KSH 0610 Epigenomics

 Epigenomics - Epi(Outside) + Genomics(The study of genome, especially function and structure analysis)

• The study of the complete set of epigenetic modifications on the genetic material of a cell
• Epigenetic modification

1. DNA methylation by DNMT (DNA methyltransferase)
2. Histone modification - acetylation, methylation, phosphorylation and so on

• Epigenetic modifications play an important role in gene expression and regulation

         Ex) It could affect Tumorigenesis

         Ex) DNA imprinting - Parent generations put tags to next generation using DNA methylation

• The effects of chromatin structure on the function of the included genes
• Chromatin structure

1. Euchromatin - a lightly packed form of chromatin. It is often under active transcription state.
2. Heterochromatin - a tightly packed form of chromatin - inaccessible to polymerase and not transcribed
3. Nucleosome - a basic unit of DNA packing in eukaryotes, consisting of 8 histone proteins and a segment of DNA (around 147bp)

• How do we study epigenomics and DNA methylation?

1. Bisulfite treatment on DNA - Treatment of DNA with bisulfite converts Cytosine to Uracil. It cannot convert methylcytosine.
2. Sequencing

• Protein - Switch - On and off - Energy(ATP, GTP, etc.) makes switching(acetylation, phosphorylation etc.)
• To detect protein structure

1. X-ray crystallography
2. Nuclear Magnetic Resonance
3. Cryoelectron microscopy
4. Microscope
5. Sequence
6. Mass spectroscopy

• Protein secondary structure - the primary polypeptide chain (sequence of specific amino acid) gets properly foled in the form of

1. alpha helix - scaffold
2. beta sheet - scaffold
3. coil (randomly coiled, irregular) - for binding to attack something Ex) Venom, Immunoglobulin (antibody) antigen binding site

•  Interaction proteomics - using chips, microarray