1. X-linked oogenic transcripts are expressed late in the germline
X-linked oogenic genes
autosomal oogenic genes
mex-3
Jones et al., 1996
rme-2
Almost no autosomal genes have an expression pattern restricted to the proximal germline; note these autosomal germline genes, which have expression in the distal part of the germline.
Lee & Schedl, 2001

2. X-linked gene expression in the C. elegans germline

3. germline gene clustering on autosomes
sperm and oogenic germline genes cluster in regional domains (p<10-15)
Roy et al, Nature, 2002
“open”
“closed”

4. operons in bacteria
operons in worms

5. 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)
SL2
SL1

6. Operons show a chromosomal bias
dots
bars
Blumenthal et al., 2002

7. Operons tend to encode proteins of certain functional classes
Blumenthal
and Gleason, 2003

8. Why are certain genes and not others in operons?
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?
There are two broad ideas for what selects for genes to be in operons. In the first, the genes in operons are more efficiently co-regulated than genes that do not share a single promoter and regulatory site. It is possible that the genes contained in operons need to be able to respond to global signals so they can be efficiently repressed or activated as a group. In the second broad class of explanation, the selection is simply for a compact genome; operons dramatically reduce both the DNA between genes and the amount of DNA expended on regulatory sites. Operons may mostly serve to transcribe genes that do not need to be regulated at all; they just need to be turned on in all tissues at all times. Another reasonable idea is that genes that are regulated at some level other than transcription have accumulated in operons because they can be expressed from the same promoter, but then regulated differentially at the level of mRNA stability or translation. These explanations are not mutually exclusive; different modes of selection may have resulted in the creation of different operons.

9. 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

10. Operons contain similar functional classes as the oogenic germline gene set

11. 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?

12. # genes in operons
on that chromosome

13. NextDB: Nematode EXpression paTtern DataBase
Large-scale in situ hybridization
distal+
proximal
distal
NextDB: Nematode EXpression paTtern DataBase
Kohara lab
Japan
proximal
distal

14. non-germline or no data
2283 genes in 876 operons
Microarray: 32
spermatogenesis
1024
oogenic germline
1227
non-germline/
no data
1010
non-germline or no data
217
mildly germline 69
somatic 84
no data 1
132
germline
557
384
In situ:
96% of all genes in operons are expressed in the germline (1572/1642)

15. 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

16. 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

17. Germline expression, not functional domains, determines operon formation43 77 31 18 9 1 9 1
actin cytoskeleton
47% oogenic germline
90% germline operons
protein phosphatases
26% oogenic germline
90% germline operons 14
that is, operons are correlated more tightly with gene expression in the germline than with the function of the encoded protein; indicating that germline expression was a more prominent force in the formation of operons 25 17
chaperones
75% oogenic germline
100% germline operons

18. Operons cluster in the genome
17/26 genes in operons
66kb from Chromosome II

19. Operons cluster in the genome
chrom
# operons
# clustered
% in clusters
# clusters
ave # in cluster CD
p< I
192
120 63 41
2.9
1.30
0.0001 II
166 89 54 33
2.7
1.21
III
203
140 69 47
3.0
1.51 IV
151 74 49 28
2.6
1.24
0.0002 V
128 46 36 20
2.3
1.17
0.0010 X 6 17 3
2.0
1.07
0.1376
(25kb non-sliding window)
Thanks to Scott Rifkin for writing statistics program for me

20. Operons cluster with monocistronic oogenic germline and sperm genes

21. 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?

22. Oogenic germline genes have the shortest 5’ intergenic distances
all
operon (1st)
all 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

23. The REDUCE algorithm finds more putative regulatory elements in sperm genes than in oogenic germline genes
Motif Gene # Significance
AAGTCGCC
CACGTAAA
CGTGAACT
GATCTAGG
TTACGTGA
sperm
oogenic
germline
ACTACGGT
CGCGCGAA *

24. 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.