Xlinked oogenic transcripts are expressed late in the germline

1
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
2
X-linked gene expression in the C. elegans
germline
X
A
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germline gene clustering on autosomes

• sperm and oogenic germline genes cluster in
  regional domains (plt10-15)
• Roy et al, Nature, 2002

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operons in bacteria
operons in worms
5
C. elegans operons
876 identified operons (gt1000 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)
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
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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

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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
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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?
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genes in operons on that chromosome
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Large-scale in situ hybridization
NextDB Nematode EXpression paTtern
DataBase Kohara lab Japan
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2283 genes in 876 operons
Microarray
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
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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
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Germline expression, not functional domains,
determines operon formation
77
43
31
18
9
9
1
1
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
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Operons cluster in the genome
66kb from Chromosome II
17/26 genes in operons
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Operons cluster in the genome
(25kb non-sliding window)
Thanks to Scott Rifkin for writing statistics
program for me
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Operons cluster with monocistronic oogenic
germline and sperm genes
21
Chromatin status in the germline
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
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The REDUCE algorithm finds more putative
regulatory elements in sperm genes than in
oogenic germline genes
Motif Gene Significance AAGTCGCC
110 0.786 CACGTAAA 308 0.419 CGTGAACT
363 0.965 GATCTAGG 108 1.090 TTACGTGA
276 0.523
sperm
oogenic germline
ACTACGGT 242 0.465 CGCGCGAA
0.477
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Chromatin status in the germline








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.