Inside each eukaryote nucleus is genetic material (DNA) surrounded by protective and regulatory proteins. These protective and regulatory proteins and the dynamic changes to them that occur during the course of a eukaryote's existence are the epigenome.
- 1 Evolution
- 2 Lamarckism
- 3 Epigenomic theory
- 4 Genomes
- 5 Deoxyribonucleic acid molecules
- 6 Nucleosomes
- 7 Histones
- 8 Euchromatin
- 9 Heterochromatin
- 10 Constitutive heterochromatin
- 11 Facultative heterochromatin
- 12 Changes
- 13 Acetyl groups
- 14 Methyl groups
- 15 Phosphoryl groups
- 16 Ubiquityl groups
- 17 Hypotheses
- 18 See also
- 19 References
- 20 External links
Evolution, the accumulation of change, while broadly applicable to anything which accumulates changes, is often thought of as gradual change or a series of changes, such as changes in the genetic composition of a population over successive generations.
"Lamarckism (or Lamarckian inheritance) is the idea that an organism can pass on characteristics that it acquired during its lifetime to its offspring (also known as heritability of acquired characteristics or soft inheritance). It is named after the French biologist Jean-Baptiste Lamarck (1744–1829), who incorporated the action of soft inheritance into his evolutionary theories."
After "Erasmus Darwin wrote Zoonomia suggesting "that all warm-blooded animals have arisen ... with the power of acquiring new parts" in response to stimuli, with each round of "improvements" being inherited by successive generations", "Jean-Baptiste Lamarck repeated in his Philosophie Zoologique of 1809 the folk wisdom that characteristics which were "needed" were acquired (or diminished) during the lifetime of an organism then passed on to the offspring."
"Neo-Lamarckism is a theory of inheritance based on a modification and extension of Lamarckism, essentially maintaining the principle that genetic changes can be influenced and directed by environmental factors."
Def. a chemical entity anterior to, after, at, besides, near to, on, outer to, over, related to, or upon another chemical is called an epi (or epi-) chemical.
Def. "[t]he complete genetic information ... of an organism" is called a genome.
Here's a theoretical definition:
Def. a chemical entity anterior to, after, at, besides, near to, on, outer to, over, related to, or upon the complete genetic information of an organism is called an epi (or epi-) genome, or epigenome.
Genetic information is encoded as a sequence of nucleobases: adenine (A), cytosine (C), guanine (G), and thymine (T).
Deoxyribonucleic acid molecules
Deoxyribonucleic acid (DNA) is composed of nucleobases (the sequence of which is the genome), deoxyribose (a sugar), and phosphate groups. Each nucleobase is attached to one deoxyribose molecule and one (PO4) phosphate molecule to form a chain of nucleotides (nucleobase + deoxyribose + phosphate) for a haploid genome. A linking of nucleobases may occur without the phosphate or the deoxyribose. The phosphate and the sugar are part of the epigenome.
DNA often occurs as a double helix. The linking between one nitrogenous nucleobase of a DNA molecule and another nitrogenous nucleobase of a second DNA molecule is via hydrogen bonds. Each hydrogen bond ("the electromagnetic attractive interaction of a hydrogen atom and an electronegative atom, such as nitrogen [or] oxygen" of a nucleobase) is part of the epigenome.
"The nucleosome core particle consists of approximately 147 base pairs of DNA wrapped in 1.67 left-handed superhelical turns around a histone octamer consisting of 2 copies each of the core histones H2A, H2B, H3, and H4."
"Core particles are connected by stretches of "linker DNA", which can be up to about 80 bp long."
"Histone deacetylases (HDAC) ([Enzyme Commission number] EC number 3.5.1) are a class of enzymes that remove acetyl groups (O=C-CH3) from an ε-N-acetyl lysine amino acid on a histone, allowing the histones to wrap the DNA more tightly."
"[Histone deacetylase] action is opposite to that of histone acetyltransferase."
"The structure of euchromatin is reminiscent of an unfolded set of beads along a string, wherein those beads represent nucleosomes."
"[T]he presence of methylated lysine 4 on the histone tails [may act] as a general marker for euchromatin."
"One example of constitutive euchromatin that is 'always turned on' is housekeeping genes, which code for the proteins needed for basic functions of cell survival."
"Heterochromatin mainly consists of genetically inactive satellite sequences, and many genes are repressed to various extents, although some cannot be expressed in euchromatin at all. Both centromeres and telomeres are heterochromatic, as is the Barr body of the second, inactivated X-chromosome in a female."
"[S]ections of DNA that occur ... particularly at the centromeres and telomeres ... often consisting of ... repetitive DNA [that is largely] transcriptionally silent" are constitutive heterochromatin.
"[R]egions of DNA that exist as constitutive heterochromatin [are] the same for all cells of a given species."
"[A]ll human chromosomes 1, 9, 16, and the Y-chromosome contain large regions of constitutive heterochromatin. In most organisms, constitutive heterochromatin occurs around the chromosome centromere and near telomeres."
"[G]enes that are silenced through a mechanism such as histone methylation or siRNA through RNAi [produce facultative heterochromatin]."
"The regions of DNA packaged in facultative heterochromatin [are not] consistent between the cell types within a species, and thus a sequence in one cell that is packaged in facultative heterochromatin (and the genes within poorly expressed) may be packaged in euchromatin in another cell (and the genes within no longer silenced)."
"An example of facultative heterochromatin is X-chromosome inactivation in female mammals: one X chromosome is packaged as facultative heterochromatin and silenced, while the other X chromosome is packaged as euchromatin and expressed."
There are "nearly 50,000 acetylated sites [punctate sites of modified histones] in the human genome that correlate with active transcription start sites and CpG islands and tend to cluster within gene-rich loci."
"Acetylation (or in IUPAC nomenclature ethanoylation) describes a reaction that introduces an acetyl functional group into a chemical compound. (Deacetylation is the removal of the acetyl group.)"
"In histone acetylation and deacetylation, histone proteins are acetylated and deacetylated on lysine residues in the N-terminal tail as part of gene regulation. Typically, these reactions are catalyzed by enzymes with histone acetyltransferase (HAT) or histone deacetylase (HDAC) activity, although HATs and HDACs can modify the acetylation status of non-histone proteins as well."
"[L]ysine acetylation almost always correlates with chromatin accessibility and transcriptional activity".
Methylation is "the addition of a methyl group ... replacing a hydrogen atom."
"DNA methylation in vertebrates typically occurs at CpG sites (cytosine-phosphate-guanine sites, that is, where a cytosine is directly followed by a guanine in the DNA sequence). This methylation results in the conversion of the cytosine to 5-methylcytosine. The formation of Me-CpG is catalyzed by the enzyme DNA methyltransferase. Human DNA has about 80%-90% of CpG sites methylated, but there are certain areas, known as CpG islands, that are GC-rich (made up of about 65% CG residues), wherein none are methylated. These are associated with the promoters of 56% of mammalian genes, including all ubiquitously expressed genes. One to two percent of the human genome are CpG clusters, and there is an inverse relationship between CpG methylation and transcriptional activity."
"Non-CpG methylation (CNG and CNN) ... has been observed at a low frequency in the early mouse embryo"
"Protein methylation typically takes place on arginine or lysine amino acid residues in the protein sequence. Arginine can be methylated once (monomethylated arginine) or twice, with either both methyl groups on one terminal nitrogen (asymmetric dimethylated arginine) or one on both nitrogens (symmetric dimethylated arginine) by peptidylarginine methyltransferases (PRMTs). Lysine can be methylated once, twice or three times by lysine methyltransferases. Protein methylation has been most-studied in the histones. The transfer of methyl groups from S-adenosyl methionine to histones is catalyzed by enzymes known as histone methyltransferases. Histones that are methylated on certain residues can act epigenetically to repress or activate gene expression."
"Kinases phosphorylate proteins and phosphatases dephosphorylate proteins."
Phosphoryl groups attach to histones at serine and threonine sites.
"The core histones that make up the nucleosome are subject to ... modifications, including ubiquitination [that occurs] primarily at specific positions within the amino-terminal histone tails."
- The epigenome around A1BG is opened as if for any gene rather than a specific promoter, enhancer, or other transcription related factor.
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