Localized Domains of G9a-Mediated Histone Methylation Are Required for Silencing of Neuronal Genes

Abstract

Negative regulation of transcription is an important strategy in establishing and maintaining cell-specific gene expression patterns. Many neuronal genes are subject to active transcriptional repression outside the nervous system to establish neuronal specificity. NRSF/REST has been demonstrated to regulate at least 30 genes and contribute to their neuronal targeting by repressing transcription outside the nervous system. Further, human genome database searches reveal that over 800 genes contain an NRSE. Here we report that NRSF recruits the histone methylase G9a to silence NRSF target genes in nonneuronal cells. We show that G9a generates a highly localized domain of dimethylated histone H3-K9 around NRSEs, but H3-K27 remains unmethylated. The NRSEs are also associated with HP1. Finally, we demonstrate that dominant-negative G9a abrogates silencing of chromosomal neuronal genes. These findings implicate a role for histone methylation in targeting neuronal gene expression to the nervous system.

Heterochromatin and its Relationship to Cell Senescence and Cancer Therapy

“…58 This model does not propose a primary role in steady-state gene expression, perhaps explaining the relative dearth of HP1 proteins at transcriptionally repressed genes. 12,59,60 Finally, according to our model, HP1 proteins might localize to transcriptionally active genes to facilitate restoration of a closed, transcriptionally silent chromatin structure after a round of transcription. 61 This suggests that HP1 proteins can respond to defects in chromatin structure at other sites in the genome, aside from pericentromeres.…”

“…Also, despite the presumed role of these proteins in gene silencing, HP1 proteins have only been found bound to relatively few transcriptionally-repressed genes. 12,59,60 Even more surprising, HP1g is localized to some transcriptionally active genes. 61 A model to explain these paradoxical results was developed from additional experiments that we performed in cells stably expressing HP1bDN.…”

Epigenetic Mechanisms in Stroke and Epilepsy

“…HDACs deacetylate core histone proteins and affect dynamic and reversible gene silencing (Roopra et al, 2001;Ooi and Wood, 2007). REST mediates long-term gene silencing by associating with the site-specific histone methyltransferase G9a, which promotes dimethylation of histone 3 at lysine 9 (H3K9me2) via CoREST-dependent (Lunyak et al, 2002; and -independent (Roopra et al, 2004) mechanisms and with LSD1, which removes mono-and dimethyl groups from lysine 4 of H3 Shi, 2005). In addition, REST recruits methyl-CpG-binding protein 2 (MeCP2) (Lunyak et al, 2002;, a transcriptional repressor, which binds to hotspots of methylated CpG dinucleotides in gene promoters where it complexes with other repressors (Feng and Nestler, 2010).…”

Differential Promoter Methylation and Histone Modification Contribute to the Brain Specific Expression of the Mouse Mbu-1 Gene

“…Within the developing nervous system, REST transiently repressed the synaptotagmin 4 brain-derived neurotrophic factor and calbindin genes in dividing progenitors, and its loss at terminal differentiation allowed their expression in mature neurons (Ballas et al, 2005;Tan et al, 2010). In contrast, outside of the nervous system, REST normally mediates long-term silencing of these genes (Lunyak et al, 2002;Roopra et al, 2004).…”