Epigenetics mol2.ppt how . how epigenetics alter the expression
- 1. What is epigenetics? • heritable changes in gene expression that don’t involve a change in DNA sequence. • The current definition of epigenetics is ‘the study of heritable changes in gene expression that occur independent of changes in the primary DNA sequence. – Epigenetic changes regulategene expression by hindering the availability of transcription factors towards DNA. These modifications occur at different regions encircling the genome. – The fact that epigenetic aberrations, unlike genetic mutations, are potentially reversible and can be restored to their normal state by epigenetic therapy
- 2. •: •The epigenetic regulation of DNA-templated processes has been intensely studied over the last 15 years. •1- DNA methylation •2- , histone modification, •2- nucleosome remodeling, •4- RNA-mediated targeting regulate many biological processes that are fundamental to the genesis of cancer (microRNA).
- 3. DNA methylation • is perhaps the most extensively studied epigenetic modification in mammals • . It provides a stable gene silencing mech anism that plays an important role in regulating gene expression and chromatin architecture. • primarily occurs by the covalent modification of cytosine residues in CpG dinucleotides. • CpG dinucleotides are not evenly distributed across the human genome but are instead concentrated in short CpG-rich DNA stretches called ‘CpG islands’ and regions of large repetitive sequences (e.g. centromeric repeats, retrotransposon elements.)
- 4. • CpG islands are preferentially located at • the 5 end of genes and occupy 60% of human gene promoters. – CpG islands: • transcription starting sites (UTR-areas): hypo-/hypermethylation • imprinting (X-inactivation): hypermethylation – Repetitive sequences: • Transposable elements: hypermethylation • The conversion of cytosine into 5-methyl cytosine (5mC) is carried out by the catalytic activity of a group of enzymes called DNA methyl- transferases (DNMTs).
- 5. • DNA methylation silence gene expression directly by impeding the binding of various transcription factors and indirectly by enrolling methyl-CpG binding domain (MBD) proteins. The MBD family contains five core proteins which include MBD1, MBD2, MBD3, MBD4 and the methyl cytosine binding protein 2 . • Recent sequencing of cancer genomes has identified recurrent mutations in DNMT3A in up to 25% of patients with acute myeloid leukemia (AML).
- 7. Histone modifications: Mark Transcriptionally relevant sites Biological Role Methylated cytosine (meC) CpG islands Transcriptional Repression Acetylated lysine (Kac) H3 (9,14,18,56), H4 (5,8,13,16), H2A, H2B Transcriptional Activation Phosphorylated serine/threonine (S/Tph) H3 (3,10,28), H2A, H2B Transcriptional Activation Methylated argine (Rme) H3 (17,23), H4 (3) Transcriptional Activation Methylated lysine (Kme) H3 (4,36,79) H3 (9,27), H4 (20) Transcriptional Activation Transcriptional Repression Ubiquitylated lysine (Kub) H2B (123/120) H2A (119) Transcriptional Activation Transcriptional Repression Sumoylated lysine (Ksu) H2B (6/7), H2A (126) Transcriptional Repression
- 8. • Unlike DNA methylation, histone modifications can lead to either activation or repression depending upon which residues are modified and the type of modifications present. For example, lysine acetylation correlates with transcriptional activation (12,29), whereas lysine methylation leads to transcriptional activation or repression depending upon which residue is modified and the degree of methylation. • For example, trimethylation of lysine 4 on histone H3 (H3K4me3) is enriched at transcriptionally active gene promoters whereas trimethylation of H3K9 (H3K9me3) and H3K27 (H3K27me3) is present at gene promoters that are transcriptionally repressed). The latter two modifications together constitute the two main silencing mechanisms in mammalian cells, H3K9me3 working in concert with DNA methylation and H3K27me3 largely working exclusive of DNA methylation.
- 9. - Histone modification patterns are dynamically regulated by enzymes that add and remove covalent modifications to histone proteins. Histone acetyltransferases (HATs) and histone methyltransferases (HMTs) add acetyl and methyl groups, respectively, wherea HDACs and histone demethylases (HDMs) remove acetyl and methyl groups,respectively (.A number of histone-modifying enzymes including various HATs, HMTs, HDACs and HDMs have been identified in the past decade . These histone-modifying enzymes interact with each other as well as other DNA regulatory mechanisms to tightly link chromatin state and transcription.
- 10. • 3- Nucleosome positioning and histone variants: - Non-covalent mechanisms, such as nucleosome remodeling and replacement of canonical histone proteins with specialized histone variants, also play an important role in how chromatin structure regulates gene activity. In addition to serving as the basic modules for DNA packaging within a cell, nucleosomes regulate gene expres- sion by altering the accessibility of regulatory DNA sequences to transcription factors.
- 11. Nucleosome-free regions (NFRs) present at the 5 and 3 ends of genes are thought to provide the sites for assembly and dis-assembly of the transcription machinery .The loss of a nucleosome directly upstream of the transcription start site is tightly correlated with gene activation .Furthermore, the presence of an NFR at gene promoters with basal level of transcription correlates with their ability for rapid activation upon stimulation .Incontrast, occlusion of the transcription start site within the NFR by a nucleosome is associated with gene repression .. Modulation of the NFRs is orchestrated by ATP- dependent chromatin-remodeling complexes, which modify the accessibility of DNA regulatory sites through both sliding and ejection of nucleosomes.
- 12. 4- miRNAs:
- 13. miRNAs are small, 22 nt, non-coding RNAs that regulate gene expression through posttranscriptional silencing of target genes. - Sequence-specific base pairing of miRNAs with 3 end untranslated re- gions of target messenger RNA within the RNA-induced silencing complex results in target messenger RNA degradation or inhibition of translation . - miRNAs are expressed in a tissue-specific manner and control a wide array of biological processes including cell proliferation, apoptosis and differentiation. The list of miRNAs identified in the human genome and their potential target genes is growing rapidly, demonstrating their extensive role in maintaining global gene expression patterns.
- 14. • Like normal genes, the expression of miRNAs can be regulated by epigenetic mechanisms (. In addition,miRNAs can also modulate epigenetic regulatory mechanisms inside a cell by targeting enzymes responsible for DNA methylation (DNMT3A and DNMT3B) and histone modifications (EZH2).