Genome-wide disruption of 5-hydroxymethylcytosine in a mouse model of autism

Abstract

The autism spectrum disorders (ASD) comprise a broad group of behaviorally related neurodevelopmental disorders affecting as many as 1 in 68 children. The hallmarks of ASD consist of impaired social and communication interactions, pronounced repetitive behaviors and restricted patterns of interests. Family, twin and epidemiological studies suggest a polygenetic and epistatic susceptibility model involving the interaction of many genes; however, the etiology of ASD is likely to be complex and include both epigenetic and environmental factors. 5-hydroxymethylcytosine (5hmC) is a novel environmentally sensitive DNA modification that is highly enriched in post-mitotic neurons and is associated with active transcription of neuronal genes. Here, we used an established chemical labeling and affinity purification method coupled with high-throughput sequencing technology to generate a genome-wide profile of striatal 5hmC in an autism mouse model (Cntnap2(-/-) mice) and found that at 9 weeks of age the Cntnap2(-/-) mice have a genome-wide disruption in 5hmC, primarily in genic regions and repetitive elements. Annotation of differentially hydroxymethylated regions (DhMRs) to genes revealed a significant overlap with known ASD genes (e.g. Nrxn1 and Reln) that carried an enrichment of neuronal ontological functions, including axonogenesis and neuron projection morphogenesis. Finally, sequence motif predictions identified associations with transcription factors that have a high correlation with important genes in neuronal developmental and functional pathways. Together, our data implicate a role for 5hmC-mediated epigenetic modulation in the pathogenesis of autism and represent a critical step toward understanding the genome-wide molecular consequence of the Cntnap2 mutation, which results in an autism-like phenotype.

Sex-specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress

“…Read density mapping showed no visible differences among the chromosomes, except depletion on the X chromosome, which is consistent with previous observations (Supplementary Fig. 1b, data not shown) (Li et al, 2016; Papale et al, 2015; Szulwach et al, 2011). …”

“…To achieve this goal, we randomly divided seven-week-old C57BL/6 female mice into experimental or control groups, where the experimental mice were restrained for thirty minutes followed by a one-hour recovery period prior to tissue collection (Methods). 5hmC containing DNA sequences were enriched from whole hippocampal genomic DNA, using an established chemical labeling and affinity purification method (Li et al, 2016; Papale et al, 2015; Song et al, 2011; Szulwach et al, 2011), and sequenced using high-throughput sequencing technology. This approach yielded approximately 30 to 55 million uniquely mapped reads from each genome (Methods; Supplementary Fig.…”

“…5hmC is enriched in neuronal cells and is associated with the regulation of neuronal activity (Szulwach et al, 2011; Yao and Jin, 2014). Related to disease, 5hmC functions independently from 5mC in neurological disorders ( e.g., Rett syndrome and Autism) (Mellen et al, 2012; Papale et al, 2015; Zhubi et al, 2014) and neurodegenerative diseases ( e.g., Huntington’s and Alzheimer’s) (Chouliaras et al, 2013; Condliffe et al, 2014; Wang et al, 2013). We recently reported a genome-wide disruption of 5hmC in the hippocampus of male mice exposed to acute stress followed by a one-hour recovery (Li et al, 2016).…”

Assessment of ‘one-step’ versus ‘sequential’ embryo culture conditions through embryonic genome methylation and hydroxymethylation changes

“…In particular, it seems important for pluripotence of mouse embryonic stem cells (Tahiliani et al ., 2009; Ito et al ., 2010; Koh et al ., 2011; Dawlaty et al ., 2014) and is preferentially associated with transcriptionally active genes (Ficz et al ., 2011; Pastor et al ., 2011; Wu et al ., 2011; Xu et al ., 2011; Kubiura et al ., 2012; Mellén et al ., 2012). Studies reporting a link between 5hmeC and many diseases, in particular cancers (review (Vasanthakumar and Godley, 2015)) and neurologic disorders such as autism (Papale et al ., 2015), have also greatly increased over the last few years. Due to its link to DNA demethylation and to these functions, 5hmeC appears as a potential crucial mark during early development.…”

An epigenetic view of developmental diseases: new targets, new therapies

“…[37] These findings are further validated in autism mouse model, in which DhMRs showed a high overlap with autism associated genes including Nrxn1 and Reln. [39] Together, these studies indicate 5hmC-mediated epigenetic regulation could play important roles in autism.…”