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Cell and Molecular Neuroscience > Gregg > Flashcards

Gregg Flashcards

1
Q

Anatomy of a gene

A

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

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2
Q

role of epigenetic mechanisms

A

maintain cellular
identity

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3
Q

Protocadherin Gene Clusters (PCDHG) are responsible for what in mammalian neurons?

A

Self-Recognition

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4
Q

BRAIN DERIVED NEUROTROPHIC FACTOR

A

*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

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5
Q

Olfactory monoallelic

A
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6
Q

Imprinted Genes

A
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7
Q

lncRNAs - long non-coding RNAs

A

*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

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8
Q

How do lncRNAs regulate gene expression

A

lncRNAs Regulate Expression of Neighboring Protein Coding
Genes By Forming Scaffolds to Regulate Chromatin

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9
Q

micro RNAs

A

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

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10
Q

miRNA biogenesis

A
  1. Primary miRNA transcribed by Pol II
  2. Pasha + Drosha RNase III form
    microprocessor
  3. Microprocessor cleaves pri-RNA to
    form precursor mirRNA (60-70 nt)
  4. Exportin 5 transports pre-miRNA to
    cytoplasm
  5. Dicer + Loquacious (co-factor) cleaves
    pre-miRNA to form miRNA:miRNA
    duplex (22-23 nt)
  6. miRNA duplex is sorted into
    Argonaute proteins to form RISC
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11
Q

miRNAs = ?
siRNAs = ?

A

miRNAs = imperfect duplexes => AGO1
siRNAs = perfect duplexes => AGO2

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12
Q

Epigenetics (MODERN meaning)

A

an epigenetic trait is a stably
inherited phenotype resulting from changes in a chromosome without
alterations in the DNA sequence

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13
Q

Epigenetics studies:

A

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

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14
Q

Epigenetic mechanisms maintain ______

A

cellular
identity

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15
Q

Heritability = ?

A

Heritability = 2 x (MZ - DZ)

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16
Q

Non-DNA parts of genome (w/ image)

A

Chromatin
Solenoid
Nuclesome
Histone Ocamer
Histones

17
Q

Chromatin

A

mass of DNA and protein that composes a chromosome

18
Q

Solenoid

A

packing of nucleosomes + DNA as a 30 nm fiber of chromatin resulting from helical winding of at least 5 nucleosome strands

19
Q

Nucleosome

A

146 bp of DNA wrapped 1.76 times around a histone octamer

20
Q

Histone Octamer

A

two H2A-H2B dimers and a H3-H4 tetramer

21
Q

Histones

A

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)

22
Q

2 types of chromatin

A

euchromatin

heterochromatin

23
Q

euchromatin

A

Less condensed
@ chromsome arms
contains unique sequences
gene-rich
replicated throughout S phase
Recombination during meiosis

24
Q

Heterochromatin

A

highly condensed
at centromeres/telomers
contains repetitious sequences
gene-poor
replicated in late S phase
no meiotic recombination

25
Q
A
26
Q

Epigenetic processes can be divided into:

A
  1. Signals that trigger the establishment of an epigenetic mark
  2. Epigenetic initiator factors that define the location of the mark in the genome.
  3. Maintenance signals that sustain the epigenetic mark
27
Q

Where does DNA methylation occur?

A

DNA methylation occurs on the 5th carbon of
cytosine = 5mC

  1. 5mC consitutes ~1% of all bases and is found almost exclusively as symmetrical
    methylation of the dinucleotide CpG
28
Q

What is CpG island?

A

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.

29
Q
A

DNA methyl transferase (DNMT) 3A and DNMT3B = de novo
methylation
DNMT1 = maintenance methylation (affinity for hemi-methylated DNA)

30
Q

Effects of methylination on DNA

A

*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

31
Q

Which proteins are responsible for active DNA-demethylation

A

ten-eleven translocation (Tet) dependent demthylation (tet1,2,3)

32
Q

5hmc

A

Formed by adding methyl group to cytosine and
then an hydroxyl group

33
Q

Tet mechanism

A

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

34
Q
A
35
Q

4 major post translational histone modifications

A
  1. acetylation
  2. methylation
  3. ubiquitylation
  4. phsphorylation
36
Q

Expressed Gene

A
37
Q

Repressed Gene

A

Cell and Molecular Neuroscience (15 decks)

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