Kourosh L1 Flashcards
what is epigenetics
study of how heritable changes in GENE EXPRESSION or CELLULAR PHENOTYPE occurs without changes in BASE PAIRING
what is the most important example of epigenetic effect
DUTCH FAMINE STUDY
- showed that children of mothers who survived the famine had:
- inc risk of schizophrenia
- overweight
- cardiovascular disease
shows epigenetics
how are DNA and histone proteins associated together
electrostatic interactions
DNA wraps around the histone proteins, whose tails protrude from structure and are modified
what did Conrad Waddington propose epigenetics was about
nt the process of cellular decision-making during development. At various points in this dynamic metaphor, the cell can take specific permitted trajectories, leading to different outcomes or cell fate
ie a link between genotype and phenotype
what are histones
Proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes
what are nucleosomes
Fundamental unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight histone protein cores
what is chromatin
the complex of DNA and its intimately associated proteins
describe DNA methylation
what catalyses
where
what does this act as
- adding methyl to DNA
- catalysed by DNA METHYLTRANSFERASES
- on position 5 of CYTOSINE nt
- next to guanine
- linked by phosphate group to form CpG dinucleotide
- forms 5-methyl-cytosine
acts as: BINDING SITE for other proteins which “read” the modification and recruit other proteins which modify histones
describe histone modification
- multiple types, catalysed by multiple enzymes
- eg ACETYLATION and METHYLATION of histones H3 AND H4
- directly alters DNA-protein interactions to change chromatin structure O alters the ability for a gene to be transcribed and expressed
acetylation of histones is performed by what
HISTONE ACYLTRANSFERASES (HATs) - adds an an acetyl group to lysine amino acids in this histone tail which causes loosening of chromatin to promote gene activation
how is acetylation of histones reversed
by HISTONE DEACETYLASES
- causes chromatin condensation, gene inactivation
describe methylation of histones
what is methylated
what doe sit cause
on LYSINE or ARGININE aa
- in mono, di or tri methylation events
- METHYLTRANSFERASES
- gene activation and inactivation
relaxation of chromatin happens why
- replication
- transcription
- repair
condensation of chromatin happens why
- inhibit transcription
- cell division
how does chromatin remodelling occur
chromatin remodelling
- change the position of the nucleosome
- nucleosome sliding:
- Histone chaperones (Nucleosome Assembly Protein (NAP-1))
- ATP dependent chromatin remodelers (SWI2, SWF2)
both interact with histones DIRECTLY
how does histone variant exchange occur
what is it controlled by
- change the composition of the nucleosome
- core histones (2 of eaach: H2A, H2B, H3 AND H4)
(H2AZ present at ACTIVE GENE PROMOTORS
H2AX X present where DNA repair occurs) - controlled by:
1) HISTONE CHAPERONES (eg Asf1)
2) ATP dependent chromatin remodelers (eg SWR complex)
how does histone tail modification occur
what is it controlled by
- histone tails are flexible regions that flank both ends of the histone fold- Lysine (K) and Arginine (R) residues are modified on histone tails by:
- Acetylation +
- Methylation -
- Phosphorylation ±
- Ubiquitination
- Degradation
how does chromatin distribution affect protein exression
affects access of proteins to DNA seq
- Process specific transcription factors (e.g. JAK/STAT transcription factors)
- General transcription factors (e.g. TFIID)
- RNA polymerase
what is the name of the case study on methods used to detect histone changes
Encode Project
- how proteins and DNA interact
- which genes are coding etc
why do we want to learn about protein-DNA interaction
- interaction= important in normal development and function, and important in disease
Important mechanism: DIRECT BINDING eg when proteins bind to DNA
what does ChIP stand for
chromatin imuunoprecipitation
what is ChIP
a method to investigate protein-
- DNA interaction in vivo, find WHERE ON THE DNA seq a protein is acting
- output is is enriched fragments of DNA that were bound by a particular protein
- The identity of DNA fragments need to be further determined by a second method
- formaldehyde used to covalently cross link proteins to DNA
- bind the protein you are looking for to specific ANTIBODIES
- covalent linking=reversed
- wash everything else away
- recovered DNA can be PCR amplified and map to reference genome (ChIP-seq)
or hybridise to microarray (ChIP-chip)
case study 1:amyotrophic lateral sclerosis (ALS)
- rare neurological (motor nerve) disease, involvs neurons for VOLUNTARY muscle control
- gradual deterioration
- early symptoms: muscle weakness, stiffness
- late: all voluntary muscles affected, cannot speak, eat, move, breathe
treatment for ALS
- no cure
- no effective treatment
- most patients die from resp. failure (3-5 years after first symptoms, 10% survive for 10+ years)
what are risk factors for ALS
age
gender
ethnicity
military veterans (exposure to lead, pesticides env toxins)
what causesALS generally
- GENETICS: familial and sporadic: SOD1 gene
- ENV: - Exposure to toxic or infectious agents, physical trauma, diet, and behavioural/occupational factor
what causes ALS to be progressive
DECREASE in acylated histone
- p300 transcriptional co-activator proteins
- FUS is an RNA-binding protein that regulates transcription, alternative splicing. Aberrations of FUS are causally associated with familial and sporadic ALS/FTLD.
- Reduction in histone acetyl transferase (HAT) activity OR Increased HDAC activity
