Epigenetic methodologies for behavioral scientists

CHD6 promotes broad nucleosome eviction for transcriptional activation in prostate cancer cells

Despite being a member of the chromodomain helicase DNA-binding protein family, little is known about the exact role of CHD6 in chromatin remodeling or cancer disease. Here we show that CHD6 binds to chromatin to promote broad nucleosome eviction for transcriptional activation of many cancer pathways. By integrating multiple patient cohorts for bioinformatics analysis of over a thousand prostate cancer datasets, we found CHD6 expression elevated in prostate cancer and associated with poor prognosis. Further comprehensive experiments demonstrated that CHD6 regulates oncogenicity of prostate cancer cells and tumor development in a murine xenograft model. ChIP-Seq for CHD6, along with MNase-Seq and RNA-Seq, revealed that CHD6 binds on chromatin to evict nucleosomes from promoters and gene bodies for transcriptional activation of oncogenic pathways. These results demonstrated a key function of CHD6 in evicting nucleosomes from chromatin for transcriptional activation of prostate cancer pathways.

A Molecular Perspective on Procedures and Outcomes with Assisted Reproductive Technologies

The emerging association of assisted reproductive technologies with adverse perinatal outcomes has prompted the in-depth examination of clinical and laboratory protocols and procedures and their possible effects on epigenetic regulatory mechanism(s). The application of various approaches to study epigenetic regulation to problems in reproductive medicine has the potential to identify relative risk indicators for particular conditions, diagnostic biomarkers of disease state, and prognostic indicators of outcome. Moreover, when applied genome-wide, these techniques are likely to find novel pathways of disease pathogenesis and identify new targets for intervention. The analysis of DNA methylation, histone modifications, transcription factors, enhancer binding and other chromatin proteins, DNase-hypersensitivity and, micro- and other noncoding RNAs all provide overlapping and often complementary snapshots of chromatin structure and resultant "gene activity." In terms of clinical application, the predictive power and utility of epigenetic information will depend on the power of individual techniques to discriminate normal levels of interindividual variation from variation linked to a disease state. At present, quantitative analysis of DNA methylation at multiple loci seems likely to hold the greatest promise for achieving the level of precision, reproducibility, and throughput demanded in a clinical setting.

High cortisol in 5-year-old children causes loss of DNA methylation in SINE retrotransposons: a possible role for ZNF263 in stress-related diseases

Background

Childhood stress leads to increased risk of many adult diseases, such as major depression and cardiovascular disease. Studies show that adults with experienced childhood stress have specific epigenetic changes, but to understand the pathways that lead to disease, we also need to study the epigenetic link prospectively in children.

Results

Here, we studied a homogenous group of 48 5-year-old children. By combining hair cortisol measurements (a well-documented biomarker for chronic stress), with whole-genome DNA-methylation sequencing, we show that high cortisol associates with a genome-wide decrease in DNA methylation and targets short interspersed nuclear elements (SINEs; a type of retrotransposon) and genes important for calcium transport: phenomena commonly affected in stress-related diseases and in biological aging. More importantly, we identify a zinc-finger transcription factor, ZNF263, whose binding sites where highly overrepresented in regions experiencing methylation loss. This type of zinc-finger protein has previously shown to be involved in the defense against retrotransposons.

Conclusions

Our results show that stress in preschool children leads to changes in DNA methylation similar to those seen in biological aging. We suggest that this may affect future disease susceptibility by alterations in the epigenetic mechanisms that keep retrotransposons dormant. Future treatments for stress- and age-related diseases may therefore seek to target zinc-finger proteins that epigenetically control retrotransposon reactivation, such as ZNF263.

Electronic supplementary material

The online version of this article (doi:10.1186/s13148-015-0123-z) contains supplementary material, which is available to authorized users.

Preoptic inputs and mechanisms that regulate maternal responsiveness

The preoptic area is a well-established centre for the control of maternal behaviour. An intact medial preoptic area (mPOA) is required for maternal responsiveness because lesion of the area abolishes maternal behaviours. Although hormonal changes in the peripartum period contribute to the initiation of maternal responsiveness, inputs from pups are required for its maintenance. Neurones are activated in different parts of the mPOA in response to pup exposure. In the present review, we summarise the potential inputs to the mPOA of rodent dams from the litter that can activate mPOA neurones. The roles of potential indirect effects through increased prolactin levels, as well as neuronal inputs to the preoptic area, are described. Recent results on the pathway mediating the effects of suckling to the mPOA suggest that neurones containing the neuropeptide tuberoinfundibular peptide of 39 residues in the posterior thalamus are candidates for conveying the suckling information to the mPOA. Although the molecular mechanism through which these inputs alter mPOA neurones to support the maintenance of maternal responding is not yet known, altered gene expression is a likely candidate. Here, we summarise gene expression changes in the mPOA that have been linked to maternal behaviour and explore the idea that chromatin remodelling during mother-infant interactions mediates the long-term alterations in gene expression that sustain maternal responding.

Ecological genomics of host behavior manipulation by parasites

Among the vast array of niche exploitation strategies exhibited by millions of different species on Earth, parasitic lifestyles are characterized by extremely successful evolutionary outcomes. Some parasites even seem to have the ability to 'control' their host's behavior to fulfill their own vital needs. Research efforts in the past decades have focused on surveying the phylogenetic diversity and ecological nature of these host-parasite interactions, and trying to understand their evolutionary significance. However, to understand the proximal and ultimate causes of these behavioral alterations triggered by parasitic infections, the underlying molecular mechanisms governing them must be uncovered. Studies using ecological genomics approaches have identified key candidate molecules involved in host-parasite molecular cross-talk, but also molecules not expected to alter behavior. These studies have shown the importance of following up with functional analyses, using a comparative approach and including a time-series analysis. High-throughput methods surveying different levels of biological information, such as the transcriptome and the epigenome, suggest that specific biologically-relevant processes are affected by infection, that sex-specific effects at the level of behavior are recapitulated at the level of transcription, and that epigenetic control represents a key factor in managing life cycle stages of the parasite through temporal regulation of gene expression. Post-translational processes, such as protein-protein interactions (interactome) and post translational modifications (e.g. protein phosphorylation, phosphorylome), and processes modifying gene expression and translation, such as interactions with microRNAs (microRNAome), are examples of promising avenues to explore to obtain crucial insights into the proximal and ultimate causes of these fascinating and complex inter-specific interactions.

Neuroplasticity in addiction: cellular and transcriptional perspectives

Drug addiction is a chronic, relapsing brain disorder which consists of compulsive patterns of drug-seeking and taking that occurs at the expense of other activities. The transition from casual to compulsive drug use and the enduring propensity to relapse is thought to be underpinned by long-lasting neuroadaptations in specific brain circuitry, analogous to those that underlie long-term memory formation. Research spanning the last two decades has made great progress in identifying cellular and molecular mechanisms that contribute to drug-induced changes in plasticity and behavior. Alterations in synaptic transmission within the mesocorticolimbic and corticostriatal pathways, and changes in the transcriptional potential of cells by epigenetic mechanisms are two important means by which drugs of abuse can induce lasting changes in behavior. In this review we provide a summary of more recent research that has furthered our understanding of drug-induced neuroplastic changes both at the level of the synapse, and on a transcriptional level, and how these changes may relate to the human disease of addiction.

Aging effects on DNA methylation modules in human brain and blood tissue

Background

Several recent studies reported aging effects on DNA methylation levels of individual CpG dinucleotides. But it is not yet known whether aging-related consensus modules, in the form of clusters of correlated CpG markers, can be found that are present in multiple human tissues. Such a module could facilitate the understanding of aging effects on multiple tissues.

Results

We therefore employed weighted correlation network analysis of 2,442 Illumina DNA methylation arrays from brain and blood tissues, which enabled the identification of an age-related co-methylation module. Module preservation analysis confirmed that this module can also be found in diverse independent data sets. Biological evaluation showed that module membership is associated with Polycomb group target occupancy counts, CpG island status and autosomal chromosome location. Functional enrichment analysis revealed that the aging-related consensus module comprises genes that are involved in nervous system development, neuron differentiation and neurogenesis, and that it contains promoter CpGs of genes known to be down-regulated in early Alzheimer's disease. A comparison with a standard, non-module based meta-analysis revealed that selecting CpGs based on module membership leads to significantly increased gene ontology enrichment, thus demonstrating that studying aging effects via consensus network analysis enhances the biological insights gained.

Conclusions

Overall, our analysis revealed a robustly defined age-related co-methylation module that is present in multiple human tissues, including blood and brain. We conclude that blood is a promising surrogate for brain tissue when studying the effects of age on DNA methylation profiles.

DNA methylation: an epigenetic risk factor in preterm birth

Spontaneous preterm birth (PTB; birth prior to 37 weeks of gestation) is a complex phenotype with multiple risk factors that complicate our understanding of its etiology. A number of recent studies have supported the hypothesis that epigenetic modifications such as DNA methylation induced by pregnancy-related risk factors may influence the risk of PTB or result in changes that predispose a neonate to adult-onset diseases. The critical role of timing of gene expression in the etiology of PTB makes it a highly relevant disorder in which to examine the potential role of epigenetic changes. Because changes in DNA methylation patterns can result in long-term consequences, it is of critical interest to identify the epigenetic patterns associated with adverse pregnancy outcomes. This review examines the potential role of DNA methylation as a risk factor for PTB and discusses several issues and limitations that should be considered when planning DNA methylation studies.

CRACKing the histone code: cocaine's effects on chromatin structure and function

Epigenetics, the nongenetic component of how chromatin structure influences gene expression, is amazingly complex, and linking how environmental stimuli can influence epigenetic 'gene programs' in specific nerve cells to ultimately control behavior is a seemingly insurmountable puzzle. Cocaine is a highly potent stimulus capable of influencing behavior for the lifetime of an organism. Not surprisingly, psychostimulant-induced epigenetic regulation of gene expression has thus been identified as key to understanding the pathology of addiction. In addition to identifying this essential role of epigenetics in addiction, several important concepts have emerged such as the importance of global, temporal, and spatial control of mRNA expression in considering any given histone modification's influence on a given gene. Adding to this complexity, one has to account for the cumulative influence of other epigenetic modifications on a gene's transcription in addition to the interplay between transcription factors and chromatin structure. This review highlights how bioinformatic, molecular, and behavioral studies on addiction provide new insight into these concepts and outlines two distinct psychostimulant-induced patterns of chromatin regulation which are thought to underlie unique programs of gene expression that contribute importantly to the addicted state.