Transcription, epigenetics and ameliorative strategies in Huntington's Disease: a genome-wide perspective

Abstract

Transcriptional dysregulation in Huntington's disease (HD) is an early event that shapes the brain transcriptome by both the depletion and ectopic activation of gene products that eventually affect survival and neuronal functions. Disruption in the activity of gene expression regulators, such as transcription factors, chromatin-remodeling proteins, and noncoding RNAs, accounts for the expression changes observed in multiple animal and cellular models of HD and in samples from patients. Here, I review the recent advances in the study of HD transcriptional dysregulation and its causes to finally discuss the possible implications in ameliorative strategies from a genome-wide perspective. To date, the use of genome-wide approaches, predominantly based on microarray platforms, has been successful in providing an extensive catalog of differentially regulated genes, including biomarkers aimed at monitoring the progress of the pathology. Although still incipient, the introduction of combined next-generation sequencing techniques is enhancing our comprehension of the mechanisms underlying altered transcriptional dysregulation in HD by providing the first genomic landscapes associated with epigenetics and the occupancy of transcription factors. In addition, the use of genome-wide approaches is becoming more and more necessary to evaluate the efficacy and safety of ameliorative strategies and to identify novel mechanisms of amelioration that may help in the improvement of current preclinical therapeutics. Finally, the major conclusions obtained from HD transcriptomics studies have the potential to be extrapolated to other neurodegenerative disorders.

Fig. 1

Summary of the gene profiling and other genome-wide studies in HD. The graph represents the number of studies per publication year with the most relevant milestones in the field of HD transcriptional dysregulation. Note that a few studies may contain more than one approach, categorized as “Array” (expression and ChIP-on-chip), “NGS” (next-generation sequencing, RNA-seq, ChIP-seq, sequencing of methylated DNA) and “Others” (PCR-based: differential display, adapter-tagged competitive PCR, panels). Reports with solely reanalysis (i.e., without generating data de novo) or chemically lesioned striatal models are not considered. References per year: 2000, [22]; 2001, [10, 15]; 2002: [12, 23, 24, 31, 65]; 2003, [173, 193]; 2004, [11]; 2005, [9, 25, 51, 135, 159, 194]; 2006, [26, 34, 36, 37, 157, 195]; 2007, [32, 38, 52, 54, 72, 110, 133, 154, 196]; 2008, [13, 27, 33, 39, 56, 103, 125, 155]; 2009, [35, 151, 152, 197]; 2010, [14, 16, 158, 165, 174, 192]; 2011, [18, 19, 30, 50, 57, 67, 119, 127, 156, 198]; 2012, [17, 66, 99, 111, 112, 181, 199]; 2013, [20, 21, 28, 29, 49, 53, 68, 113, 116, 124, 128, 180, 200]

Fig. 2

Convergent disruption of regulatory mechanisms for differentially expressed genes in HD. Schematic representation of a hypothetical deregulated gene in HD, which transcriptional dysregulation may be the result of correlated changes in the complex genomic redistribution and occupancy of transcription factors, epigenetic marks, and miRNAs. SNPs, although invariant, may contribute to the susceptibility to the expression change. Arrow, direction of the gene; shade box, CpG island