Chromatin and Epigenetics

Chromatin and Epigenetics

1. Epigenetics - The study of mitotically (between cells) and/or meiotically (between generations) heritable changes in gene function that are not explainable by changes in DNA sequence

   • All somatic cells in an organism have identical genes, but these are used differently depending on the cell
     • Genes become programmed during development
   • Genetic inheritance allows the daughter cells to retain a memory of the gene expression patterns present in the parent cell
     • Cells can be reprogrammed to produce something different
       • Developmental events can be influenced by the epigenetic state of the cell
         • Some events are stochastic gene programming events, meaning that there is a random probability distribution of different versions occurring

2. X Chromosome Inactivation

   • Males (XY) and females (XX) have different numbers of X chromosomes
     • Cells are sensitive to gene dosage, and this can sometimes be lethal
   • Dosage compensation mechanism in mammals to equalise this difference in gene quantity
   • One of the two X chromosomes in female somatic cells are transcriptionally inactive
     • Once inactivated, it will remain that way in all of the daughter cells that it produces
     • Random inactivation
     • Inactivated by being condensed
     • Many parts to the process
       • Chromatin
         • Complex of DNA, histones and other non-histone proteins found in the nucleus of a eukaryotic cell
         • This is the material from what chromosomes are made
           • Condensed and packed into compact chromosomes
             • These contain nucleosomes, which are regularly repeating protein-DNA complexes
               • Nucleosomes consist of a histone octamer with two turns of DNA wrapped around it (147bp)
                 • The histone octamer consists of two copies each of histones H2A, H2B, H3 and H4 (eight in total)
                   • H2A and H2B bind to form two dimers, and H3 and H4 form another two dimers
                   • Each of the core histones has an N-terminal tail, which extrudes from the surface of the nucleosome, which may help to pack the nucleosomes, forming higher order chromatin structures
                     • These tails can also be subjected to various forms of covalent modifications such as acetylation, methylation and phosphorylation
                   • A combination of different modifications can be found on histones, all of which are reversible and created by a specific enzyme
                     • e.g. an acetyl group is added to specific lysines by a set of different histone acetyl transferases (HATs)
       • Histone Modifications
         • A series of coordinated histone modifications can modulate the chromatin, and thereby the transcriptional activity of a gene
           • This hypothesis is known as the histone code
           • The DNA sequence of an individual stores the genetic information and is invarient and so different cell types have differetn eipgenomes (overall genetic state of a cell)
       • DNA Methylation
       • Non-coding RNAs

3. Cytosine Methylation

   • Common form of post-replicative DNA modification
   • Adds information without changing the actual DNA sequence
   • S-adenosyl methionine (SAM) donates the methyl group
     • DNA methylation depends on the availability of methyl groups from SAM
   • Other modifications exist and each has its own function
   • Predominant sites of cytosine methylation are the CpG dinucleotides
     • CpG islands are regions of high CpG density that lack methylation
       • They are found at promoters of most human genes
         • Long-term silencing of the gene can be established by methylation of the CpG island region
           • Genes on the inactive X chromosome and certain imprinted genes are silenced in this way
   • Reversible, but can be inherited to the daughter cells after replication
     • There are many potential sites along the DNA for methylation
       • Methylating the gene inactivates it and prevents transcription

4. Genomic Imprinting

   • Epigenetic mechanism that induces parental-specific gene expression in diploid cells
   • Maternal and paternal genomes are required for mammalian reproduction, and so all offspring are diploid maternal/paternal
     • Nuclear transfer techniques have been used to replace the male nucleus in the zygote with another female nucleus, resulting in a diploid maternal/maternal (gynogenetic) embyro
       • These die during early developmental stages, as do diploid paternal/paternal (androgenetic) embryos
         • Proves that imprinted genes are needed for successful development, which are specific to either the maternal or paternal genome
   • Most imprinted genes are clustered, and controlled by a cis-acting imprint control element (ICE)
     • These carry an epigenetic imprint (i.e. methylated region) that has been inherited from one of the parental gametes
       • If the paternal allele's ICE is methylated, and the maternal allele's ICE is unmethylated, the maternal allele with be transcribed
     • Mostly cluster together with a non-coding RNA, and play a vital role in mammalian development
   • Maintenance methylation
     • Occurs after DNA replication
     • New strand is methylated so that it matches the old one, in preparation for future replications
     • A class of proteins called the methyl-CpG binding proteins are attached to methylated cytosines instead of being repelled by them
       • They share a methyl-CpG binding domain (MBD)
         • Some of these proteins are involved in the repression of transcription

5. Double stranded RNA is produced by special types of transcription of the DNA strand, such as bidirectional transcription, inverted repeat transcription, and aberrant transcription

   • RNA interference is a defence mechanism aimed to degrade foreign, dsRNA, which is often derived from viruses and other transposable elements
     • Protein complex contains Dicer nuclease, which cuts dsRNA into fragments called small interfering RNAs (siRNA)