X-linked oogenic transcripts are expressed late in the germline
autosomal oogenic genes
X-linked oogenic genes
mex-3
Jones et al., 1996
rme-2
Lee & Schedl, 2001
X-linked gene expression in the
C. elegans germline
X
A
germline gene clustering on autosomes
sperm and oogenic germline genes cluster in
regional domains (p<10-15)
Roy et al, Nature, 2002
“open”
“closed”
operons in bacteria
operons in worms
C. elegans operons
876 identified operons
(>1000 extrapolated)
2270 genes (~15% of genome)
2.6 genes/operon average
Unlike bacterial operons, operon
genes in C. elegans do not show
strong co-expression.
(Blumenthal et al., 2002; Blumenthal and Gleason 2003)
SL1
SL2
SL2
Operons show a chromosomal bias
bars
dots
Blumenthal et al., 2002
Operons tend to encode proteins of certain
functional classes
Blumenthal
and Gleason, 2003
C. elegans operons lack an organizing principle
• Relatively poor co-expression
• Low frequency of common functions for genes within an
operon
• No functional class of proteins completely represented in
operons
Why are certain genes and not
others in operons?
Similarities between germline and operon gene sets
Show similar genomic organization: biased against the X
Show similar frequency of nonviable phenotypes by RNAi: ~30%
Encode similar types of gene products: oogenic germline set only
Operons contain similar functional classes as the
oogenic germline gene set
Similarities between germline and operon gene sets
Show similar genomic organization: biased against the X
Show similar frequency of nonviable phenotypes by RNAi: ~30%
Encode similar types of gene products: oogenic germline set only
So, how many genes in operons are expressed in the germline?
# genes in operons
on that chromosome
Large-scale in situ hybridization
NextDB: Nematode
EXpression paTtern DataBase
Kohara lab
Japan
distal
proximal
distal
distal+
proximal
proximal
2283 genes in 876 operons
Microarray:
32
1227
spermatogenesis non-germline/
no data
1010
non-germline or no data
In situ:
557
no data
1024
oogenic germline
217
mildly germline
In situ:
69
somatic
384
84
1
germline no data somatic
132
germline
96% of all genes in operons are expressed in the
germline (1572/1642)
876 operons
510 completely classified operons
(microarray or in situ data for ALL genes)
456
all-germline
operons
54
mixed or somatic
operons by in
situ
89% of all operons are completely expressed in the
germline (456/510)x100
Which came first?
Expression: Germline gene expression
actively promoted operon formation
Function: Genes are in operons because
of their encoded protein products, which
happen to be commonly expressed in the
germline.
Test: look within a functional category for expression bias
Germline expression, not functional domains,
determines operon formation
77
43
1 9
31
1 9 18
actin cytoskeleton
47% oogenic germline
90% germline operons
protein phosphatases
26% oogenic germline
90% germline operons
14
25
17
chaperones
75% oogenic germline
100% germline operons
Operons cluster in the genome
17/26 genes in operons
66kb from Chromosome II
Operons cluster in the genome
chrom # operons
#
% in
#
ave # in
clustered clusters clusters cluster
CD
p<
I
192
120
63
41
2.9
1.30 0.0001
II
166
89
54
33
2.7
1.21 0.0001
III
203
140
69
47
3.0
1.51 0.0001
IV
151
74
49
28
2.6
1.24 0.0002
V
128
46
36
20
2.3
1.17 0.0010
X
36
6
17
3
2.0
1.07 0.1376
(25kb non-sliding window)
Thanks to Scott Rifkin for writing statistics program for me
Operons cluster with monocistronic oogenic
germline and sperm genes
Chromatin status in the germline
“open”
“closed”
= operon
= oogenic
germline
= sperm
Sperm genes are expressed in the right place (the germline)
and are are organized similarly to oogenic germline genes.
Then why are they not in operons?
Oogenic germline genes have the shortest 5’ intergenic distances
all
operon
all
(1st) non-op
oog gl
non-op
oog gl
sperm
non-op
sperm
mean
2051
1206
2215
1186
1468
1578
1602
SD
2964
1934
3080
2120
2501
2773
2802
median
972
539
1096
532
656
772
782
N
19484
870
17565
2901
1877
1278
1245
The REDUCE algorithm finds more putative regulatory
elements in sperm genes than in oogenic germline genes
sperm
oogenic
germline
Motif
AAGTCGCC
CACGTAAA
CGTGAACT
GATCTAGG
TTACGTGA
ACTACGGT
CGCGCGAA
Gene #
110
308
363
108
276
242
Significance
0.786
0.419
0.965
1.090
0.523
0.465
0.477*
Chromatin status in the germline
*
*
* *
*
*
*
*
“open”
“closed”
= operon
= germline
= sperm
The requirement for sequence-specific transactivation (*)
prevents operon formation, but the dependence on
chromatin status and post-transcriptional regulation in
the oogenic germline for gene regulation removes this
requirement and allows operon formation when the
trans-splicing machinery is present.