NUDT21-spanning CNVs lead to neuropsychiatric disease and altered MeCP2 abundance via alternative polyadenylation

Abstract

The brain is sensitive to the dose of MeCP2 such that small fluctuations in protein quantity lead to neuropsychiatric disease. Despite the importance of MeCP2 levels to brain function, little is known about its regulation. In this study, we report eleven individuals with neuropsychiatric disease and copy-number variations spanning NUDT21, which encodes a subunit of pre-mRNA cleavage factor Im. Investigations of MECP2 mRNA and protein abundance in patient-derived lymphoblastoid cells from one NUDT21 deletion and three duplication cases show that NUDT21 regulates MeCP2 protein quantity. Elevated NUDT21 increases usage of the distal polyadenylation site in the MECP2 3′ UTR, resulting in an enrichment of inefficiently translated long mRNA isoforms. Furthermore, normalization of NUDT21 via siRNA-mediated knockdown in duplication patient lymphoblasts restores MeCP2 to normal levels. Ultimately, we identify NUDT21 as a novel candidate for intellectual disability and neuropsychiatric disease, and elucidate a mechanism of pathogenesis by MeCP2 dysregulation via altered alternative polyadenylation.DOI: http://dx.doi.org/10.7554/eLife.10782.001

New Perspectives on Genomic Imprinting, an Essential and Multifaceted Mode of Epigenetic Control in the Developing and Adult Brain

“…Genetic analyses of behavioral and neurological defects highlight that normal brain development and function require a fine regulation of gene dosages, such that even small deviations may disturb the balance of the biological pathways they control, leading to striking neural dysfunctions. This has been observed for nonimprinted genes such as MECP2 in Rett syndrome and MECP2 duplication disorder (Chao & Zoghbi 2012), as well as variation in posttranscriptional regulation of MECP2 levels (Gennarino et al 2015). In fragile X intellectual disability (FXS), FMRP mutations lead to increased metabotropic glutamate receptor (mGLUR) signaling, and reductions in mGluR dosage in an FXS mouse model was shown to rescue cognitive phenotypes (Dölen et al 2007).…”

Widespread Translational Remodeling during Human Neuronal Differentiation

“…For example, expression of variants of the TLS/ FUS RNA binding protein found in amyotrophic lateral sclerosis patients causes aberrant gene expression in human cells, including of MECP2 (Coady and Manley, 2015). Similarly, copy-number variations in the NUDT21 gene found in patients with neurological disease increase the fraction of MECP2 mRNA molecules with long 3′ UTRs (Gennarino et al, 2015). Total MECP2 mRNA levels are elevated in patient-derived cells (Gennarino et al, 2015) or human cells expressing TLS/FUS variants (Coady and Manley, 2015), but MeCP2 protein levels are decreased in both cases.…”

“…Similarly, copy-number variations in the NUDT21 gene found in patients with neurological disease increase the fraction of MECP2 mRNA molecules with long 3′ UTRs (Gennarino et al, 2015). Total MECP2 mRNA levels are elevated in patient-derived cells (Gennarino et al, 2015) or human cells expressing TLS/FUS variants (Coady and Manley, 2015), but MeCP2 protein levels are decreased in both cases. Thus, measuring translation changes in the manner described here that can detect and quantify alternative transcripts and 3′ UTRs is essential when studying diseases involving genetic alterations to post-transcriptional control factors.…”

“…Transcript 3′ UTRs regulate translation level, RNA degradation, RNA localization, and protein complex formation, therefore this expansion in 3′ UTR size also increases the post-transcriptional regulatory potential of the brain (Mayr, 2016; Tian and Manley, 2017). Defective 3′ UTR formation leads to nervous system dysfunction (Van Epps et al, 2010) and widespread shortening of 3′ UTRs is observed upon a shift to proliferation in diverse contexts including cancers and other diseases (Elkon et al, 2013; Gennarino et al, 2015; Mayr and Bartel, 2009; Sandberg et al, 2008; Singh et al, 2009). …”

An RNA interference screen identifies druggable regulators of MeCP2 stability

“…To evaluate the feasibility of incisively isolating modifiers of dose-sensitive disease drivers, we began with MECP2 due to the wealth and validity of available mouse models of disease (48). Additionally, even without a direct genetic basis, abnormalities in MeCP2 levels have been observed in ASD, Prader-Willi (49, 50) and ID patients with NUDT21 -spanning CNVs (51), suggesting modulation of MeCP2 levels may serve a broader therapeutic purpose. Here we have identified four regulators of MeCP2 stability, validating regulation of MeCP2 by PP2A and HIPK2 in vivo and demonstrating that pharmacological inhibition of PP2A was sufficient to partially rescue MeCP2 overexpression and motor abnormalities in a mouse model of MDS.…”