MECP2, a multi-talented modulator of chromatin architecture

Briefings in Functional Genomics, 15(6), 2016, 420–431 doi: 10.1093/bfgp/elw023 Advance Access Publication Date: 12 June 2016 Review paper MECP2, a multi-talented modulator of chromatin architecture Corresponding author: Floriana Della Ragione, Institute of Genetics and Biophysics “A.Buzzati Traverso”, CNR, Via Pietro Castellino, 111, 80131, Italy. Tel.: þ39 081 6132338; Fax: þ39 081 6132607; IRCCS Neuromed, Pozzilli (Is), Italy. E-mail: Abstract It has been a long trip from 1992, the year of the discovery of MECP2, to the present day. What is surprising is that some of the pivotal roles of MeCP2 were already postulated at that time, such as repression of inappropriate expression from repetitive elements and the regulation of pericentric heterochromatin condensation. However, MeCP2 performs many more functions. MeCP2 is a reader of epigenetic information contained in methylated (and hydroxymethylated) DNA, moving from the ’classical’ CpG doublet to the more complex view addressed by the non-CpG methylation, which is a feature of the postnatal brain. MECP2 is a transcriptional repressor, although when it forms complexes with the appropriate molecules, it can become a transcriptional activator. For all of these aspects, Rett syndrome, which is caused by MECP2 mutations, is considered a paradigmatic example of a ‘chromatin disorder’. Even if the hunt for bona-fide MECP2 target genes is far from concluded today, the role of MeCP2 in the maintenance of chromatin architecture appears to be clearly established. Taking a cue from the non-scientific literature, we can firmly attest that MeCP2 is a player with ’a great future behind it’*. *V. Gassmann ‘Un grande avvenire dietro le spalle’. TEA Eds Key words: MECP2; DNA methylation; pericentric heterochromatin; Rett syndrome; neurological diseases Introduction Epigenetic regulation of the genome acts at different levels of complexity and cross-talk, which are responsible for the establishment of cell and tissue identity [1]. Among the major epigenetic modifications, DNA methylation [2] and histone modifications [3] are of particular interest. Mammalian genomes are globally methylated, except for short hypomethylated regions known as CpG islands [4]. Methylation of cytosine residues (the most characterized DNA methylation site) is catalyzed by the DNA methyltransferase (DNMT) enzymes [5], which can be thought of as the ‘writers’. Generally, methylation of CpG sites (mCGs) in the promoters and enhancers is associated with chromatin compaction and Floriana Della Ragione obtained her master’s degree in Biology in 2000, then her PhD in Biology in 2005. From 2015 she has been a PI at IGB “A. Buzzati Traverso”, CNR, Naples. Her current scientific interests include epigenetic changes in RTT focusing on the role of MECP2 in heterochromatin architecture. Institute of Genetics and Biophysics “A.Buzzati Traverso”, CNR, via Pietro Castellino, 111, 80131, Naples, Italy; IRCCS Neuromed, Pozzilli (Is), Italy. Marcella Vacca obtained her master’s degree in Biology in 1998 and her PhD in Neuroscience in 2003, working on Rett syndrome. From 2015 she has been a PI at IGB “A. Buzzati Traverso”, CNR, Naples. Her current interests are focused on the molecular circuits controlled by MECP2. Institute of Genetics and Biophysics “A.Buzzati Traverso”, CNR, via Pietro Castellino, 111, 80131, Naples, Italy. Salvatore Fioriniello obtained his master’s degree in Biology in 2016, with a thesis entitled: ‘Pericentric heterochromatin condensation: role of interactions between MeCP2 and molecular partners in neural differentiation’. Institute of Genetics and Biophysics “A.Buzzati Traverso”, CNR, via Pietro Castellino, 111, 80131, Naples, Italy. Giuseppe Pepe obtained his master’s degree in Biology in 2015, with a thesis entitled: ‘The role and the molecular targets of MeCP2 in response to stress in animal models’. He is currently a PhD student at I.R.C.C.S. Neuromed. IRCCS Neuromed, Pozzilli (Is), Italy. Maurizio D’esposito obtained his PhD in Biology in 1986, working on human HOX loci. In 1992, he moved to St. Louis, USA, working on PAR2 regulation. He has been a PI since 1998 at IGB “A. Buzzati Traverso”, CNR, Naples, and his current interests concern the molecular alterations underlying chromatin diseases. Institute of Genetics and Biophysics “A.Buzzati Traverso”, CNR, via Pietro Castellino, 111, 80131, Naples, Italy; IRCCS Neuromed, Pozzilli (Is), Italy. C The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please email: V 420 Floriana Della Ragione, Marcella Vacca, Salvatore Fioriniello, Giuseppe Pepe, and Maurizio D’Esposito MeCP2 as chromatin organizer MeCP2: the gene and the protein MeCP2 was the first MBD-containing protein discovered, due to its binding to a single methyl-CpG pair [13, 17]. In vitro studies showed that the high affinity binding of MeCP2 to methylated DNA requires four or more A/T sequences adjacent to the methyl-CpGs [33]. MeCP2 also contains: (i) a TRD that mediates its links with the histone modifications and co-repressors [12]; (ii) a nuclear localization signal (NLS) that imports part of the total protein into the nucleus; and (iii) a C-terminal domain that is involved in the interactions with DNA and its protein partners [34]. In addition, three AT-hook-like domains were identified in MeCP2 recently ([Figure 1]). These domains are shared with 421 chromatin-associated proteins of the high-mobility group AThook (HMGA) family, and they have roles in DNA binding [36]. The MECP2 gene is located within Xq28 and it is subjected to X inactivation [37, 38]. This gene contains four exons, that code for two protein isoforms that are produced by alternative splicing: MeCP2-e1 (i.e. MECP2B or MeCP2a) and MeCP2-e2 (i.e. MECP2A or MeCP2b). These splicing isoforms differ at their N-terminal regions, although they include both of the two main domains (i.e. MBD and TRD). The most abundant isoform is MeCP2-e1, which includes the exon 1, while the start of translation of the MeCP2-e2 isoform is in the exon 2 [39–41] (Figure 1B). Both of the MeCP2-e1 and MeCP2-e2 isoforms are ubiquitous, although their expression levels are highest in the brain [34]. Human MeCP2 was purified to homogeneity and its structure was characterized in detail by ultracentrifugation, circular dichroism and protease digestion [42]. MeCP2 has a monomeric state under a wide range of conditions, it appears to be intrinsically disordered and it contains at least six distinct domains that are organized in a tertiary structure that is 60% unstructured. Nonetheless, it has also been shown more recently that MeCP2 can form homo-interactions, with itself, both in vitro and in vivo [43]. The structural autonomy of the different domains that results from the disordered structure of the protein might explain its multi-functionality [42]. Taking these findings together, it is highly likely that the ability of MeCP2 to establish interac (...truncated)