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Publication: Applied Epigenetics for Mental Health Professionals
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- 15q11-q13:
- Denotation of the area of chromosome 15’s long arm, close to the centromere at region 1, covering bands 1–3. This section contains many genes relevant for neurodevelopment, several of which are subject to genomic imprinting, leading to parent-of-origin–specific expression. Genetic errors affecting this region before conception may lead to the development of PWS, Angelman syndrome, or dup15q.
- 15q11-q13 duplication syndrome (dup15q):
- A neurodevelopmental disorder that, like Angelman syndrome and PWS, is associated with genes in 15q11-q13. In dup15q, maternal and paternal copies of the chromosome are imprinted, and one copy contains a duplication of the genes in this region, leading to an increased copy number.
- adaptation:
- The genetically programmed development of neural networks based on an experience-dependent maturation process, with subsequent impact on behavior.
- age acceleration:
- The characteristic of a person’s epigenetic age (DNA methylation age) being older than their chronological age.
- age deceleration:
- The characteristic of a person’s epigenetic age (DNA methylation age) being younger than their chronological age.
- allele:
- One form of two or more variants of the same gene. Alleles are typically heritable and vary from one another in their DNA base sequence, which may result from a difference of a single base or nucleotide, as in a SNP, or deletions or insertions of longer portions of DNA in the gene.
- alternative splicing:
- The condition in which multiple different forms of RNA transcripts may emerge from the same gene. In RNA splicing, some exons may be rearranged or even removed, creating multiple variants or isoforms of mature RNA, which may then be translated into different proteins.
- Angelman syndrome:
- A neurodevelopmental disorder that, like PWS and dup15q, is associated with silencing of genes located in 15q11-q13. In Angelman syndrome, the maternally expressed genes are dysfunctional or absent.
- anticipation:
- The symptoms and features of a genetic condition appearing earlier in life or manifesting more severely as the condition affects subsequent generations. Examples include Huntington’s disease and FXS.
- anticodon:
- The three-base-pair sequence complementary to a codon; for example, CAU is the anticodon for AUG.
- antiparallel:
- Oriented in opposite directions.
- aryl hydrocarbon receptor repressor (AHRR):
- Gene involved in cell growth, differentiation, immune function, and response to environmental toxins. DNA methylation patterns of this gene appear to correlate with smoking and smoking cessation, as well as PTSD.
- autism spectrum disorder (ASD):
- A neurodevelopmental disorder that emerges in early childhood, with features such as deficient social-emotional reciprocity, abnormal communication, restrictive behaviors, and fixed interests, among others.
- autosome:
- A non-sex chromosome; humans typically carry 22 pairs of autosomes, inheriting one copy from each parent.
- base sequence:
- The order of nucleotide bases of DNA; genetic information.
- biallelic expression:
- The condition in which gene copies (alleles) from both parents are concurrently expressed.
- biological aging:
- Changes with age that are not reliably predicted by chronological age.
- bisulfite sequencing:
- A variant of NGS with an extra step, allowing for location of methylated cytosines in a DNA sample. The addition of sodium bisulfite converts unmethylated cytosine to uracil, while methylated/hydroxymethylated cytosines and other bases remain unchanged. After sequencing, the output shows a sequence of bases that is compared to known standards, revealing the location of unmethylated cytosine bases compared with methylated cytosines.
- brain-derived neurotrophic factor (BDNF):
- A neuronal growth factor widely expressed in the central nervous system that stimulates neuron differentiation, development, plasticity, synaptogenesis, and long-term potentiation. Dysregulated BDNF has been tied to a variety of mental illnesses (e.g., major depressive disorder) in addition to neurodegenerative disorders (e.g., amyotrophic lateral sclerosis, Parkinson’s disease, Alzheimer’s disease, Huntington’s disease) and lack of neuroprotection following cerebrovascular accident.
- catechol-O-methyltransferase (COMT):
- An enzyme (and associated gene, COMT) that breaks down catecholamines, including dopamine and norepinephrine. COMT is located on 22q11, and polymorphisms are associated with increased risk for development of schizophrenia.
- central dogma of molecular biology:
- Genetic information is passed from DNA to RNA through transcription and RNA to protein through translation. Genetic information is not passed between proteins or backward from protein to DNA.
- chromatin:
- A strand of DNA that has undergone some level of condensation and organization by interactions with proteins (i.e., histones). Chromatin ranges from lightly packed euchromatin to more coiled, condensed heterochromatin. The most condensed form of this structure is referred to as the chromosome.
- chromatin remodeling:
- A dynamic, reversible process by which accessibility of nucleosomes is increased or decreased, with possible influences on rates of gene expression. Mechanisms of chromatin remodeling may include histone modifications (e.g., histone methylation or acetylation) and the effects of other chromatin remodeling complexes.
- chromosome:
- A long, heritable strand of DNA in its most condensed form. Humans typically carry 23 pairs of chromosomes, inheriting one from each parent.
- codon:
- A sequence of three nucleotides, usually abbreviated as the sequence of three bases, that corresponds to a specific amino acid or stop signal during translation. For example, CGA corresponds to arginine; UAG provides a stop signal.
- copy number variant (CNV):
- In sections of the genome that are duplicated or repeated, an individual may carry a different number of copies than the typical population. Major examples include duplications (an extra copy of one portion of the genome) and deletions (one less copy of one portion of the genome). Sections may be short, as in the case of trinucleotide repeats, or long, encompassing multiple genes.
- core promoter:
- A major segment of the promoter, located just upstream of the transcription start site, that is relevant for staging the preinitiation complex.
- CpG island:
- A sequence of ~ 1,000 base pairs containing an elevated proportion of cytosine-[phosphate]-guanine (CpG) dinucleotides. CpG islands are mostly unmethylated; however, patterns of CpG island methylation may affect rates of gene expression. About half of CpG islands are within known promoter regions, and the other half (orphan CpG islands) are outside of promoters.
- de novo mutation:
- A mutation, or change to the base sequence of DNA, that is new—that is, not inherited from either parent.
- deoxyribonucleic acid (DNA):
- A chain of nucleotides comprising deoxyribose, a nitrogen base (guanine [G], adenine [A], cytosine [C], and thymine [T]), and a phosphate group, oriented in such a way that the phosphate group forms the backbone and confers a negative charge (acidic property) to the polynucleotide. The bases are usually oriented to face the medial position when forming a helix.
- deoxyribose:
- A pentose sugar essential for DNA. Differs from ribose in the absence of a hydroxyl group on the carbon atom in the second position.
- Developmental Origins of Health and Disease (DOHaD):
- A frequently cited research framework and conceptual model in epigenetic literature that pays particular attention to nutrition and stress in early development with respect to later development of preventable chronic disease.
- diathesis-stress model:
- A framework positing the interactive effect of the underlying predisposition to disease (diathesis) with the degree of exposure to stress.
- distal promoter:
- A major segment of the promoter, located farther upstream of the transcription start site than other promoter segments, that includes regulatory sequences such as enhancers, insulators, and silencers.
- DNA methyltransferase (DNMT):
- An enzyme that facilitates the transition of a methyl group from a methyl donor to a select cytosine base in a sequence of DNA.
- downstream:
- Next in the sequence, relative to the 5′-to-3′ direction.
- enrichment analysis:
- Examples are gene set enrichment analysis (GSEA), network enrichment analysis, or functional enrichment analysis. An application of genomewide DNA analysis in which patterns of over- or underrepresented findings (e.g., DNA methylation) in a sample are compared with previously identified patterns across a network of regions of interest or a gene set. Patterns may be tied to general biological processes, which may then be compared to the study sample.
- epigenetic clock:
- A means of estimating biological age using DNA methylation patterns of specific CpG sites across the epigenome. This complex biomarker, which may help to estimate biological age, suggests factors that may accelerate, decelerate, or even reverse biological aging.
- epigenetics:
- The study of changes in gene products and gene expression without any alteration to the genome base sequence. Epigenetic mechanisms are susceptible to environmental triggers and include DNA methylation and histone modification, which affect a gene’s ability to interact with transcriptional machinery, as well as functions of noncoding RNA such as miRNAs, which affect gene expression.
- epigenome:
- The entire compilation of epigenetic marks carried by an individual. The epigenome includes all DNA methylation and histone modification patterns across every chromatin. Some marks of the epigenome are reset before reproduction; others are transmitted to subsequent generations.
- epimutation:
- Errors in epigenetic methylation or imprinting patterns.
- euchromatin:
- A lightly packed, typically more transcriptionally active form of chromatin.
- exon:
- Portion of a gene joined together during RNA splicing into a final mature RNA transcript that may ultimately undergo translation into a protein. Exons are often referred to as coding regions within genes.
- expression:
- 1. The appearance in a phenotype of a characteristic or effect attributed to a particular gene. 2. The process by which genetic information is transmitted from DNA to functional end products including proteins or noncoding RNA.
- fetal alcohol spectrum disorder (FASD):
- A set of developmental consequences caused by in utero exposure to alcohol.
- fetal alcohol syndrome (FAS):
- A disorder considered to be at the extreme end of FASD, following chronic and heavy alcohol use during gestation.
- fetal programming:
- The effect that environment has in the developing fetus with respect to later pathology, through developmental, genetic, and epigenetic changes.
- FK506 binding protein 51 (FKBP5):
- Co-chaperone of the glucocorticoid receptor complex that inhibits glucocorticoid receptor signaling. FKBP5 hinders the interaction between intracellular glucocorticoid receptor and glucocorticoid, ultimately disrupting the signal pathway by impeding translocation to the nucleus. FKBP5 plays an integral role in the negative feedback loop of the glucocorticoid signal pathway.
- fragile X messenger ribonucleoprotein 1 (FMR1):
- Gene encoding FMRP, located on the q arm of the X chromosome. FMR1 may undergo a trinucleotide expansion of CGG repeats in a region upstream from the coding region, where the number of repeats is associated with decreased expression of FMRP and emergence of symptoms: < 45 repeats is the wild-type variant, 45–200 repeats is considered a premutation and may be associated with symptoms, and > 200 repeats is a full mutation associated with development of FXS.
- fragile X messenger ribonucleoprotein (FMRP):
- An RNA-binding protein understood to interact with many proteins relevant for proper dendrite maturation, synaptic plasticity, and overall neurological development. FMRP is encoded by FMR1, which is susceptible to trinucleotide expansions. These expansions occur outside of the coding region and affect the rate of expression, not the structure, of the protein.
- fragile X–related elements 1 and 2 (FREE1 and FREE2):
- Epigenetic boundaries flanking FMR1. FREE1 is upstream and FREE2 downstream of the promoter region. Typically, DNA methylation patterns show a notable transition from methylated to nonmethylated at these boundaries, but in FXS, methylation crosses these boundaries, transcending FREE1 and the entirety of the promoter region including the CpGs, transcription start site, CGG repeats, and FREE2.
- fragile X syndrome (FXS):
- A heritable, single-gene disorder associated with FMR1.
- γ-aminobutyric acid (GABA):
- The primary neurotransmitter of the brain and spinal cord. GABA plays a role in motor signaling, respiratory rate, proprioception sleep, and anxiety, among others.
- gene:
- A section of DNA that may be expressed. Expression may occur after translation into functional RNA (as in miRNAs and noncoding RNA) or transcription into a protein.
- gene set enrichment analysis (GSEA):
- A method using statistical approaches to identify genes or proteins that are overrepresented and thus may be associated with different phenotypes.
- genotype:
- The particular gene variant (allele) or combination of alleles that an individual carries.
- gestational stress:
- See prenatal stress.
- glucocorticoid receptor:
- A nuclear receptor that may bind to a glucocorticoid hormone. Upon binding to a glucocorticoid, the glucocorticoid receptor may move into the nucleus and bind to a particular DNA sequence known as the glucocorticoid response element (GRE), then activate or repress transcription of the associated site.
- glutamate decarboxylase 1 (GAD1):
- An enzyme (and associated gene, GAD1, located on chromosome 2) that converts glutamate to GABA. Differential expression of GAD1 has been associated with schizophrenia, among other disorders.
- glutamate receptor subunit ε-2 (GRIN2B):
- A subunit of the N-methyl-d-aspartate (NMDA) receptor that appears to be susceptible to methylation changes from environmental stressors. Mutations of GRIN2B have been associated with a variety of neurodevelopmental and psychiatric disorders.
- heterochromatin:
- A more condensed, typically less transcriptionally active, form of chromatin.
- heteroduplex:
- Hybridization of the RNA and DNA; the genetic recombination of single complementary strands derived from different sources.
- histone:
- A protein essential for chromatin organization. DNA winds around an octamer of core histones (a combination of H2A, H2B, H3, and H4) to form nucleosomes. Linker histones (H1 and H5) further stabilize the nucleosome structure and bind to linker DNA, which joins adjacent nucleosomes.
- histone acetyltransferase (HAT):
- An enzyme that facilitates the addition of an acetyl group to a histone.
- histone deacetylase (HDAC):
- An enzyme that facilitates the removal of an acetyl group from a histone.
- histone demethylase:
- An enzyme that facilitates the removal of a methyl group from a histone.
- histone methyltransferase (HMT):
- An enzyme that facilitates the transition of a methyl group from a methyl donor to a histone.
- Huntingtin gene (HTT):
- A gene located on chromosome 4 that contains a repeating CAG segment within the coding region. CAG coincides with the amino acid glutamine, so the protein product contains a polyglutamine chain that corresponds to the number of CAG repeats within the gene. Having 10–35 repeats is the wild-type variant; higher numbers of repeats, > 40, are associated with development of Huntington’s disease. With more repeats (longer polyglutamine chains), the protein’s three-dimensional conformational structure is altered, although it continues to function. The structural alteration leads to the formation of inclusions within the nucleus and other cell compartments.
- Huntington’s disease:
- A neurodevelopmental disorder attributed to a repeating CAG segment within the coding region of a single gene (HTT).
- hypothalamic-pituitary-adrenal axis (HPA axis):
- A hormone-secreting neuroendocrine chain, which includes the hypothalamus, pituitary gland, and adrenal glands, that tightly feeds back on itself and is associated with the body’s stress response.
- imprinting:
- The epigenetically controlled preferential expression of one parental allele over the other (i.e., monoallelic expression based on parent-of-origin). The process of imprinting begins in gametogenesis, during which genes may be tagged based on the parent-of-origin. Some genes in some tissues may then be imprinted if only one of the copies is expressed based on these parent-of-origin epigenetic marks. If the maternal gene is imprinted, it is silenced, leaving the gene copy from the father to be expressed (paternally expressed gene). If the paternal gene is imprinted, then the maternal allele is expressed (maternally expressed gene). Imprinting does not refer to the parent-of-origin marks on the genes but rather the entire regulatory process of gene expression based on the parent-of-origin markings.
- imprinting control region (ICR):
- A DNA sequence, found on the genome near imprinted genes, that regulates their expression.
- intergenerational transmission:
- Epigenetic inheritance in gametes formed before trauma exposure.
- intergenic:
- 1. (describing orphan CpG islands) Found between genes; 2. (describing miRNAs) Transcribed independently from neighboring genes.
- intragenic:
- Found within genes (describing orphan CpG islands).
- intron:
- A portion of a gene that is removed from an RNA transcript before translation into a protein. Introns are often referred to as noncoding regions within genes.
- intronic:
- Transcribed along with another gene before being excised during posttranscriptional modification (describing miRNAs).
- l-acetylcarnitine (LAC):
- (aka acetyl-l-carnitine, l-carnitine, carnitine) A compound available through diet and biosynthesis that acts similarly to an HDAC inhibitor. Some research has suggested that LAC has an antidepressant effect through promoting acetylation of histones bound at promoters of genes, increasing expression of the glutamate receptor gene and BDNF in neural tissue.
- long interspersed element 1 (LINE-1):
- A repetitive portion of DNA duplicated widely across the genome. In research, methylation of LINE-1 may be used as a proxy measurement for global DNA methylation patterns.
- maladaptation:
- Responses to experiences—commonly toxic environmental stimuli—leading to impacts on neural networks and subsequent behavior patterns that may be dysfunctional across other environments.
- messenger RNA (mRNA):
- An RNA transcript that is translated into a protein.
- methyl-CpG-binding domain protein (MBDP):
- A protein that contains a region able to bind to methylated CpG sites of DNA. After binding to DNA, MBDPs typically attract additional complexes that generally downregulate expression of the associated gene through repressively modifying histones or otherwise increasing chromatin organization. Therefore, MBDPs are essential for the epigenetic regulation of gene expression.
- methyl CpG binding protein 2 (MeCP2):
- An MBDP that binds to methylated cytosine within CpG islands, affecting regulation of associated genes. The function of MeCP2 is of particular importance for neurodevelopment. Mutations of MeCP2 (located on the X chromosome) have been implicated in the development of Rett syndrome.
- microarray (chip):
- A method for genotyping or estimating DNA methylation at multiple sites of a DNA sample at once. A prepared, fragmented DNA sample is washed over a chip containing a library of DNA probes. If the sample contains strands that are complementary to the probes, they bind (hybridize) to those probes. When used for DNA methylation, binding strength at the locations is measured, showing the proportion of methylated cytosines in a given region of interest on the genome. The DNA probes used include many sites of interest on the epigenome, including CpG islands, coding regions, promoters, and enhancers.
- microRNA (miRNA):
- Small (~ 18–25 nucleotides), single-stranded, regulatory RNA segments that can silence a gene by posttranscriptionally degrading mRNA or by preventing the attachment of ribosomal subunits, inhibiting translation.
- monoallelic expression:
- The condition in which only one gene copy (allele) is expressed, while the other is silenced. Examples of monoallelic expression include imprinting and X-inactivation.
- monoamine oxidase (MAO):
- A human enzyme (and MAO, the gene encoding it) that breaks down monoamines (in particular, serotonin, dopamine, and norepinephrine). MAO includes two isoforms, encoded by monoamine oxidase A (MAOA) and monoamine oxidase B (MAOB). Polymorphisms of both isoforms have been associated with development of psychiatric illnesses, and MAOB has been found to be susceptible to effects of smoking, with reductions in DNA methylation and subsequent increases in expression. MAOI = monoamine oxidase inhibitor.
- mutation:
- A potentially heritable change to the base sequence of DNA that consists of a substitution, deletion, or insertion of one or more bases.
- neuroapoptosis:
- The functional programmed death of neurons.
- next-generation sequencing (NGS):
- Also called next-gen sequencing, second-generation sequencing, or massive parallel sequencing. A technique used to determine the sequence of a DNA sample. The sample is broken down into fragments that are fixed to a plate and replicated while being monitored. Data reveal the DNA sequences of the complementary strands synthesized during this process, which are then combined and processed through specialized computational programs, determining the DNA sequence of the entire sample.
- nitrogen base:
- (aka nitrogenous base, base) Nitrogen-containing molecules that are essential components of nucleosides and nucleotides. They include purine bases—guanine (G) or adenine (A)—and pyrimidine bases—cytosine (C), thymine (T), or uracil (U). DNA consists of bases G, A, C, and T; RNA consists of G, A, C, and U.
- noncoding RNA:
- A functional RNA transcript that is not translated into a protein end-product. Noncoding RNAs may serve regulatory functions; examples include miRNAs and Xist.
- nuclear receptor subfamily 3 group C member 1 (NR3C1):
- Glucocorticoid receptor gene, named based on its classification within steroid receptors.
- nucleoside:
- A molecule comprising a nitrogenous base and a pentose sugar (a nucleotide without a phosphate group). Examples include adenosine, guanosine, thymidine, cytidine, and uridine.
- nucleosome:
- A compact unit of DNA wound around a histone octamer. The appearance of a series of nucleosomes is often compared to beads on a string.
- nucleotide:
- Basic building blocks of the human genome, comprising a nitrogen base, a pentose sugar, and a phosphate group.
- orphan CpG island:
- A section of the genome outside of known gene promoter regions with elevated proportions of CpG dinucleotides. Orphan CpG islands are intragenic (found within genes) or intergenic (found between genes). Although they are outside of promoter regions, methylation of orphan CpG islands may affect regulation of transcriptional activity.
- p arm:
- Conventional name for the shorter of a chromosome’s two arms.
- penetrance:
- Of all people with a particular genotype (i.e., carrying a particular gene variant or allele), penetrance is the proportion of those who exhibit the associated phenotype.
- pentose sugar:
- A ring molecule of carbon, hydrogen, and oxygen that may be used in nucleosides and nucleotides. Ribose is used in RNA; deoxyribose is used in DNA.
- pharmacoepigenetics:
- The application of epigenetics to understanding medical treatment response.
- phenotype:
- An observable trait that is an outcome of gene expression and environment. A phenotype may be observable at the cellular level; at developmental, morphological, and functional levels; and at the behavioral level.
- pleiotropic:
- Variants of a single gene locus that produce differences in more than one trait.
- polygenic inheritance:
- A pattern of inheritance in which a trait is passed along by the cumulative effects of multiple genes.
- polynucleotide:
- A chain of nucleotides connected to each other via phosphodiester bonds.
- Prader-Willi syndrome (PWS):
- A neurodevelopmental disorder that, like Angelman syndrome, is associated with silencing of genes located in 15q11-q13. In PWS, the paternally expressed genes are mutated or absent.
- preconception stress:
- Stressful experiences occurring within a short window of time just before conception.
- preinitiation complex:
- A large group of proteins, including Pol II and multiple transcription factors, that bind to the core promoter, allowing for initiation of transcription of DNA to RNA by Pol II.
- pre-mRNA:
- An initial, precursor mRNA transcript that undergoes posttranscriptional modification, including removal of introns and splicing, before becoming mature mRNA, which may then be translated into a protein.
- premutation:
- A sequence of repeated nucleotides that is longer than in the wild-type allele but may produce no or attenuated disease symptoms. Premutations have a risk of transmitting a full mutation to offspring.
- prenatal stress:
- Stressful experiences occurring after conception but before birth.
- primer:
- Short, single strand of nucleic acid needed to initiate DNA synthesis.
- pro-BDNF:
- A precursor protein to brain-derived neurotrophic factor (BDNF). BDNF is a complex gene, with multiple exons and promoters, allowing for multiple different variants (isoforms) of BDNF mRNA transcript. Despite the multiple transcripts being translated into a variety of proteins (pre-pro-BDNF), these products undergo posttranslational cleavage to become the same pro-BDNF protein. Pro-BDNF undergoes further cleavage to yield the functional, mature BDNF protein.
- promoter:
- A DNA sequence along the genome that lies upstream from the transcription start site of a gene. Within this region, proteins including Pol II and transcription factors interact with DNA to carry out translation into RNA. The promoter includes core, distal, and proximal promoter segments.
- proximal promoter:
- A major segment of the promoter located upstream of the core promoter, near the transcription start site, that contains gene regulatory sequences, including CpG islands.
- q arm:
- Conventional name for the longer of a chromosome’s two arms.
- reelin (RELN):
- A protein (and associated gene, RELN) expressed by GABA neurons key to neurodevelopment (Cajal–Retzius cells), which regulate neuronal migration and synaptic plasticity. Downregulation of reelin, as with disrupted DNA methylation, has been associated with schizophrenia in addition to other neurodevelopmental disorders.
- resilience:
- A buffer for the risk of developing pathological responses to adverse events, containing elements across biological, psychological, and social systems.
- Rett syndrome (RTT):
- A neurodevelopmental disorder caused by mutation of a single gene (methyl CpG binding protein 2 [MeCP2]) on the X chromosome.
- ribonucleic acid (RNA):
- A chain of nucleotides comprising ribose, a nitrogen base (guanine [G], adenine [A], cytosine [C], and uracil [U]), and a phosphate group, oriented in such a way that the phosphate group forms the backbone and confers a negative charge (acidic property) to the polynucleotide. The bases are usually oriented to face the medial position when forming a helix.
- ribose:
- A pentose sugar essential for RNA, ribose differs from deoxyribose by the presence of a hydroxyl group on the carbon atom in the second position.
- RNA polymerase II (Pol II):
- A complex of proteins that translates DNA to RNA. Initiation of transcription is facilitated by a group of proteins known as a preinitiation complex. After initiation of transcription, Pol II leaves behind most of the preinitiation complex to continue elongating the transcribed strand of RNA based on the DNA sequence of the gene until reaching a termination signal.
- s-adenosylmethionine (SAM or SAM-e):
- A compound that acts as a methyl group donor for DNA and histone methylation, among other biochemical pathways. SAM is produced through enzymatic reaction of amino acid methionine with adenosine triphosphate (ATP).
- sex chromosome:
- Chromosomes (designated as X or Y in humans) typically carrying genes that determine biological sex characteristics.
- schizophrenia:
- A psychiatric disorder, conceived in recent years as a neurodevelopmental disorder, diagnosed based on the presence of positive (e.g., hallucinations, delusions) and negative (e.g., prosody of speech, social withdrawal, anhedonia) symptoms.
- Simons Foundation Autism Research Initiative (SFARI Gene):
- A frequently updated database available to researchers that tracks potential ASD risk genes.
- single-nucleotide polymorphism (SNP):
- A variation in a single base pair at a specified location on DNA which may be inherited or arise as a result of a mutation. Many SNPs have no effect on the individual (either they occur outside of a coding or regulatory region of a gene or they do not lead to a change in amino acid sequence during translation). Sometimes, SNPs can have effects on phenotype, including drug metabolism or development of pathology.
- skewed X-inactivation:
- An imbalance between maternally versus paternally expressed X chromosomes.
- sodium butyrate:
- (aka butyrate) A compound available from dietary sources or through biosynthesis that acts as an HDAC inhibitor, in addition to further enzymatic effects possibly leading to downstream DNA demethylation. Sodium butyrate may yield antidepressant effects through upregulation of BDNF expression.
- solute carrier family 6 member 4 (SLC6A4):
- A gene encoding the serotonin transporter (SERT), also known as 5-hydroxytryptamine transporter (5-HTT), which allows reuptake of serotonin into presynaptic neurons and plays a crucial role in the regulation of emotion, affect, and behavior. Variation in expression of SLC6A4 has been linked to a variety of mental illnesses including major depressive disorder.
- splicing (RNA splicing):
- A type of posttranscriptional modification in which portions of precursor RNA (introns) are selectively removed and the remaining portions (exons) are joined together in a process that ultimately yields mature RNA.
- stop codon:
- A sequence of three nucleotides that provide a signal to terminate translation at the end of a gene sequence.
- stress:
- Some force or event that disrupts homeostasis.
- stress response:
- Physiological actions occurring in tandem with protective behaviors necessary to maintain homeostasis.
- toxic stress:
- Prolonged, frequent, or intense adversity.
- transcription:
- The process of converting the base sequence of DNA into RNA.
- transcription factor:
- A protein that regulates the rate of gene expression by binding to DNA. Transcription factors contain DNA binding domains, which allow attachment to particular DNA sequences called response elements. The transcription factors may also form complexes with additional proteins and may act to upregulate or downregulate the rate of transcription of the associated gene.
- transgenerational transmission:
- Epigenetic inheritance in gametes formed after trauma exposure.
- translation:
- The process of converting mRNA into a protein.
- trauma:
- High-intensity stress.
- trinucleotide repeat expansion:
- A DNA mutation in which a series of three nucleotides is duplicated in tandem because of slipped strand mispairing during replication; associated with neurodevelopmental disorders including Huntington’s disease and FXS.
- tropomyosin receptor kinase B (TrkB):
- (aka tyrosine receptor kinase B, tropomycin receptor kinase B, neurotrophic receptor tyrosine kinase 2 [NTRK2]) A receptor bound to the neuron’s cell membrane that binds to BDNF extracellularly, leading to a cascade of intracellular effects, ultimately modulating gene expression and influencing neural growth and synaptic plasticity.
- upstream:
- Previous in the sequence, relative to the 5′-to-3′ direction.
- variant of uncertain significance (VUS):
- A gene form identified in an individual or sample that lacks enough data to indicate whether it is related to the development of a health condition or other clinically relevant outcome.
- X-inactivation:
- In individuals with two X chromosomes, the process by which one X chromosome is markedly condensed, with the effect of significantly downregulating expression of the genes on that chromosome. The process of X-inactivation takes place during embryonic development and involves a combination of both parent-of-origin and random mechanisms. Whichever X chromosome is inactivated is typically maintained over cell replications consistently across life.
- X-inactive specific transcript (Xist):
- A DNA sequence on the X chromosome encoding a functional long noncoding RNA that works to recruit and interact with protein complexes and other repressive epigenetic factors, ultimately leading to chromatin compaction.
- X-inactivation escape:
- Expression of a gene from the otherwise silenced X chromosome despite X-inactivation; evokes a dose difference, which can lead to phenotypic differences and consequences ranging from various disease states to cell death.
Information & Authors
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Published In
Applied Epigenetics for Mental Health Professionals
Pages: 153 - 168
Editors: Sallie G. De Golia, M.D., M.P.H., and Raziya S. Wang, M.D.
History
Published in print: 20 November 2023
Published online: 5 December 2024
© American Psychiatric Association Publishing
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