be characterized regulators of snRNA processing including those encoding nuclear protein complex. Given the expansion of a broad role for the Integrator complex in gene expression control beyond snRNA processing, and its emerging implication in human diseases [8,14], it will ultimately be of interest to determine whether these novel regulators may also influence snRNA independent function of the Integrator in contributing to transcriptome stability.…”

“…Phenotypically, human mutations to the Integrator complex have been linked to severe neurodevelopmental syndrome and developmental ciliopathies resulting in oral-facial digital syndromes [8,14]. Analysis of the Cancer Genome Atlas has also revealed an increase in nonsynonymous mutations to the Integrator subunits in primary tumour samples [12,15].…”

“…The Integrator is a metazoan conserved protein complex that is composed of at least 15 distinct subunits in humans and was discovered in 2005 as the elusive molecular machinery for snRNA 3’ processing [6]. The Integrator catalytic module includes subunits 4, 9, and 11 that are directly involved in snRNA cleavage, while the functions of non-catalytic subunits are not well defined [7,8]. Knockdown of both catalytic and non-catalytic subunits of the Integrator leads to RNA polymerase II termination failure and 3’ misprocessing of the snRNA transcripts.…”

“…Beyond snRNA 3’ processing, recent evidence has elucidated a broader role for the Integrator in contributing to transcriptional homeostasis; these functions include the 3’ processing of non-coding Piwi-interacting RNAs as well as cleavage of nascent mRNAs at RNA polymerase II paused sites to facilitate either gene transcription activation or repression [11–13]. Phenotypically, human mutations to the Integrator complex have been linked to severe neurodevelopmental syndrome and developmental ciliopathies resulting in oral-facial digital syndromes [8,14]. Analysis of the Cancer Genome Atlas has also revealed an increase in non-synonymous mutations to the Integrator subunits in primary tumour samples [12,15].…”