Misregulation of Alternative Splicing in a Mouse Model of Rett Syndrome

Abstract

Mutations in the human MECP2 gene cause Rett syndrome (RTT), a severe neurodevelopmental disorder that predominantly affects girls. Despite decades of work, the molecular function of MeCP2 is not fully understood. Here we report a systematic identification of MeCP2-interacting proteins in the mouse brain. In addition to transcription regulators, we found that MeCP2 physically interacts with several modulators of RNA splicing, including LEDGF and DHX9. These interactions are disrupted by RTT causing mutations, suggesting that they may play a role in RTT pathogenesis. Consistent with the idea, deep RNA sequencing revealed misregulation of hundreds of splicing events in the cortex of Mecp2 knockout mice. To reveal the functional consequence of altered RNA splicing due to the loss of MeCP2, we focused on the regulation of the splicing of the flip/flop exon of Gria2 and other AMPAR genes. We found a significant splicing shift in the flip/flop exon toward the flop inclusion, leading to a faster decay in the AMPAR gated current and altered synaptic transmission. In summary, our study identified direct physical interaction between MeCP2 and splicing factors, a novel MeCP2 target gene, and established functional connection between a specific RNA splicing change and synaptic phenotypes in RTT mice. These results not only help our understanding of the molecular function of MeCP2, but also reveal potential drug targets for future therapies.

Activity-dependent aberrations in gene expression and alternative splicing in a mouse model of Rett syndrome

“…Therefore, a tight regulation of the ratios of different alternatively spliced isoforms is highly important for proper functioning of the neuronal networks. Indeed, aberrant ratios between the flip and flop isoforms of the Gria1-4 subunits of AMPAR have been linked recently to abnormal synaptic transmission in RTT (12). Our study showed widespread aberrations in alternative splicing, specifically in response to neuronal activity in RTT mice.…”

“…This conundrum has led to other studies, some of which have suggested that MeCP2 is not a gene-specific transcriptional repressor but rather a global repressor that abundantly binds methylated DNA and dampens transcriptional noise genomewide (6), that MeCP2 acts as both a repressor and an activator (5,7,8), that MeCP2 functions in a celltype-specific manner (9,10), and that MeCP2 is a long-gene-specific repressor (4). Other studies have suggested that MeCP2 functions posttranscriptionally as a regulator of alternative splicing (11,12), or as a regulator of microRNA expression (13)(14)(15). Although these studies advanced our understanding of the function of MeCP2, they also clearly emphasize that the molecular mechanism which mediates RTT is likely complex and has yet to be deciphered.…”

Chromatin-mediated alternative splicing regulates cocaine reward behavior

“…Neuron-specific isoform expression is essential to proper cell-type specification as shown from recent studies in neuronal development (Furlanis and Scheiffele, 2018;Saito et al, 2019;Schwartzentruber et al, 2018), disease (Gandal et al, 2018;de la Torre-Ubieta et al, 2016;Parikshak et al, 2016;Voineagu et al, 2011) and activity Parikshak et al, 2016;Quesnel-Vallières et al, 2016). While many neurological diseases, including autism (Quesnel-Vallières et al, 2016;Voineagu et al, 2011), Rett syndrome (Cheng et al, 2017;Kriaucionis and Bird, 2004;Li et al, 2016), Huntington's disease (Lin et al, 1993;Sathasivam et al, 2013;Wood, 2013), spinal muscular atrophy (Cartegni et al, 2006;Lorson et al, 1999;Parente and Corti, 2018;Xiong et al, 2015) and schizophrenia (Gandal et al, 2018;Glatt et al, 2011;Morikawa and Manabe, 2010;Nakata et al, 2009;Wu et al, 2012) have been linked to disruptions in alternative splicing, this mechanism of gene regulation is understudied in the context of drug abuse and addiction. Only one study thus far has reported that investigator administered cocaine results in greater changes in isoform expression than gene expression in the NAc (Feng et al, 2014).…”

“…Alternative splicing is a key mechanism for gene regulation in brain. Aberrant splicing is implicated in myriad neurological diseases, such as autism (Gonatopoulos-Pournatzis et al, 2018;Quesnel-Vallières et al, 2016;Voineagu et al, 2011), Rett syndrome (Cheng et al, 2017;Kriaucionis and Bird, 2004;Li et al, 2016), Huntington's disease (Lin et al, 1993;Sathasivam et al, 2013;Wood, 2013), spinal muscular atrophy (Cartegni et al, 2006;Lorson et al, 1999;Parente and Corti, 2018;Xiong et al, 2015) and schizophrenia (Gandal et al, 2018;Glatt et al, 2011;Morikawa and Manabe, 2010;Nakata et al, 2009;Wu et al, 2012). However, this mechanism of gene regulation is understudied in neuropsychiatric diseases, including drug addiction.…”

Modeling and Predicting the Activities of Trans-Acting Splicing Factors with Machine Learning

“…We have previously constructed engineering splicing factors (ESFs) by fusing functional domains of known splicing factors to an RBD with programmable specificity (PUF domain from human PUM1). The resulting ESFs have been successfully used in manipulating AS of endogenous genes in cultured cells and model animals (Li et al, 2016;Wang et al, 2009). Additionally, this strategy also provides a convenient and standard system to assess the function of splicing regulatory domains.…”