MeCP2 and the enigmatic organization of brain chromatin. Implications for depression and cocaine addiction

Abstract

Methyl CpG binding protein 2 (MeCP2) is a highly abundant chromosomal protein within the brain. It is hence not surprising that perturbations in its genome-wide distribution, and at particular loci within this tissue, can result in widespread neurological disorders that transcend the early implications of this protein in Rett syndrome (RTT). Yet, the details of its role and involvement in chromatin organization are still poorly understood. This paper focuses on what is known to date about all of this with special emphasis on the relation to different epigenetic modifications (DNA methylation, histone acetylation/ubiquitination, MeCP2 phosphorylation and miRNA). We showcase all of the above in two particular important neurological functional alterations in the brain: depression (major depressive disorder [MDD]) and cocaine addiction, both of which affect the MeCP2 homeostasis and result in significant changes in the overall levels of these epigenetic marks.

Fig. 1

a Gene organization of MeCP2. Two isoforms E1 and E2 result from alternative splicing. The red arrows indicate the starting sites of transcription. The domain organization of the resulting protein isoforms is also shown. CTD; C-terminal domain; ID: intervening domain; MBD: methyl-binding domain; NTD; N-terminal domain; TRD: transcriptional repression domain. b Number of publications since MeCP2 was first described

Fig. 2

The involvement of MeCP2 in Rett syndrome neurodevelopmental disease represents just the tip of the iceberg. The high abundance of MeCP2 in the brain [8, 9] has implications for many other neuropathological disorders [4]

Fig. 3

a After micrococcal nuclease (MNase) digestion of cellular nuclei, small-sized nucleosomes chromatin (nI) (see Fig. 4) that leak through the nuclear membrane pores can be recovered in the supernatant (SI) after centrifugation. The nuclear pellet can next be hypotonically lysed in the presence of 0.25 mM EDTA and centrifuged once more to yield a supernatant (SE) fraction and an insoluble pellet (P). b Protein composition of the SI, SE and P fractions as analysed by polyacrylamide gel electrophoresis (PAGE) in the presence of SDS detergent. Histones H1, H2A, H2B, H3 and H4 are indicated, as well as myelin (M). c Analysis of the SI, SE and P fractions during a time-course Mnase digestion of rat whole brain nuclei. The upper part of the Figure shows a Western blot analysis using MeCP2 and H4 antibodies. The lower part shows a native PAGE analysis of the DNA composition of the fractions obtained at different time of digestion. CE: chicken erythrocyte histones used as a control; M: pBR322-Cfo I–digested DNA used as a marker. The numbers on the right had side of the native PAGE indicate the DNA fragment sizes in base pairs (bp). The red lines highlight the shift in the center of the mononucleosome DNA (nI) distribution in SE and P. d Relative meC/C percentile composition of the SI, Se and P fractions at limit Mnase digestion. (Section c was reproduced from Fig. 2A from [9], with permission)

Fig. 4

Hypothetical model for the MeCP2 distribution within the neuronal chromatin organization. MeCP2 is sparsely distributed in the chromatin fibers in the nucleoplasm binding to DNA methylated sites that are depleted of H1. An important fraction of MeCP2 binds preferentially to the periphery of chromocenters/nucleoli. Upon micrococcal nuclease (MNase) digestion, MeCP2 is very quickly released from the insoluble pellet-able (P) chromocenter periphery and leaks through the nuclear membrane pores into the SI fraction (see Fig. 2). MeCP2 associated to nucleosomes is also released from nuclear chromatin fibers (SE fraction), albeit at a much lower level as indicated by the thickness of the arrows. nl: mononucleosome