5. DNA and Histone Protein Modifications.pdf

SC4102 Regulation of Gene Expression Dr. Ruvini Mathangadeera  Transcriptional control When and how often a gene sequence is copied into RNA is termed transcriptional control. 1. Structural-chemical modifications of genetic material - Modificat...

SC4102 Regulation of Gene Expression Dr. Ruvini Mathangadeera  Transcriptional control When and how often a gene sequence is copied into RNA is termed transcriptional control. 1. Structural-chemical modifications of genetic material - Modifications made to DNA - Modifications made to histone proteins 2. DNA binding proteins modulate gene expression to turn transcription on and off DNA Modification: Methylation  Methylation of DNA In eukaryotes, cytosine bases in chromosomal DNA molecules are sometimes changed to 5- methylcytosine by the addition of methyl groups by enzymes called DNA methyltransferases. Methylating the cytosine of a CpG (cytosine– guanine dinucleotide) motif silences the genes. Methyl groups added to the promoter regions of genes prevents it from being “seen” – Genes are switched off.  Methylation of DNA Two types of methylation activity have been distinguished as follows. - Maintenance methylation Addition of methyl groups to the newly synthesized DNA strand in replication to make sure the new strand is identical to the older strand in all aspects. - de novo methylation Addition of methyl groups to totally new positions. Modification of Histone Proteins  Histone modifications A histone modification is a covalent PTM made to a histone protein which includes - Acetylation - Methylation - Phosphorylation - Ubiquitination The PTMs made to histone proteins can impact the gene expression by altering chromatin structure or recruiting histone modifiers.  I. Acetylation of Histone proteins Enables transcription. Attachment of negatively charged acetyl groups to lysine amino acids in the N-terminal regions of each of the core histone molecules.  Acetylation of Histone proteins These N-termini form tails that protrude from the nucleosome core octamer and their acetylation reduces the affinity of the histones for DNA and possibly also reduces the interaction between individual nucleosomes, destabilizing the 30 nm chromatin fiber. The histones in heterochromatin are generally unacetylated whereas those in active domains are acetylated, a clear indication that this type of modification is linked to DNA packaging. Wikimedia commons.  II. Methylation of Histone proteins Represses transcription generally but methylation of some residues of histones enables transcription. Methylation of histone proteins occurs on Lysine and Arginine residues in the H3 and H4 histone tails. Done by Histone Methyltransferases (HMTs)  Methylation of Histone proteins Tri-methylation of histone H3 at lysine 27 (H3K27me3) leads to silencing and repression of gene expression while Tri-methylation of histone H3 at lysine 4 (H3K4me3) leads to transcriptional activation. Wikimedia commons.  III. Phosphorylation of Histone proteins Occurs on Serine, Threonine or Tyrosine residues of Histones. Histone phosphorylation confers a negative charge to the histone, resulting in a more open chromatin conformation, as increased negative charge of histone proteins will decrease their interactions with DNA. Protein kinases add phosphate groups to histones while, protein phosphatases remove phosphate groups.  IV. Ubiquitination of Histone proteins Ubiquitination of lysine residues at the C-terminal regions of H2A and H2B. This modification involves addition of the small, common (ubiquitous) protein called ubiquitin or a related protein. H2A ubiquitination through PRC1 typically represses gene expression, while H2B ubiquitination can both activate and inhibit target gene expression.  V. Citrullination of Histone proteins Citrullination in the N-terminal regions of H3 and H4. Citrullination is the conversion of arginine to the related amino acid called citrulline, by replacement of the terminal =NH group of the arginine side chain with an =O group. Citrullination, which is also known as deimination, is one type of histone modification that leads to a reduction in hydrogen-bonding and a looser chromatin structure. The citrullination of histone H3, for example, has been shown to open up the chromatin and promote gene transcription.