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The evolution of selfishness

The evolution of selfishness. HW#5: FASTA sequence Function. Human genome. Klug & Cummings 2000. Transposable elements in bacteria- Insertion Sequence (IS). http://bio3400.nicerweb.com/Locked/media/ch15/insertion_sequences.html.

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The evolution of selfishness

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  1. The evolution of selfishness • HW#5: • FASTA sequence • Function

  2. Human genome

  3. Klug & Cummings 2000

  4. Transposable elements in bacteria- Insertion Sequence (IS) http://bio3400.nicerweb.com/Locked/media/ch15/insertion_sequences.html

  5. Transposable elements in bacteria- Insertion Sequence (IS) replicative transposition Shapiro, J. 1979. Molecular model for the transposition and replication of bacteriophage Mu and other transposable elements. Proc. Natl. Acad. Sci. USA 76:1933-1937

  6. Repetitive DNA- Transposable elements http://www.uni-kiel.de/Botanik/Kempken/researchtranspos-e.shtml

  7. Transposable elements- transposition machinery Retrotransposition

  8. Virus vs. Retrotransposon

  9. Transposition machinery Henry S Levin 2011

  10. Classes of species specific transposons in human and chimpanzees A, The overall composition of species-specific insertions in humans and chimpanzees. Note that 97.2% of all insertions in humans and 95.6% of all insertions in chimpanzees are Alu, L1, and SVA insertions. B, The distributions of Alu and L1 subfamilies for humans. C, The distributions of Alu and L1 subfamilies for chimpanzees Mills et al. 2006

  11. Mills et al. 2007

  12. How can we control them?

  13. Why do we need them?

  14. Retrotransposon- L1 • Non-LTR retroelement (Class I) • Comprises 17% of the human genome. • ORF1 encodes 40KD nucleic acid binding protein. • ORF2 encodes for both reverse transcriptase (RT) and endonuclease (EN).

  15. L1 retrotranspositionin hCNS-SCns (hCNS-SCns) human fetal brain stem cells Coufal et al. 2010

  16. PCR of genomic DNA 1,243bp product contains the intron 342bp product indicates intron loss and retrotransposition 1 weight standards 2 hCNS-SCns transfected with JM111/L1RP 3-5, three hCNS-SCns lines transfected with L1RP 6-7, primary astrocytes and fibroblasts transfected with L1RP 8, positive control 9, water Coufal et al. 2010

  17. Time course of L1 retrotransposition Coufal et al. 2010

  18. EGFP-positive hCNS-SCns also could be differentiated to cells of boththe neuronal and glial lineages EGFP-positive cells express Nestin and Sox2 EGFP-positive cells can differentiate to neurons EGFP-positive cells can differentiate into glia Coufal et al. 2010

  19. L1 retrotransposition in hESC-derived NPCsand some HUES6-derived NPCs are functional hESC human embryonic stem cell L1 5′ UTR is induced upon differentiation. voltage step depolarizations Suprathreshold responses to somatic current injections Spontaneous action potentials Coufal et al. 2010

  20. Methylation analysis for the endogenous human L1 5′ UTR Coufal et al. 2010

  21. Methylation analysis for the endogenous human L1 5′ UTR Coufal et al. 2010

  22. Multiplex quantitative PCR analyses of L1 copy number in human tissues Coufal et al. 2010

  23. Multiplex quantitative PCR analyses of L1 copy number in human tissues Coufal et al. 2010

  24. So, why do we need them?

  25. Clustering options and stringency Genes involved in individual term Related term Every term in the annotation cluster A group of terms having similar biological meaning due to sharing similar gene members

  26. Highly common of annotation Difference of annotation Genes in the gene group

  27. All genes Genes in one gene term Genes in my list ? P-value

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