Genomes

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Genomes
http//www.ornl.gov
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Each cell within an organism contains a complete
genome, but only deploys a fraction of the genes
Positive selective activation of a gene at a
particular place and time to produce a gene
product Negative selective silencing of a gene
or removal of a gene product at a particular
place and time
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Gene expression regulation at the level of DNA
Sequence-dependent cis-acting factors
promoters/regulatory sequences of
genes trans-acting factors proteins and RNAs
that bind cis-elements and promote or repress
gene expression DNA methylation methylation of
CpG islands promotes silencing Range Usually
functions at level of single gene, or at most a
local group of genes
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(No Transcript)
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Regulatory network from early sea urchin
development
Levine and Davidson, PNAS, 2005
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DNA is embedded in chromatin
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Regulation of gene expression at the level of
chromatin
Sequence-independent linker histones control
DNA compaction and accessibility to trans-acting
factors post-translational modifications of
histone tails control compaction of DNA and
serve as docking sites for trans-acting
factors Range Can act at the level of a single
gene, often acts over groups of genes and over
larger domains (20-200kb), and can affect gene
expression over an entire chromosome
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Regulation of gene expression at the level of RNA
mRNA Stability/decay length of poly A tail,
binding of proteins and RNAs that either protect
or degrade transcripts Subcellular localization
sequestration by proteins, ribosome stalling
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RNA also acts as a regulator of gene expression
miRNA
siRNA
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DNA is silenced at the level of histone
modifications through an RNAi-like mechanism
centromere repeats
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Genomics Technologies
systematic gene mutation/RNAi screens
sequence analyses
Functional Networks
genome-wide expression profiling
global protein analysis
genotyping
nucleic acid/ protein interactions
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Genome organization is non-random with respect to
gene expression in multiple organisms
local
chromatin
chromosome
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Germ cells act to maintain the species
somatic cells
somatic cells
gametes
embryo
gametes
embryo
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C. elegans hermaphrodite germ line
stem cells
meiosis
embryos
sperm
oocytes
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germline formation during larval development
L1
L2
L3
L3/L4
late L4
meiosis
stem cells
young adult
oocytes
sperm
somatic gonad
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Levels of gene regulation in the germline
Chromosome silencing of the X Large domain
clustering of germline-expressed genes Local
domain operon formation
stem cells
meiosis
embryos
sperm
oocytes
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C. elegans DNA microarrays
20,000 genes in the worm genome 18,000 genes on
the array
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Germline mutant comparisons
wild type
no germ line (glp-4)
vs.
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C. elegans hermaphrodite germ line
oogenic germline 3003 genes
sperm 1380 genes
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Sperm genes are different from oogenic germline
genes
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Large-scale in situ hybridization
NextDB Nematode EXpression paTtern
DataBase Kohara lab Japan
98 of all genes in oogenic germline category
show germline expression by in situ
distal
proximal
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Why?
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The oogenesis genes on the X chromosome express
at lower levels than those on the autosomes
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The hermaphrodite paired X does not stain with
antibodies against transcriptionally active
chromatin conformation
DNA
Merge
a
-H3methylK4
diplotene
stem cells
diakinesis
pachytene
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Hermaphrodite X is silenced early in meiotic
prophase but not late
diakinesis
diplotene
inactive transgene
diakinesis
diakinesis
active transgene
?
-H3methylK4