It seems that everyone has MeCP2 on the brain – as evidenced by its starring role in two new Molecular Cell papers – but it’s in your brain too! The MeCP2 protein is essential for neuronal function and consistent with this, loss-of-function mutations in MeCP2 cause the neurodevelopmental disorder Rett syndrome. Unfortunately, because MeCP2 acts genome-wide and causes only subtle changes, it has been difficult to understand the mechanistic details and the breadth of its effects.
MeCP2 and NCoR Work Together to Repress Transcriptional Initiation of Target Genes
MeCP2 may be a tough protein to study, but the lab of Michael Greenberg (Harvard Medical School, USA) put their collective brainpower to the task. In neurons, MeCP2 preferentially binds long, highly methylated genes and interacts with the transcriptional co-repressor NCoR, suggesting that MeCP2 acts as a transcriptional repressor at these specific genes. To investigate this potential function of MeCP2 and how it regulates gene expression, they compared brain tissue from wild type (WT) and MeCP2 knockout mice (MeCP2-KO).
Here are the highlights:
- RNA-seq confirmed that loss of MeCP2 results in the upregulation of long genes with higher-than-average methylation of cytosine followed by adenine (mCA)
- Upregulated genes show an accompanying increase in H3K36me3 (a marker of actively transcribed genes), confirming that MeCP2 functions to repress transcription in this context
- A point mutation in MeCP2 that abolishes NCoR binding resulted in similar upregulation of genes compared to MeCP2 knockouts, indicating that repression is mediated through NCoR
- This repression is, at least in part, due to the histone deacetylase component of the NCoR complex
- MeCP2 and NCoR are recruited by the presence of mCA
- MeCP2 represses transcription by reducing the rate of transcriptional initiation, rather than affecting elongation
- MeCP2-KO upregulated genes have increased precision run-on sequencing (PRO-seq) signal and increased Pol II (ChIP-seq) at transcription start sites and within genes
- Hi-C analysis revealed an enrichment of contacts between gene bodies and transcription start sites in MeCP2-KO upregulated genes
- The gene body sites are also enriched for H3K27ac, suggesting that these are intragenic enhancers
This work gives us a glimpse into how loss-of-function mutations in MeCP2 may play a role in Rett syndrome. At long genes, loss of MeCP2 results in a loss of transcriptional repression. This leads to increased transcriptional initiation and therefore increased gene expression. This research, in combination with future work, will lead to a better understanding of how MeCP2 regulates gene expression in repressive contexts, and potentially give rise to therapeutic advancements for Rett Syndrome patients.
MeCP2 Blocks Enhancer Activation of Long, Highly Methylated Genes
In the second paper, MeCP2 still takes center stage, but with an additional focus on 3-dimensional chromatin structure and the role of DNMT3A–the methyltransferase responsible for de novo, postnatal mCA. This team of brainiacs, led by Harrison Gabel (Washington University School of Medicine, USA) compared data from the cerebral cortex of normal mice, MeCP2 knockout mice, and mice overexpressing MeCP2. After confirming that MeCP2 represses highly methylated long genes, they went on to investigate how exactly these gene targets are modulated.
Here’s what they found:
- Overlaying genome-wide methylation profiles with Hi-C data from the mice revealed an enrichment of mCA in TADs with MeCP2-repressed genes
- TAD structures govern DNMT3A binding and in turn, the distribution of mCA
- TADs with higher mCA levels show a modest enrichment of MeCP2 binding
- MeCP2 represses transcription of highly methylated long genes by downregulating promoter activation, and does not alter polymerase activity
- For these genes, loss of MeCP2 increased the RNA-seq reads across the entire length of pre-mRNA, indicating that full-length transcripts are being generated and that polymerase processivity is unaffected by loss of MeCP2
- ChIP-seq of MeCP2 knockouts showed markers of active gene transcription (H3K36me3) and promoter activation (H3K27ac and H3K4me3) at MeCP2-repressed genes
- The repressive effect of MeCP2 is achieved by blocking enhancer activation
- MeCP2 binds at intragenic enhancers with high mCA or mCG
- Hi-C data showed a preference for promoters to interact with intragenic sequences as opposed to extragenic sequences
MeCP2 acts most strongly on highly methylated intragenic enhancers, which may explain MeCP2’s preference for long genes due to their higher number of intragenic enhancer regions.
MeCP2 is a Key Regulator of Gene Expression in Neurons
Together, these papers construct a model for MeCP2 function, acting to repress highly methylated long genes in neurons. Adding NCoR, TADs, and DNMT3A into the mix gives us even more insight into the mechanistic details, but there is still more to uncover. Future work will be directed towards a better understanding of how MeCP2 acts on enhancers and how the preference for intragenic enhancers is established, as well as identifying the numerous target genes. Interestingly, some genes are activated rather than repressed by MeCP2, and a better understanding of this mechanism could also be useful in the treatment of Rett syndrome.
If this has your neurons firing, you can read more about MeCP2’s effect on transcriptional initiation and its long-ranging enhancer effects online in Molecular Cell, November 2019.