Obesity: Genetic and Environmental Factors

• Americans sought to treat obesity and it's link to chronic heart disease with treatments.
• Overeating was believed to be the cause of being overweight by Experts, and behavior modification was seen as the right treatment.
• The development of genome-wide association studies (GWAS) has led to discovering genetic associations and awareness of monogenic and polygenic obesity causes.
• Approximately 127 sites in the human genome show linkage with obesity by GWAS.
• More than 500 obesity-related genes are recognized in humans.
• Obesity can be influenced via obesogenic exposures, unhealthy dietary habits, sedentary lifestyle, and sleep disorders.
• Epigenetic regulations of targeted genes related to obesity are responsive to a healthy environment, healthy nutrition, regular physical activity and regular sleep/wake cycles.
• Environmentally-induced epigenetic transgenerational inheritance of obesity can occur.
• Epigenetics refers to the study of molecular processes influencing information flow between a constant DNA sequence and variable gene expression patterns.
• Nuclear organization, DNA methylation, histone modification, and RNA transcription are all studied in epigenetics.
• Epigenetic processes can result in intergenerational effects.
• While the genome is the same in all cell types, cells differ because the genome is regulated differently in each cell type, a process controlled by epigenetics.
• Epigenetic modifications, referred to as the "epigenome", occur within an organism's genome.
• Most epigenetic modifications are temporary and reversible, allowing cells to respond and adapt to environmental and behavioral changes.
• Environmental factors can imprint the genome and impact the epigenome.
• Exposing an F0 generation gestating female to an environmental insult exposes the developing F1 generation embryo.
• Epimutations from a gestating female exposed to environmental factors can influence the F2/F3 generations by altering methylation patterns.
• Transmission of epimutations from a gestating female to future generations is considered epigenetic transgenerational inheritance.
• In males, the germline becomes the F1 generation and is directly exposed to the environmental toxicant, not considered to be transgenerational.
• Therefore, the F2 generation is the first transgenerational offspring in males.

Epigenetic Code

• The most recognized epigenetic regulations: DNA tagging, Histone modifications, Non-coding RNAs (ncRNAs), RNA modifications (post-transcriptional modifications)

DNA Methyl Transferases

• DNA methyltransferases (DNMTs) enzymes catalyze the transfer of a methyl group to DNA.
• All DNMTs share a conserved catalytic domain.

Target CpG Islands

• CpG islands are DNA regions with a high frequency of CpG sites, where a cytosine nucleotide is followed by a guanine nucleotide.
• CpG Islands are usually 200 to 2000 base pairs long and have a higher-than-average GC content.
• CpG islands are typically found near gene promoters.
• CpG islands play a crucial role in gene regulation, with their unmethylation allowing active transcription and methylation leading to gene silencing.

DNA Tagging: Functional Differences

• DNMT1 preserves the methylation pattern during cell division
• Histone modifications can be inherited through cell divisions that provide a mechanism for maintaining gene expression patterns across generations of cells.
• DNMT2/3 induce de novo DNA methylation to control differentiation and reprogramming.
• De novo DNA methylation can include methylation of new CpG sites or increased methylation levels of previous CpG sites.

DNA Tagging: DNMT1

• DNA methyltransferase 1 (DNMT1) maintains existing methylation during DNA replication, distinguishing it from other DNMTs.
• DNMT1 recognizes hemimethylated DNA (where only one strand is methylated) and adds methyl groups to the newly synthesized strand.
• DNMT1 ensures methylation patterns are faithfully copied to daughter cells.

DNA Tagging: Impact of Methylation on Gene Expression

• DNA methylation inhibits transcription and its control depends on the location of the methylation relative to genes.
• Methylation of DNA at the promoter region is seen in repressed genes, and methylated CpGs near transcription initiation sites prevent transcription.
• Gene body methylation is strongly correlated with gene expression.
• Gene body methylation has a role in splicing, with exons being more heavily methylated than introns and a transition at exon-intron boundaries.
• DNMTs play a key role in silencing (transcriptional repression) of transposons ("jumping genes") that change position within the genome.
• Transposable elements are upregulated in DNMT1-deficient mice.
• In mammals, transposons are silenced through bulk de novo methylation (for evolutionary 'old' transposons) and PIWI protein recognition (for evolutionarily young retrotransposons).

DNA Methylation and X-Chromosome Inactivation

• X-chromosome inactivation (XCI) occurs when female mammals silence one of the two X chromosomes to achieve dosage compensation.
• DNA methylation is essential for XCI.
• Sexual dimorphisms at low methylation levels (0-50%) on the X chromosomes are primarily reflected by differences at promoter-proximal CpG islands.
• Methylation levels at non-CpG islands on the X chromosome are similar in both males and females.
• Both sexes show comparable DNA methylation on autosomal chromosome 3.

Histone Modifications

• The Protein Data Bank (PDB) provides access and tools for the exploration visualization, and analysis of 3D molecular structures.
• The nucleosomal DNA path in a human nucleosome core particle illustrates positioning, mobility, and packaging of nucleosomes.
• Detailed information about the human nucleosome core particle (NCP) structure elucidates the impact of chromatin properties on gene regulation mechanisms.
• The covalent post-translational modifications (PTMs) of the histone tails (methylation, acetylation, and ubiquitination) allow enzymes to catalyze the addition of the PTMs.
• Histone modifications regulate gene expression by altering chromatin structure, influence the accessibility of DNA to transcription factors and other regulatory proteins.
• Histone modifications lead to condensed or relaxed chromatin.
• Specific histone modifications can serve as binding sites for proteins that either activate or repress transcription.
• Combinations of different histone modifications can create a complex code that is read by other proteins to regulate gene expression, and allow cells to respond to environmental changes and developmental cues by modulating gene expression.

Non-Coding RNAs

• Gene transcriptional regulation by non-coding RNAs (NCRs) is a relatively recently discovered mode of regulation.
• Most human transcripts are not translated into peptides, but the NCRs serve vital functions.
• Many recent studies suggest that NCRs are the most common regulatory RNAs.
• NCRs include miRNAs, piRNAs, endogenous siRNAs, and long non-coding RNAs.
• NCRs are processed through the RNA-induced silencing complex (RISC) together with a member of the Argonaute (AGO) protein family.
• An empty Argonaute (AGO) loads a small RNA duplex to form pre-RISC.
• The passenger strand is ejected from AGO.
• The complex consisting of AGO and a guide strand is called mature RISC, or simply RISC.
• RISC is directed by its bound small RNA to target complementary RNAs, represses their expression through mRNA cleavage, degradation, and/or translational repression.
• The silencing mechanism can be mediated by micro RNA (miRNA) and silencing RNA (siRNA)
• MIRNA is produced by endogenous genes containing hairpin structures of 65–70 nt pre-miRNA
• The hairpin structure is processed into pre-miRNA in the nucleus, where it is processed into miRNA by Dicer and loaded to protein Argonaute (AGO2).
• SIRNA derived from the long double stranded RNA molecule is cut into fragments of 21–25 nt by the Dicer enzyme and then loaded to protein Argonaute (AGO2).
• The loaded Argonaute protein recognizes and degrades mRNA that is complementary to the loaded guide strand.
• Non-coding RNAs (NcRNAs) regulate expression at the gene and chromosome level.
• Piwi-interacting RNAs (piRNAs) and long non-coding RNAs (lncRNAs) are types of non-coding RNAs with distinct characteristics and functions.
• RNA modifications affect either the base or sugar moiety and regulate gene expression at the post-transcriptional level.
• Over 170 modifications have been identified on RNA, methylation account for two-thirds of total cases and exist on all RNAs.