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

iro, J

. 197

9. M

olec

ular

mod

el fo

r the

tran

spos

ition

and

repl

icati

on o

f bac

terio

phag

e M

u an

d ot

her t

rans

posa

ble

elem

ents

. Pro

c. N

atl.

Acad

. Sci

. USA

76:

1933

-193

7

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