Gregg Flashcards
Anatomy of a gene
5’ end - promoter
5’-UTR
Start codon (ATG) (encodes M)
next exon has an accepter site
introns are regions that don’t make it into protein
stop codon
3’-UTR
poly-A site
role of epigenetic mechanisms
maintain cellular
identity
Protocadherin Gene Clusters (PCDHG) are responsible for what in mammalian neurons?
Self-Recognition
BRAIN DERIVED NEUROTROPHIC FACTOR
*Regulates cell differentiation, survival, migration, dendritic arborization, synaptogenesis, and
activity-dependent plasticity
*Expression is induced by neuronal activity
long 3’UTR targets transcript to dendrites
*BDNF val66met polymorphism is associated with altered hippocampal volume and anxiety
behavior (Chen et al. Science 2006; Egan et al., Cell 2003)
impaired episodic memory and hippocampal function
Olfactory monoallelic
Imprinted Genes
lncRNAs - long non-coding RNAs
*thousands of lncRNAs in the human
genome (Guttman et al. 2009)
*can be megabases in length, but defined as non-coding RNA > 200 bps
low sequence conversion
involved in regulating gene expresison
How do lncRNAs regulate gene expression
lncRNAs Regulate Expression of Neighboring Protein Coding
Genes By Forming Scaffolds to Regulate Chromatin
micro RNAs
defined as 21-24 nucleotides in length
*Discovered by Victor Ambros, Gary
Ruvkan and David Baulcombe (Lasker Prize
2008)
*one miRNA can influence many genes
miRNAs regulate the translation of target RNAs by triggering transcript translation-interference or
degradation depending on the degree of matching.
1. Complete complementation = RNA degradation by Ago2
2. Incomplete complementation = translation-interference by Ago1
miRNA biogenesis
- Primary miRNA transcribed by Pol II
- Pasha + Drosha RNase III form
microprocessor - Microprocessor cleaves pri-RNA to
form precursor mirRNA (60-70 nt) - Exportin 5 transports pre-miRNA to
cytoplasm - Dicer + Loquacious (co-factor) cleaves
pre-miRNA to form miRNA:miRNA
duplex (22-23 nt) - miRNA duplex is sorted into
Argonaute proteins to form RISC
miRNAs = ?
siRNAs = ?
miRNAs = imperfect duplexes => AGO1
siRNAs = perfect duplexes => AGO2
Epigenetics (MODERN meaning)
an epigenetic trait is a stably
inherited phenotype resulting from changes in a chromosome without
alterations in the DNA sequence
Epigenetics studies:
Reversible heritable changes in gene function
that occur without a change in the sequence of
nuclear DNA
How environmental factors and signals result
in long-term gene expression changes
How cellular identity is maintained
Epigenetic mechanisms maintain ______
cellular
identity
Heritability = ?
Heritability = 2 x (MZ - DZ)
Non-DNA parts of genome (w/ image)
Chromatin
Solenoid
Nuclesome
Histone Ocamer
Histones
Chromatin
mass of DNA and protein that composes a chromosome
Solenoid
packing of nucleosomes + DNA as a 30 nm fiber of chromatin resulting from helical winding of at least 5 nucleosome strands
Nucleosome
146 bp of DNA wrapped 1.76 times around a histone octamer
Histone Octamer
two H2A-H2B dimers and a H3-H4 tetramer
Histones
5 major families - H2A, H2B, H3, H4 (core histones); H1/H5 (linker histones). Amino termini tails project out of the nucleosome core and can be epigenetially modified (acetylation, methylation, phosphorylation)
2 types of chromatin
euchromatin
heterochromatin
euchromatin
Less condensed
@ chromsome arms
contains unique sequences
gene-rich
replicated throughout S phase
Recombination during meiosis
Heterochromatin
highly condensed
at centromeres/telomers
contains repetitious sequences
gene-poor
replicated in late S phase
no meiotic recombination
Epigenetic processes can be divided into:
- Signals that trigger the establishment of an epigenetic mark
- Epigenetic initiator factors that define the location of the mark in the genome.
- Maintenance signals that sustain the epigenetic mark
Where does DNA methylation occur?
DNA methylation occurs on the 5th carbon of
cytosine = 5mC
- 5mC consitutes ~1% of all bases and is found almost exclusively as symmetrical
methylation of the dinucleotide CpG
What is CpG island?
a sequence of >200bp with a greater number of CpG sites than
expected for its GC content. ~60% of human genes have CpG islands at their
promoters.
DNA methyl transferase (DNMT) 3A and DNMT3B = de novo
methylation
DNMT1 = maintenance methylation (affinity for hemi-methylated DNA)
Effects of methylination on DNA
*DNA methylation at CpG islands in promoters
leads to chromatin structure changes that inhibit
gene expression
*Methylated DNA promotes DNA binding by
some proteins:
Methyl CpC-binding domain proteins (MBD 1, 2, 3 and 4)
Methyl CpG-binding protein 2 (MeCP2)
*Methylated DNA inhibits DNA binding by
some proteins:
CCCTC-binding factor (CTCF) - an insulator protein
ETS1 - a transcription factor
Which proteins are responsible for active DNA-demethylation
ten-eleven translocation (Tet) dependent demthylation (tet1,2,3)
5hmc
Formed by adding methyl group to cytosine and
then an hydroxyl group
Tet mechanism
Role for TET enzymes in 5mC conversion to 5hmC was discovered by
Tahiliani et al. 2009
*Trypanosomes contain base J - a modified thymine produced by the
JBP1 and JBP2 enzymes
*Mammalian JBP paralogous proteins were identified TET1, TET2, TET3
4 major post translational histone modifications
- acetylation
- methylation
- ubiquitylation
- phsphorylation
Expressed Gene
Repressed Gene
