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The Parts and the Whole: How Genes Allow an Animal to Build Itself

The Parts and the Whole: How Genes Allow an Animal to Build Itself. Itai Yanai Biology, Technion. The parts relative to the whole: The ship of Theseus.

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The Parts and the Whole: How Genes Allow an Animal to Build Itself

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  1. The Parts and the Whole: How Genes Allow an Animal to Build Itself Itai Yanai Biology, Technion

  2. The parts relative to the whole: The ship of Theseus "The ship wherein Theseus and the youth of Athens returned had thirty oars, and was preserved by the Athenians down even to the time of Demetrius Phalereus, for they took away the old planks as they decayed, putting in new and stronger timber in their place, insomuch that this ship became a standing example among the philosophers, for the logical question of things that grow; one side holding that the ship remained the same, and the other contending that it was not the same." —Plutarch, Theseus

  3. The Development of an Animal http://www.wormclassroom.org/files/worm/EmbryoHatch.swf

  4. Introducing C. elegans C. elegans is studied as a model organism for a variety of reasons. It is a amulticellular eukaryotic organism that is simple enough to be studied in great detail. Strains are cheap to breed and can be frozen. When subsequently thawed they remain viable, allowing long-term storage.

  5. Research from the humble worm has proved fruitful 3 Nobel Prizes in the past 10 years

  6. The development of the nematode C. elegans is comprised of five somatic founder lineages

  7. Evidence for mosaic development: segregation of developmental potential in the embryo ABs Dissociate cells C MS P3 E Expresses the genes expected from the gut Laufer, Bazzicalupo and Wood. Cell 1980

  8. Evidence for mosaic development: segregation of developmental potential in the embryo ABs Dissociate cells C MS P3 E med-1,2 end-1,3 elt-2,7 Expresses the genes expected from the gut Maduro & Rothman. Dev. Bio. 2002

  9. Evidence for regulative development: blastomere swapping experiment ABa Makes half of the pharynx ABp Makes half of the pharynx ABp ABa Priess and Thomson. Cell 1987

  10. Cost per megabase of DNA sequence

  11. The reason for the drop in cost: sequencing occurs in a massively parallel fashion

  12. Illumina HiSeq 2000 Image: www.illumina.com

  13. With generous support from: Yvgenia Lapis Lab technician Dr. Tal Katz-Ezov Head of Center Karen Chait Bioinformatician Dr. Maayan Duvshani-Eshet Head of LS&E Infrastructure Unit Rachelly Normand Bioinformatician Anastasia Diviatis Lab technician Noa Henig Bioinformatician Maya Abraham Bioinformatician

  14. Now possible to gauge gene expression levels for all genes by sequencing the transcriptome. genome sequence Reads lowly expressed gene highly expressed gene

  15. Which genes are expressed at which time in development? Levin, Hashimshony, Wagner and Yanai. Developmental Cell (2012)

  16. Which genes are expressed at which time in development? Different genes Gene expression levels Time

  17. Which gene expression is conserved?

  18. Stage 7 in mid-development that is uniquely conserved across different nematodes.

  19. Our lab developed a method for single cell RNA-Seq Hashimshony, Wagner, Sher and Yanai. Cell Reports (2012)

  20. Our lab developed a method for single cell RNA-Seq Cell 1 Cell 2 Cell 3 Gene 1 Gene 2 Gene 3 Expression n level high low Gene 20,000 . .

  21. Using the method we can identify differential expression between the sister cells mex-3 Bowerman et al. Cell 1996

  22. CEL-Seq for multiplexed single cell RNA-Seq • CEL-Seq is a single cell transcriptomics method using in vitro transcription. • CEL-Seq is linear, sensitive and reproducible. • CEL-Seq is highly multiplexed allowing for the parallel examination of hundreds of cells. Hashimshony, Wagner, Sher and Yanai. Cell Reports (2012)

  23. We are able to isolate and culture blastomeres

  24. Which developmental pathways are dependent upon interaction among the lineages? Whole embryo Separated embryo time ABs C MS P3 E ?

  25. Gene expression analysis on the C. elegans blastomere lineages

  26. The developmental expression profiles distinguish the contribution of the founder lineages unc-120 Whole embryo Expression level (log10) Time

  27. The expression of many genes is lineage specific Whole embryo Exp. level Developmental stages

  28. The expression of most genes is not specific to particular lineages and adds up to the whole-embryo expression Whole embryo Whole embryo Exp. Level Exp. level Developmental Stages Developmental stages

  29. The sum of the parts of the embryo generally matches the whole embryo. Number of molecules Time Whole embryo Parts + + +

  30. An example of a gene with missing expression Whole embryo pha-4 Exp. Level Developmental Stages

  31. Over time, fewer genes are recapitulated completely Sum analysis Ratio (Sum of Parts / Whole) Time

  32. Genes involved in morphogenesis, such as the fusogeneff-1, are also missing in the parts. eff-1 Exp. Level Developmental Stages

  33. Genes that are temporally restricted • are also spatially restricted time-specific Not time-specific Spatial specificity

  34. Known pathways can be recovered by detecting lineage specific expression ABs C MS P3 E med-1,2 end-1,3 elt-2,7 Expresses the genes expected from the gut

  35. We are currently validating a predicted AB neurogenesis pathway Exp. Level Developmental Stages

  36. Extending the evolutionary synthesis GB Muller. Nature Reviews Genetics (2008)

  37. The evolution of pathways can be studied by comparing across distantly related species

  38. Currently we are studying an entire phylum with Tardigrades as an outgroup.

  39. Our group at the Technion Dr. Tamar Hashimshony Assist. Prof. Itai Yanai Sally Khair Naftalie Senderovich Gal Avital Natalia Mostov Vlad Grishkevich Michal Levin Shay Ben-Elazar Leon Anavy David Silver Avital Polsky Martin Feder

  40. Thank you!

  41. The vitellogenins are expressed in the whole embryo but not in the cells, even early on. Whole Parts AB P 1 High expression No expression

  42. How is the pharynx programmed? P0 P1 AB GLP-1/Notch P2 ABp ABa EMS APX-1/Delta A first Notch signal is received by ABp but not ABa apx-1 glp-1

  43. How is the pharynx programmed? P0 P1 AB GLP-1/Notch P2 ABp ABa EMS APX-1/Delta tbx-37,38 hlh-27 lag-2 Without the signal, no hlh-27 and extra lag-2 and tbx-37,38 tbx-37,38 lag-2 hlh-27

  44. lag-1 is present throughout though, another signal is missing? P0 P1 AB GLP-1/Notch P2 ABp ABa EMS APX-1/Delta GLP-1/Notch MS E DSL-1??/Delta ABa descendants pha-4 lag-1 tbx-37,38 lag-1 pha-4 ceh-22 ceh-22 AnteriorPosterior

  45. Why doesn’t the MS blastomere make pharynx? P0 P1 AB GLP-1/Notch P2 ABp ABa EMS APX-1/Delta GLP-1/Notch med-1,2 MS E DSL-1??/Delta ABa descendants tbx-35 MS descendants tbx-35 tbx-37,38 lag-1 pha-4 pha-4 ceh-22 pha-4 AnteriorPosterior

  46. How many genes overall are missing? Number of genes Fraction covered (log2)

  47. C. elegans development proceeds by an invariant cell lineage Sulston et al. Dev. Bio. 1983

  48. C. elegans embryos develop according to an invariant cell lineage P0 P0

  49. CEL-Seq reads have “sense” orientation Chromosome II 500 bp

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