Genomes
Organism
Estimated size
(in bases)
Estimated
gene #
Average gene
density/base
Diploid
chromosome #
Human
2.9 x 109
~30,000
1/100,000
46
Rat
2.8 x 109
~30,000
1/100,000
42
Mouse
2.5 x 109
~30,000
1/100,000
40
Drosophila
1.8 x 108
13,600
1/9,000
8
Arabidopsis
1.2 x 108
25,500
1/4,000
10
C. elegans
9.7 x 107
19,100
1/5,000
12
S. cerevisiae
1.2 x 107
6,300
1/2,000
32
E. coli
4.7 x 106
3,200
1/1400
1
H. influenzae
1.8 x 106
1,700
1/1000
1
http://www.ornl.gov
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
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
Regulatory network from early sea urchin development
Levine and Davidson, PNAS, 2005
DNA is embedded in chromatin
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
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
RNA also acts as a regulator of gene expression
siRNA
miRNA
DNA is silenced at the level of histone modifications
through an RNAi-like mechanism
centromere
repeats
Genomics Technologies
systematic gene
mutation/RNAi screens
sequence
analyses
Functional
Networks
genome-wide
expression profiling
genotyping
global protein
analysis
nucleic acid/
protein interactions
Genome organization is non-random with respect
to gene expression in multiple organisms
local
chromatin
chromosome
Germ cells act to maintain the species
somatic cells
embryo
somatic cells
gametes
embryo
gametes
C. elegans hermaphrodite germ line
embryos
sperm
germline formation during larval development
L1
L2
L3
L3/L4
late L4
stem cells
meiosis
young adult
somatic gonad
sperm
oocytes
Levels of gene regulation in the germline
Chromosome: silencing of the X
Large domain: clustering of germline-expressed genes
Local domain: operon formation
embryos
sperm
C. elegans DNA microarrays
~20,000 genes in the worm genome
~18,000 genes on the array
Germline mutant comparisons
wild type
vs.
no germ line (glp-4)
sperm only (fem-3gf)
vs.
oocytes only (fem-1lf)
C. elegans hermaphrodite germ line
oogenic
germline
3003
genes
sperm
1380
genes
Sperm genes are different from oogenic
germline genes
Large-scale in situ hybridization
NextDB: Nematode
EXpression paTtern DataBase
Kohara lab
Japan
distal
distal+
proximal
98% of all genes in
oogenic germline
category show germline
expression by in situ
proximal
distal
proximal
Why?
The oogenesis genes on the X chromosome express at
lower levels than those on the autosomes
A
B
The hermaphrodite paired X does not stain with antibodies against
transcriptionally active chromatin conformation
DNA
Merge
α -H3methylK4
diplotene
stem cells
pachytene
diakinesis
Hermaphrodite X is silenced early in meiotic prophase but not late
diplotene
A
diakines
inactive
B
Transgene
1
2
5
6
3
4
C
D
diakinesis
 -H3methylK4
diakines
active tra