Contribution of epigenetic modifications to evolution

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Epigenetics is the study of changes in gene expression that occur via mechanisms such as DNA methylation, histone acetylation, and microRNA modification. When these epigenetic changes are heritable, they can influence evolution. Current research indicates that epigenetics has influenced evolution in a number of organisms, including plants and animals. [1]

Contents

In plants

Overview

DNA methylation is a process by which methyl groups are added to the DNA molecule. Methylation can change the activity of a DNA segment without changing the sequence. Histones are proteins found in cell nuclei that package and order the DNA into structural units called nucleosomes.[ citation needed ]

DNA methylation and histone modification are two mechanisms used to regulate gene expression in most organisms which includes plants and animals. DNA methylation can be stable during cell division, allowing for methylation states to be passed to other orthologous genes in a genome. DNA methylation can be reversed via enzymes known as DNA de-methylases, while histone modifications can be reversed by removing histone acetyl groups with deacetylases. The process of DNA methylation reversal is known DNA demethylation. [2] Interspecific differences due to environmental factors are shown to be associated with the difference between annual and perennial life cycles. There can be varying adaptive responses based on this. [3]

Arabidopsis thaliana

Forms of histone methylation cause repression of certain genes that are stably inherited through mitosis but that can also be erased during meiosis or with the progression of time. The induction of flowering by exposure to low winter temperatures in Arabidopsis thaliana shows this effect. Histone methylation participates in repression of expression of an inhibitor of flowering during cold. In annual, semelparous species such as Arabidopsis thaliana, this histone methylation is stably inherited through mitosis after return from cold to warm temperatures giving the plant the opportunity to flower continuously during spring and summer until it senesces. However, in perennial, iteroparous relatives the histone modification rapidly disappears when temperatures rise, allowing expression of the floral inhibitor to increase and limiting flowering to a short interval. Epigenetic histone modifications control a key adaptive trait in Arabidopsis thaliana, and their pattern changes rapidly during evolution associated with reproductive strategy. [3]

Another study tested several epigenetic recombinant inbred lines (epiRILs) of Arabidopsis thaliana - lines with similar genomes but varying levels of DNA methylation - for their drought sensitivity and their sensitivity to nutritional stress. It was found that there was a significant amount of heritable variation in the lines in regards to traits important for survival from drought and nutrient stress. This study proved that variation in DNA methylation could result in heritable variation of ecologically important plant traits, such as root allocation, drought tolerance, and nutrient plasticity. It also hinted that epigenetic variation alone could result in rapid evolution. [4]

Dandelions

Scientists found that changes in DNA methylation induced by stress were inherited in asexual dandelions. Genetically similar plants were exposed to different ecological stresses, and their offspring were raised in an unstressed environment. Amplified fragment-length polymorphism markers that were methylation-sensitive were used to test for methylation on a genome-wide scale. It was found that many of the environmental stresses caused induction of pathogen and herbivore defenses, which caused methylation in the genome. These modifications were then genetically transmitted to the offspring dandelions. The transgenerational inheritance of a stress response can contribute to the heritable plasticity of the organism, allowing it to better survive environmental stresses. It also helps add to the genetic variation of specific lineages with little variability, giving a greater chance of reproductive success. [5]

In animals

Primates

A comparative analysis of CpG methylation patterns between humans and primates found that there were more than 800 genes that varied in their methylation patterns among orangutans, gorillas, chimpanzees, and bonobos. Despite these apes having the same genes, methylation differences are what accounts for their phenotypic variation. The genes in question are involved in development. It is not the protein sequences that account for the differences in physical characteristics between humans and apes; rather, it is the epigenetic changes to the genes. Since humans and the great apes share 99% of their DNA, it is thought that the differences in methylation patterns account for their distinction. So far, there are known to be 171 genes that are uniquely methylated in humans, 101 genes that are uniquely methylated in chimpanzees and bonobos, 101 genes that are uniquely methylated in gorillas, and 450 genes that are uniquely methylated in orangutans. For example, genes involved in blood pressure regulation and the development of the inner ear's semicircular canal are highly methylated in humans, but not in apes. There are also 184 genes that are conserved at the protein level between humans and chimpanzees, but have epigenetic differences. Enrichments in multiple independent gene categories show that regulatory changes to these genes have given humans their specific traits. This research shows that epigenetics plays an important role in the evolution of primates. [6] It has also been shown that cis-regulatory elements changes affect the transcription start sites (TSS) of genes. 471 DNA sequences are found to be enriched or depleted in regards to histone trimethylation at the H3K4 histone in chimpanzee, human, and macaque prefrontal cortexes. Among these sequences, 33 are selectively methylated in neuronal chromatin from children and adults, but not from non-neuronal chromatin. One locus that was selectively methylated was DPP10, a regulatory sequence that showed evidence of hominid adaptation, such as higher nucleotide substitution rates and certain regulatory sequences that were missing in other primates. Epigenetic regulation of TSS chromatin has been identified as an important development in the evolution of gene expression networks in the human brain. These networks are thought to play a role in cognitive processes and neurological disorders. [7] An analysis of methylation profiles of humans and primate sperm cells reveals epigenetic regulation plays an important role here as well. Since mammalian cells undergo reprogramming of DNA methylation patterns during germ cell development, the methylomes of human and chimp sperm can be compared to methylation in embryonic stem cells (ESCs). There were many hypomethylated regions in both sperms cells and ESCs that showed structural differences. Also, many of the promoters in human and chimp sperm cells had different amounts of methylation. In essence, DNA methylation patterns differ between germ cells and somatic cells as well as between human and chimpanzee sperm cells. Meaning, differences in promoter methylation could possibly account for the phenotypic differences between humans and primates. [8] Research has also shown surprisingly amounts of conserved tissue-specific methylation, in line with phylogenetic relatedness [9]

Chickens

Red Junglefowl, an ancestor of domestic chickens, show that gene expression and methylation profiles in the thalamus and hypothalamus differed significantly from that of a domesticated egg-laying breed. Methylation differences and gene expression were maintained in the offspring, depicting that epigenetic variation is inherited. Some of the inherited methylation differences were specific to certain tissues, and the differential methylation at specific loci was not altered much after intercrossing between Red Junglefowl and domesticated laying hens for eight generations. The results hint that domestication has led to epigenetic changes, as domesticated chickens maintained a higher level of methylation for more than 70% of the genes. [10]

Role in evolution

The role of epigenetics in evolution is clearly linked to the selective pressures that regulate that process. As organisms leave offspring that are best suited to their environment, environmental stresses change DNA gene expression that is further passed down to their offspring, allowing for them also to better thrive in their environment. The classic case study of the rats who experience licking and grooming from their mothers pass this trait to their offspring shows that a mutation in the DNA sequence is not required for a heritable change. [11] Basically, a high degree of maternal nurturing makes the offspring of that mother more likely to nurture their own children with a high degree of care as well. Rats with a lower degree of maternal nurturing are less likely to nurture their own offspring with so much care. Also, rates of epigenetic mutations, such as DNA methylation, are much higher than rates of mutations transmitted genetically [12] and are easily reversed. [13] This provides a way for variation within a species to rapidly increase, in times of stress, providing opportunity for adaptation to newly arising selection pressures.[ citation needed ]

Lamarckism

Lamarckism supposes that species acquire characteristics to deal with challenges experienced during their lifetimes, and that such accumulations are then passed to their offspring. In modern terms, this transmission from parent to offspring could be considered a method of epigenetic inheritance. Scientists are now questioning the framework of the modern synthesis, as epigenetics to some extent is Lamarckist rather than Darwinian. While some evolutionary biologists have dismissed epigenetics' impact on evolution entirely, others are exploring a fusion of epigenetic and traditional genetic inheritance. [14]

See also

Related Research Articles

<span class="mw-page-title-main">Heredity</span> Passing of traits to offspring from the species parents or ancestor

Heredity, also called inheritance or biological inheritance, is the passing on of traits from parents to their offspring; either through asexual reproduction or sexual reproduction, the offspring cells or organisms acquire the genetic information of their parents. Through heredity, variations between individuals can accumulate and cause species to evolve by natural selection. The study of heredity in biology is genetics.

Genomic imprinting is an epigenetic phenomenon that causes genes to be expressed or not, depending on whether they are inherited from the female or male parent. Genes can also be partially imprinted. Partial imprinting occurs when alleles from both parents are differently expressed rather than complete expression and complete suppression of one parent's allele. Forms of genomic imprinting have been demonstrated in fungi, plants and animals. In 2014, there were about 150 imprinted genes known in mice and about half that in humans. As of 2019, 260 imprinted genes have been reported in mice and 228 in humans.

<span class="mw-page-title-main">Epigenetics</span> Study of DNA modifications that do not change its sequence

In biology, epigenetics is the study of heritable traits, or a stable change of cell function, that happen without changes to the DNA sequence. The Greek prefix epi- in epigenetics implies features that are "on top of" or "in addition to" the traditional genetic mechanism of inheritance. Epigenetics usually involves a change that is not erased by cell division, and affects the regulation of gene expression. Such effects on cellular and physiological phenotypic traits may result from environmental factors, or be part of normal development. They can lead to cancer.

<span class="mw-page-title-main">Euchromatin</span> Lightly packed form of chromatin that is enriched in genes

Euchromatin is a lightly packed form of chromatin that is enriched in genes, and is often under active transcription. Euchromatin stands in contrast to heterochromatin, which is tightly packed and less accessible for transcription. 92% of the human genome is euchromatic.

<span class="mw-page-title-main">Cellular differentiation</span> Developmental biology

Cellular differentiation is the process in which a stem cell changes from one type to a differentiated one. Usually, the cell changes to a more specialized type. Differentiation happens multiple times during the development of a multicellular organism as it changes from a simple zygote to a complex system of tissues and cell types. Differentiation continues in adulthood as adult stem cells divide and create fully differentiated daughter cells during tissue repair and during normal cell turnover. Some differentiation occurs in response to antigen exposure. Differentiation dramatically changes a cell's size, shape, membrane potential, metabolic activity, and responsiveness to signals. These changes are largely due to highly controlled modifications in gene expression and are the study of epigenetics. With a few exceptions, cellular differentiation almost never involves a change in the DNA sequence itself. However, metabolic composition does get altered quite dramatically where stem cells are characterized by abundant metabolites with highly unsaturated structures whose levels decrease upon differentiation. Thus, different cells can have very different physical characteristics despite having the same genome.

A maternal effect is a situation where the phenotype of an organism is determined not only by the environment it experiences and its genotype, but also by the environment and genotype of its mother. In genetics, maternal effects occur when an organism shows the phenotype expected from the genotype of the mother, irrespective of its own genotype, often due to the mother supplying messenger RNA or proteins to the egg. Maternal effects can also be caused by the maternal environment independent of genotype, sometimes controlling the size, sex, or behaviour of the offspring. These adaptive maternal effects lead to phenotypes of offspring that increase their fitness. Further, it introduces the concept of phenotypic plasticity, an important evolutionary concept. It has been proposed that maternal effects are important for the evolution of adaptive responses to environmental heterogeneity.

<span class="mw-page-title-main">Epigenome</span> Biological term

An epigenome consists of a record of the chemical changes to the DNA and histone proteins of an organism; these changes can be passed down to an organism's offspring via transgenerational stranded epigenetic inheritance. Changes to the epigenome can result in changes to the structure of chromatin and changes to the function of the genome.

<span class="mw-page-title-main">Paramutation</span>

In epigenetics, a paramutation is an interaction between two alleles at a single locus, whereby one allele induces a heritable change in the other allele. The change may be in the pattern of DNA methylation or histone modifications. The allele inducing the change is said to be paramutagenic, while the allele that has been epigenetically altered is termed paramutable. A paramutable allele may have altered levels of gene expression, which may continue in offspring which inherit that allele, even though the paramutagenic allele may no longer be present. Through proper breeding, paramutation can result in siblings that have the same genetic sequence, but with drastically different phenotypes.

Histone methylation is a process by which methyl groups are transferred to amino acids of histone proteins that make up nucleosomes, which the DNA double helix wraps around to form chromosomes. Methylation of histones can either increase or decrease transcription of genes, depending on which amino acids in the histones are methylated, and how many methyl groups are attached. Methylation events that weaken chemical attractions between histone tails and DNA increase transcription because they enable the DNA to uncoil from nucleosomes so that transcription factor proteins and RNA polymerase can access the DNA. This process is critical for the regulation of gene expression that allows different cells to express different genes.

Epigenomics is the study of the complete set of epigenetic modifications on the genetic material of a cell, known as the epigenome. The field is analogous to genomics and proteomics, which are the study of the genome and proteome of a cell. Epigenetic modifications are reversible modifications on a cell's DNA or histones that affect gene expression without altering the DNA sequence. Epigenomic maintenance is a continuous process and plays an important role in stability of eukaryotic genomes by taking part in crucial biological mechanisms like DNA repair. Plant flavones are said to be inhibiting epigenomic marks that cause cancers. Two of the most characterized epigenetic modifications are DNA methylation and histone modification. Epigenetic modifications play an important role in gene expression and regulation, and are involved in numerous cellular processes such as in differentiation/development and tumorigenesis. The study of epigenetics on a global level has been made possible only recently through the adaptation of genomic high-throughput assays.

<span class="mw-page-title-main">Transgenerational epigenetic inheritance</span> Epigenetic transmission without DNA primary structure alteration

Transgenerational epigenetic inheritance is the transmission of epigenetic markers and modifications from one generation to multiple subsequent generations without altering the primary structure of DNA. Thus, the regulation of genes via epigenetic mechanisms can be heritable; the amount of transcripts and proteins produced can be altered by inherited epigenetic changes. In order for epigenetic marks to be heritable, however, they must occur in the gametes in animals, but since plants lack a definitive germline and can propagate, epigenetic marks in any tissue can be heritable.

Behavioral epigenetics is the field of study examining the role of epigenetics in shaping animal and human behavior. It seeks to explain how nurture shapes nature, where nature refers to biological heredity and nurture refers to virtually everything that occurs during the life-span. Behavioral epigenetics attempts to provide a framework for understanding how the expression of genes is influenced by experiences and the environment to produce individual differences in behaviour, cognition, personality, and mental health.

The epigenetics of schizophrenia is the study of how inherited epigenetic changes are regulated and modified by the environment and external factors and how these changes influence the onset and development of, and vulnerability to, schizophrenia. Epigenetics concerns the heritability of those changes, too. Schizophrenia is a debilitating and often misunderstood disorder that affects up to 1% of the world's population. Although schizophrenia is a heavily studied disorder, it has remained largely impervious to scientific understanding; epigenetics offers a new avenue for research, understanding, and treatment.

Epigenetics of human development is the study of how epigenetics effects human development.

<span class="mw-page-title-main">Epigenome-wide association study</span>

An epigenome-wide association study (EWAS) is an examination of a genome-wide set of quantifiable epigenetic marks, such as DNA methylation, in different individuals to derive associations between epigenetic variation and a particular identifiable phenotype/trait. When patterns change such as DNA methylation at specific loci, discriminating the phenotypically affected cases from control individuals, this is considered an indication that epigenetic perturbation has taken place that is associated, causally or consequentially, with the phenotype.

Epigenetics of anxiety and stress–related disorders is the field studying the relationship between epigenetic modifications of genes and anxiety and stress-related disorders, including mental health disorders such as generalized anxiety disorder (GAD), post-traumatic stress disorder, obsessive-compulsive disorder (OCD), and more. These changes can lead to transgenerational stress inheritance.

Human epigenome is the complete set of structural modifications of chromatin and chemical modifications of histones and nucleotides. These modifications affect according to cellular type and development status. Various studies show that epigenome depends on exogenous factors.

Transgenerational epigenetic inheritance in plants involves mechanisms for the passing of epigenetic marks from parent to offspring that differ from those reported in animals. There are several kinds of epigenetic markers, but they all provide a mechanism to facilitate greater phenotypic plasticity by influencing the expression of genes without altering the DNA code. These modifications represent responses to environmental input and are reversible changes to gene expression patterns that can be passed down through generations. In plants, transgenerational epigenetic inheritance could potentially represent an evolutionary adaptation for sessile organisms to quickly adapt to their changing environment.

Sleep epigenetics is the field of how epigenetics affects sleep.

Environmental epigenetics is a branch of epigenetics that studies the influence of external environmental factors on the gene expression of a developing embryo. The way that genes are expressed may be passed down from parent to offspring through epigenetic modifications, although environmental influences do not alter the genome itself.

References

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  2. ↑ Sapozhnikov, Daniel M.; Szyf, Moshe (2021-09-29). "Unraveling the functional role of DNA demethylation at specific promoters by targeted steric blockage of DNA methyltransferase with CRISPR/dCas9". Nature Communications. 12 (1): 5711. Bibcode:2021NatCo..12.5711S. doi:10.1038/s41467-021-25991-9. ISSN   2041-1723. PMC   8481236 . PMID   34588447.
  3. 1 2 Turck F, Coupland G (March 2014). "Natural variation in epigenetic gene regulation and its effects on plant developmental traits". Evolution; International Journal of Organic Evolution. 68 (3): 620–631. doi:10.1111/evo.12286. hdl: 11858/00-001M-0000-0024-04A8-4 . PMID   24117443. S2CID   10225862.
  4. ↑ Zhang YY, Fischer M, Colot V, Bossdorf O (January 2013). "Epigenetic variation creates potential for evolution of plant phenotypic plasticity". The New Phytologist. 197 (1): 314–322. doi: 10.1111/nph.12010 . PMID   23121242.
  5. ↑ Verhoeven KJ, Jansen JJ, van Dijk PJ, Biere A (March 2010). "Stress-induced DNA methylation changes and their heritability in asexual dandelions". The New Phytologist. 185 (4): 1108–18. doi: 10.1111/j.1469-8137.2009.03121.x . PMID   20003072.
  6. ↑ Hernando-Herraez I, Prado-Martinez J, Garg P, Fernandez-Callejo M, Heyn H, et al. (2013) Dynamics of DNA Methylation in Recent Human and Great Ape Evolution. PLoS Genet 9(9): e1003763. doi: 10.1371/journal.pgen.1003763
  7. ↑ Shulha HP, Crisci JL, Reshetov D, Tushir JS, Cheung I, Bharadwaj R, Chou HJ, Houston IB, Peter CJ, Mitchell AC, Yao WD, Myers RH, Chen JF, Preuss TM, Rogaev EI, Jensen JD, Weng Z, Akbarian S (2012). "Human-specific histone methylation signatures at transcription start sites in prefrontal neurons". PLOS Biology. 10 (11): e1001427. doi: 10.1371/journal.pbio.1001427 . PMC   3502543 . PMID   23185133.
  8. ↑ Molaro A, Hodges E, Fang F, Song Q, McCombie WR, Hannon GJ, Smith AD (September 2011). "Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates". Cell. 146 (6): 1029–41. doi:10.1016/j.cell.2011.08.016. PMC   3205962 . PMID   21925323.
  9. ↑ Blake LE, Roux J, Hernando-Herraez I, Banovich NE, Perez RG, Hsiao CJ, et al. (February 2020). "A comparison of gene expression and DNA methylation patterns across tissues and species". Genome Research. 30 (2): 250–262. doi:10.1101/gr.254904.119. PMC   7050529 . PMID   31953346.
  10. ↑ Nätt D, Rubin CJ, Wright D, Johnsson M, Beltéky J, Andersson L, Jensen P (February 2012). "Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens". BMC Genomics. 13: 59. doi: 10.1186/1471-2164-13-59 . PMC   3297523 . PMID   22305654.
  11. ↑ Dickins TE, Rahman Q (August 2012). "The extended evolutionary synthesis and the role of soft inheritance in evolution". Proceedings. Biological Sciences. 279 (1740): 2913–21. doi:10.1098/rspb.2012.0273. PMC   3385474 . PMID   22593110.
  12. ↑ Rando OJ, Verstrepen KJ (February 2007). "Timescales of genetic and epigenetic inheritance". Cell. 128 (4): 655–68. doi: 10.1016/j.cell.2007.01.023 . PMID   17320504. S2CID   17964015.
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  14. ↑ Pennisi E (September 2013). "Plant biology. Evolution heresy? Epigenetics underlies heritable plant traits". Science. 341 (6150): 1055. doi:10.1126/science.341.6150.1055. PMID   24009370.
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