DOSTIE - LECTURE 1 Flashcards
what do all cells have in common
- contain copies of the same genetic material
- all cells encode the same regulatory sequences (enhancers, insulators, promoters)
how do cells have the same genes but are not the same
do not all express the same genes
what is the epigenome
the reason as to why genes are transcribed in a cell type specific manner
epigenome: the information that influences gene expression but which is not encoded in the genome sequence (can be inherited but not necessarily)
what are two important epigenomic components
proteins that bind the DNA
modifications to the DNA itself (methylation)
what is DNA packaged with
packaged with histones and non histone proteins
histones are by far the most abundant proteins that bind genomic DNA
what is the chromatin
histone DNA complex
also called the 10/11nm fiber
what is in a nucleosome
146/7 bp of genomic DNA and 8 core histones
two of each of these: H2A, H2B, H3 and H4
what are histone variants
what affects the position of nucleosomes
what are linker histones
H1 and H5
genomic DNA binding to this type of histone regulates compaction
representation of one nucleosome with its tails
which regions of the histones are most extensively modified
the tails are subject to the most PTM
tails are accessible and protrude from the structure
the amino and the carboxy terminal tails
how are histone modifications identified
by mass spectrometry
what are the modifications that the histones are subjected to
acetylation
methylation
phosphorylation
ubiquitination
(modifications on H3 and H4 are the most characterised)
what do histone marks affect
transcription
DNA repair
replication
condensation (mitosis/meiosis)
what are writer complexes
enzyme complexes involved in modifying histones
what are some examples of those writer complexes
what are eraser complexes and some examples
enzymes/complexes that remove the modifications made to histones
- histone deacetylases (HDACs)
- Lys deacetylases (KDACs)
- Lys demethylases (KDMTs)
what are the general roles of lysine acetylation and methylation
what are reader complexes and some examples
protein complexes that interact with these modifications
two domains identified
bromodomain (BrD): interacts with acetylated lysine
chromodomain (ChrD): interacts with methylated lysine
how does ChIP seq reveal the role of H3K4me3
what are the proteins that are H3 lys 4 trimethylases
SET1A, SET1B, MLL1, MLL2, MLL3, MLL4
SET1A and SET1B can exist together or separate
what are the ways in which MLL can be recruited to the chromatin?
what is the role of H3K4me3 modification?
what are the different marks that can be present to show cross talk between histone modifications
explain the polycomb group complexes (PRC1 and 2) as examples of positive cross talk
PRC1 and 2 synergise to repress many genes by adding H3K27me3 and H2AK119ub
what are polycomb group proteins (PcGs) responsible for
what is obligatory heterochromatin
where is facultative heterochromatin usually located
