DNA methylation-environment interactions in the human genome

Previously, we showed that a massively parallel reporter assay, mSTARR-seq, could be used to simultaneously test for both enhancer-like activity and DNA methylation-dependent enhancer activity for millions of loci in a single experiment (Lea et al., 2018). Here, we apply mSTARR-seq to query nearly the entire human genome, including almost all CpG sites profiled either on the commonly used Illumina Infinium MethylationEPIC array or via reduced representation bisulfite sequencing. We show that fragments containing these sites are enriched for regulatory capacity, and that methylation-dependent regulatory activity is in turn sensitive to the cellular environment. In particular, regulatory responses to interferon alpha (IFNA) stimulation are strongly attenuated by methyl marks, indicating widespread DNA methylation-environment interactions. In agreement, methylation-dependent responses to IFNA identified via mSTARR-seq predict methylation-dependent transcriptional responses to challenge with influenza virus in human macrophages. Our observations support the idea that pre-existing DNA methylation patterns can influence the response to subsequent environmental exposures—one of the tenets of biological embedding. However, we also find that, on average, sites previously associated with early life adversity are not more likely to functionally influence gene regulation than expected by chance.

Chromosome 21 is the smallest human chromosome and represents a model for physical mapping of the entire human genome. Three copies of this autosome cause Down syndrome, the most frequent genetic disorder associated with significant mental retardation. Five years ago, in the framework of the international human genome project, and as an integrated part of the chromosome 21 community, a consortium, of academic groups from Japan and Germany was formed to map and sequence this chromosome. Several whole-genome and chromosome-specific DNA libraries were constructed for mapping purposes. Using a combination of nested-deletion [1] and shotgun sequencing approaches, our center determined and analyzed over 17 million bases of high-quality data. In total, over 33.5 million basepairs of DNA, distributed over four contigs, were sequenced with very high accuracy [2]. The largest of these contigs is nearly 25.5Mb long. Only three small clone gaps remain, which together comprise approximately 100kb. Thus, we achieved a coverage of 99.7% of 21q. In addition, 211,116 bp from the short arm were also sequenced. Analysis of the chromosome revealed far fewer genes than previously estimated. Instead of 800-1000 expected genes, we found only 225 genes, of which 127 are known genes and 98 are predicted genes. In addition, 59 pseudogenes were identified. The completion of the 21q sequence provides a unique resource for understanding the molecular pathophysiology of Down syndrome, as well as all other monogenic and complex disorders that map to this chromosome, including Alzheimer’s disease, leukemia, autoimmune disease, epilepsy and manic-depressive psychosis. It also stands as a structural framework from which the complete molecular architecture of the chromosome can be determined. With the announcement of the first “working draft” of the human genome by the international human genome sequencing consortium this past June, there has been a great interest in the total number of genes in the human genome[3]. Some of the current estimates range from as low as 34,000 genes to as high as 140,000 genes. The low gene-density of chromosome 21 was quite unexpected. Most striking is a 7-Mb region near the region near the centromere that contains only one gene. This region is much larger than the whole genome of some species, such as Escherichia coli, yet evolutionary processes permitted the existence of such a gene-poor SNA segment. This finding leads us to propose that there are additional large gene-less regions in other human/mammalian chromosomes. By combining the gene numbers of chromosomes 21 and 22 [4] (770genes; 2-3% of human genome) and assuming that together they represent the average gene content of the human genome, we estimate that the total number of human genes may be close to 40,000. As part of the international human genome sequencing project, we are also sequencing parts of chromosomes 11 and 18. Our high-throughput sequence production line generates about 10 Mb per day. In order to handle such a high volume of output, we have developed a system for automated data assembly, annotation and release. All the data is released through our website and through the DNA Database of Japan immediately according to the policies established by the international consortium. In addition to chromosomes 11, 18 and 21, we are also interested in the structure of the entire human genome. In collaboration with the University of Tokyo, we have developed a database called HGREP [5] (Human Genome Reconstruction Project) that contains working draft and finished sequences which cover more than 85% of the human genomic sequences. Sequence entries are aligned along the chromosomes based on sequence similarities to STS markers, BAC-end and other entry sequences. Further, biological features, such as genes, gene functions, repeats and CpG islands, are fully annotated on these entries. To identify evolutionally conserved and biologically important information in the genome, we are taking the strategy of comparative genomic sequence analysis between human and other related genomes such as those of rodents and primates. We are currently sequencing several regions of the mouse, including some regions that are counterpart to human chromosome 21, and are preparing genomic resources for sequencing of the chimpanzee. Through comparative methods, we are also trying to understand telomeric regions, structures at the end of chromosomes that play an important role in several biological functions and have been associated with human diseases like an oncogenesis and a cellular aging. The structure and function of all genes and their regulatory regions can only be fully understood by looking at how they interact under different circumstances and in several different backgrounds. Determining which genes and elements are human-specific will lead to a deeper understanding of who we are and will advance medical sciences drastically.

The relation between early life adversity, cortisol awakening response and diurnal salivary cortisol levels in postpartum women

Social bonds enhance fitness in many group-living animals, generating interest in the processes that create individual variation in sociality. Previous work on female baboons shows that early life adversity and temperament both influence social connectedness in adulthood. Early life adversity might shape sociality by reducing ability to invest in social relationships or through effects on attractiveness as a social partner. We examine how females' early life adversity predicts sociality and temperament in wild olive baboons, and evaluate whether temperament mediates the relationship between early life adversity and sociality. We use behavioural data on 31 females to quantify sociality. We measure interaction style as the tendency to produce grunts (signals of benign intent) in contexts in which the vocalization does not produce immediate benefits to the actor. Early life adversity was negatively correlated with overall sociality, but was a stronger predictor of social behaviours received than behaviours initiated. Females who experienced less early life adversity had more benign interaction styles and benign interaction styles were associated with receiving more social behaviours. Interaction style may partially mediate the association between early life adversity and sociality. These analyses add to our growing understanding of the processes connecting early life experiences to adult sociality.

Early life adversity is associated with both persistent disruptions in the hypothalamic-pituitary-adrenal (HPA) axis and psychiatric symptoms. Glucocorticoid receptors (GRs), which are encoded by the NR3C1 gene, bind to cortisol and other glucocorticoids to create a negative feedback loop within the HPA axis to regulate the body’s neuroendocrine response to stress. Excess methylation of a promoter sequence within NR3C1 that attenuates GR expression, however, has been associated with both early life adversity and psychopathology. As critical regulators within the HPA axis, GRs and their epigenetic regulation may mediate the link between early life adversity and the onset of psychopathology. The present review discusses this work as one mechanism by which stress may get under the skin to disrupt HPA functioning at an epigenetic level and create long-lasting vulnerabilities in the stress regulatory system that subsequently predispose individuals to psychopathology. Spanning prenatal influences to critical periods of early life and adolescence, we detail the impact that early adversity has on GR expression, physiological responses to stress, and their implications for long-term stress management. We next propose a dual transmission hypothesis regarding both genomic and non-genomic mechanisms by which chronic and acute stress propagate through numerous generations. Lastly, we outline several directions for future research, including potential reversibility of methylation patterns and its functional implications, variation in behavior determined solely by NR3C1, and consensus on which specific promoter regions should be studied.

BackgroundAdults with early life adversity exhibit heightened response to threat signals in the environment, which makes them vulnerable to developing stress-related mental health problems, including anxiety disorders. Yet, the impact of the COVID-19 pandemic on adults who have experienced early life adversity is understudied. Recently, researchers have characterized dysfunctional cognitions about the pandemic, which are associated with negative mental health outcomes, as coronavirus anxiety. We conducted a study to examine the relation between exposure to early life adversity, perceived threat from COVID-19, and coronavirus anxiety.MethodsAdults (N = 975; 18–78 years of age; 585 = Women) living in the United States were recruited online in October 2020. Two forms of early life adversity, maltreatment and household dysfunction, were assessed using the Adverse Childhood Experiences scale. Participants’ state anxiety was measured using the State-Trait Anxiety Inventory, and coronavirus anxiety was measured via the Coronavirus Anxiety Scale. Three items were used to measure perceived threat from COVID-19. Additionally, as reduced flexibility is implicated in the development and maintenance of anxiety disorders, participants’ cognitive flexibility was assessed using the Cognitive Flexibility Inventory.ResultsThe data were analyzed using parallel mediation regression analyses. Exposure to early life adversity, in the form of maltreatment and household dysfunction, were the key predictor variables. Coronavirus anxiety and state anxiety were the outcome variables. Perceived threat from COVID-19 and cognitive flexibility were added as parallel mediators into all the regression models. The regression analyses revealed that both perceived threat from COVID-19 and cognitive flexibility mediated the relation between early life adversity and anxiety. The data demonstrate that exposure to early life adversity, in the form of maltreatment or household dysfunction, was associated with higher levels of perceived threat from COVID-19, which, in turn, predicted increased coronavirus anxiety and state anxiety. In contrast, appraisal of everyday challenges as controllable, one of the two types of cognitive flexibility assessed, predicted lower levels of coronavirus anxiety and state anxiety. However, exposure to maltreatment and household dysfunction was associated with reduced cognitive flexibility.ConclusionThis study replicates and extends prior research showing that adults with early life adversity experienced increased anxiety during the pandemic. The findings bolster existing theories that highlight the importance of threat appraisal as a mechanism for the development of anxiety disorders in this population. Additionally, this report adds to the limited body of work on the impact of COVID-19 in adults who have experienced early life adversity.

Detail-oriented visual processing style: Its role in the relationships between early life adversity and hoarding-related dysfunctions

Objective The present study explores how and when lifetime discriminatory experience moderates the mediation effect of early life adversities and social activity on loneliness among older European adults over eight years. Method The study analyzed 13,699 respondents aged 50 years and over who were interviewed in 2009 and re-interviewed in 2017 in the European Survey of Health, Ageing, Retirement. Conditional process analysis using the PROCESS model 15 was applied to examine the moderated mediation effect of lifetime discriminatory experience in 2009 (W) on early life adversities in 2009 (X) and social activity at 2017 (M) to loneliness in 2017 (Y). Results Our moderated mediation models found that early life adversities (X) are associated with loneliness (Y) (Coeff X→Y=-0.0501, p<.001), but social activity (M) reduces its effect on loneliness (Y) (Coeff X→M→Y=-1.6391, p<.001). However, lifetime discriminatory experience (W) hampers social activity (Coeff M*W→Y = 0.0955, p<.05) and increases loneliness (Coeff X*M→Y = 0.6069, p<.05). Conclusion Older adults experiencing early life adversities may not necessarily develop later life loneliness. However, lifetime discriminatory experience due to political beliefs, religion, ethnicity, sexual orientation/background etc. may reverse the positive effect of social engagement on the relationship between early life adversities and loneliness. Early interventions should address discrimination and social inequalities and increase social participation across the life course to prevent the development of later-life loneliness among older adults.

Early life adversity (ELA) predisposes individuals to physical and mental disorders lifelong. How ELA affects brain functions, leading to these vulnerabilities, is a mystery. To understand ELA's impacts, investigations into neural activity affected by ELA must go beyond localized areas toward simultaneous recordings from multiple widely distributed regions over time. Such studies will expose relative activity between regions and discover shifts in regional activity in response to different experiences. Here, we performed longitudinal manganese-enhanced MRI (MEMRI) to measure degrees of brain-wide neural activity in ELA-exposed mice across a series of experiences in adulthood. To ascertain whether ELA resulted in atypical brain activity, results were compared to those of the standard mouse (Std). MEMRI captured activity in the freely moving home cage condition, and short- and long-term after exposure to TMT, a naturalistic predator threat. Images were normalized and aligned then analyzed with statistical mapping and automated segmentation. We found that neural activity in the home cage was greater in ELA compared to Std in multiple striatal-pallidal and hypothalamic regions. Upon acute threat, neural activity in Std increased in these regions to become more similar to that in ELA, while new hyperactive responses in ELA emerged in the midbrain and hindbrain. Nine days after acute threat, heightened neural activity in ELA persisted within locus coeruleus and increased within the posterior amygdala, ventral hippocampus, and dorsomedial and ventromedial hypothalamus. These results reveal functional imbalances that arise between multiple brain-systems after ELA, which are dependent upon context and cumulative experiences into adulthood.

BackgroundPrevious studies have linked exposure to early socioeconomic adversity to depression, but the mechanisms of this association are not well understood. Locus of control (LoC), an individual's control-related beliefs, has been implicated as a possible mechanism, however, longitudinal evidence to support this is lacking. MethodsThe study sample comprised 8803 participants from a UK cohort, the Avon Longitudinal Study of Parents and Children (ALSPAC). Indicators of early socioeconomic adversity were collected from the antenatal period to 5 years and modelled as a latent factor. Depression was assessed using the Clinical Interview Schedule-Revised (CIS-R) at 18 years. LoC was assessed with the Nowicki–Strickland Internal–External (CNSIE) scale at 16 years. ResultsUsing structural equation modelling, we found that 34% of the total estimated association between early socioeconomic adversity and depression at 18 years was explained by external LoC at 16 years. There was weak evidence of a direct pathway from early socioeconomic adversity to depression after accounting for the indirect effect via external locus of control. Socioeconomic adversity was associated with more external LoC, which, in turn, was associated with depression. LimitationsAttrition may have led to an underestimation of the direct and indirect effect sizes in the complete case analysis. ConclusionsResults suggest that external LoC in adolescence is one of the factors mediating the link between early adversity and depression at 18 years. Cognitive interventions that seek to modify maladaptive control beliefs in adolescence may be effective in reducing risk of depression following early life adversity.

Coming of Age in War: Early Life Adversity, Age at Menarche, and Mental Health

GREATER CORTICAL THICKNESS IN PATIENTS WITH FIRST-EPISODE SCHIZOPHRENIA WHO ARE RESPONSIVE TO ATYPICAL ANTIPSYCHOTICS

Early postnatal experience and DRD2 genotype affect dopamine receptor expression in the rat ventral striatum

Simple SummaryOur study aims to understand mysterious parts of our DNA, known as ultra-conserved non-coding elements. Found in the genomes of mammals and other vertebrates, these long (300 nucleotides, on average) DNA fragments have remained unchanged for hundreds of millions of years, despite numerous mutations happening within them. We do not yet know the function of these elements, but their extraordinary evolutionary stability could help us devise new approaches to preventing harmful mutations that lead to cancer and genetic disorders. We sought to discover why ultra-conserved non-coding elements are so resistant to change by studying their smaller building blocks, called dinucleotides, which play a crucial role in the shape and structure of DNA. Using a bioinformatics approach, we compared the differences in arrangement of dinucleotides in the ultra-conserved non-coding elements to the rest of the human genome. Our study revealed unique patterns within the ultra-conserved non-coding elements sections that distinguish them from the rest of our genetic code.Long human ultra-conserved non-coding elements (UCNEs) do not have any sequence similarity to each other or other characteristics that make them unalterable during vertebrate evolution. We hypothesized that UCNEs have unique dinucleotide (DN) composition and arrangements compared to the rest of the genome. A total of 4272 human UCNE sequences were analyzed computationally and compared with the whole genomes of human, chicken, zebrafish, and fly. Statistical analysis was performed to assess the non-randomness in DN spacing arrangements within the entire human genome and within UCNEs. Significant non-randomness in DN spacing arrangements was observed in the entire human genome. Additionally, UCNEs exhibited distinct patterns in DN arrangements compared to the rest of the genome. Approximately 83% of all DN pairs within UCNEs showed significant (>10%) non-random genomic arrangements at short distances (2–6 nucleotides) relative to each other. At the extremes, non-randomness in DN spacing distances deviated up to 40% from expected values and were frequently associated with GpC, CpG, ApT, and GpG/CpC dinucleotides. The described peculiarities in DN arrangements have persisted for hundreds of millions of years in vertebrates. These distinctive patterns may suggest that UCNEs have specific DNA conformations.

Age and early life adversity (ELA) are both key determinants of health, but whether they target similar physiological mechanisms across the body is unknown due to limited multi-tissue datasets from well-characterized cohorts. We generated DNA methylation (DNAm) profiles across 14 tissues in 237 semi-free ranging rhesus macaques, with records of naturally occurring ELA. We show that age-associated DNAm variation is predominantly tissue-dependent, yet tissue-specific epigenetic clocks reveal that the pace of epigenetic aging is relatively consistent within individuals. ELA effects on loci are adversity-dependent, but a given ELA has a coordinated impact across tissues. Finally, ELA targeted many of the same loci as age, but the direction of these effects varied, indicating that ELA does not uniformly contribute to accelerated age in the epigenome. ELA thus imprints a coordinated, tissue-spanning epigenetic signature that is both distinct from and intertwined with age-related change, advancing our understanding of how early environments sculpt the molecular foundations of aging and disease.