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X-linked oogenic transcripts are expressed late in the germline

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. “open”. “closed”. germline gene clustering on autosomes.

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X-linked oogenic transcripts are expressed late in the germline

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  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

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

  4. operons in bacteria operons in worms

  5. C. elegans operons SL1 SL2 SL2 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)

  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. C. elegans operons lack an organizing principle Why are certain genes and not others in operons? • Relatively poor co-expression • Low frequency of common functions for genes within an operon • No functional class of proteins completely represented in 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. Large-scale in situ hybridization distal distal+ proximal distal proximal proximal NextDB: Nematode EXpression paTtern DataBase Kohara lab Japan

  14. 32 spermatogenesis 1024 oogenic germline 1227 non-germline/ no data In situ: In situ: 1010 non-germline or no data 217 mildly germline 132 germline 384 germline 557 no data 84 no data 1 somatic 69 somatic 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

  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 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

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

  19. Operons cluster in the genome (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. “open” “closed” 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

  23. The REDUCE algorithm finds more putative regulatory elements in sperm genes than in oogenic germline genes MotifGene #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*

  24. “open” “closed” 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.

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