the evolution of selfishness
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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. - PowerPoint PPT PresentationTRANSCRIPT
The evolution of selfishnessHW#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
Transposable elements in bacteria- Insertion Sequence (IS) replicative transposition
Shap
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. Pro
c. N
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. Sci
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76:
1933
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Repetitive DNA- Transposable elements
http://www.uni-kiel.de/Botanik/Kempken/researchtranspos-e.shtml
Transposable elements- transposition machinery
Retrotransposition
Virus vs. Retrotransposon
Transposition machinery
Henry S Levin 2011
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
Mills et al. 2007
How can we control them?
Why do we need them?
•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
Coufal et al. 2010
(hCNS-SCns) human fetal brain stem cells
L1 retrotransposition in hCNS-SCns
1,243bp product contains the intron
342bp product indicates intron loss and retrotransposition
1 weight standards2 hCNS-SCns transfected with JM111/L1RP
3-5, three hCNS-SCns lines transfected with L1RP
6-7, primary astrocytes and fibroblasts transfected with L1RP8, positive control9, water
Coufal et al. 2010
PCR of genomic DNA
Coufal et al. 2010
Time course of L1 retrotransposition
EGFP-positive hCNS-SCns also could be differentiated to cells of boththe neuronal and glial lineages
EGFP-positive cells candifferentiate to neurons
EGFP-positive cells can differentiate into glia
EGFP-positive cells express
Nestin and Sox2
Coufal et al. 2010
L1 retrotransposition in hESC-derived NPCsand some HUES6-derived NPCs are functional
L1 5 UTR is induced ′upon differentiation.
voltage stepdepolarizations
Suprathreshold responses to
somatic current injections
Spontaneous action potentials
Coufal et al. 2010
hESChuman embryonic stem cell
Methylation analysis for the endogenous human L1 5 UTR′
Coufal et al. 2010
Coufal et al. 2010
Methylation analysis for the endogenous human L1 5 UTR′
Multiplex quantitative PCR analyses of L1 copy number in human tissues
Coufal et al. 2010
Multiplex quantitative PCR analyses of L1 copy number in human tissues
Coufal et al. 2010
So, why do we need them?
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
Genes in the gene group
Highly common of annotation
Difference of annotation
All genesGenes in one gene term
Genes in my list
?
P-value