Human mutations in integrator complex subunits link transcriptome integrity to brain development

Abstract

Integrator is an RNA polymerase II (RNAPII)-associated complex that was recently identified to have a broad role in both RNA processing and transcription regulation. Importantly, its role in human development and disease is so far largely unexplored. Here, we provide evidence that biallelic Integrator Complex Subunit 1 (INTS1) and Subunit 8 (INTS8) gene mutations are associated with rare recessive human neurodevelopmental syndromes. Three unrelated individuals of Dutch ancestry showed the same homozygous truncating INTS1 mutation. Three siblings harboured compound heterozygous INTS8 mutations. Shared features by these six individuals are severe neurodevelopmental delay and a distinctive appearance. The INTS8 family in addition presented with neuronal migration defects (periventricular nodular heterotopia). We show that the first INTS8 mutation, a nine base-pair deletion, leads to a protein that disrupts INT complex stability, while the second missense mutation introduces an alternative splice site leading to an unstable messenger. Cells from patients with INTS8 mutations show increased levels of unprocessed UsnRNA, compatible with the INT function in the 3’-end maturation of UsnRNA, and display significant disruptions in gene expression and RNA processing. Finally, the introduction of the INTS8 deletion mutation in P19 cells using genome editing alters gene expression throughout the course of retinoic acid-induced neural differentiation. Altogether, our results confirm the essential role of Integrator to transcriptome integrity and point to the requirement of the Integrator complex in human brain development.

Contribution of rare and common variants to intellectual disability in a high-risk population sub-isolate of Northern Finland

“…We also observed three cases that were homozygous missense variant carriers in the INTS1 gene (Table 3). Recently a loss-of-function variants in INTS1 have been identified in three unrelated moderate to severe ID patients 44 . One of our patients had mild ID and the two others had moderate/severe ID.…”

Attenuation of Eukaryotic Protein-Coding Gene Expression via Premature Transcription Termination

“…However, the underlying molecular mechanisms responsible for these phenotypes remain largely unclear. Slight increases in unprocessed snRNAs have been observed when Integrator subunits are depleted or mutated, but the levels of mature snRNAs have generally not been found to be significantly different (Ezzeddine et al 2011;Oegema et al 2017;Tatomer et al 2019). There is no denying that functional snRNAs are critical for life, but we hypothesize that Integrator's role in fine-tuning protein-coding transcription may also be critical for normal development, and that perturbation of this tuning process may lead to the phenotypes that have been observed.…”

“…Focusing specifically on the brain, depletion of Integrator subunits is associated with excess immature neuroblasts in Drosophila (Zhang et al 2019) and cortical neuron migration defects in mice (van den Berg et al 2017). Recent work has even extended these observations to humans as six individuals with severe neurodevelopmental delay have been shown to carry biallelic mutations in Integrator subunits (Oegema et al 2017).…”

Co-evolutionary analysis accurately predicts details of interactions between the Integrator complex subunits

“…The Integrator complex (INT) is an important transcriptional component in regulating 3'-end processing of non-coding RNA (Baillat and Wagner 2015), and widely participating in transcription processes at protein-coding genes through its association with RNA polymerase II (Gardini et al 2014;Stadelmayer et al 2014). Several INT subunits have been found to play important roles in human brain development (Oegema et al 2017), lung function (Kheirallah et al 2017), embryogenesis(Kapp et al 2013, and adipose differentiation (Otani et al 2013). Among at least the 14 subunits of Integrator, Here, we use DCA with our added convolution method to accurately predict the binding residues of INTS9/INTS11 heterodimer.…”