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

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

8. Transposable elements- transposition machinery Retrotransposition

9. Virus vs. Retrotransposon

10. Transposition machinery Henry S Levin 2011

11. 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 Classes of species specific transposons in human and chimpanzees

12. Mills et al. 2007

13. How can we control them?

14. Why do we need them?

16. 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). Retrotransposon- L1

17. Coufal et al. 2010 (hCNS-SCns) human fetal brain stem cells L1 retrotransposition in hCNS-SCns

18. 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 PCR of genomic DNA

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

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

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

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

23. Methylation analysis for the endogenous human L1 5′ UTR

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

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

26. So, why do we need them?

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

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

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