1. Transposon and Epigenetic Regulation
Liang Wu, Haiyun Zhang, Weizhen Cai

2. Transposon/ Transposable Elements
All mobile DNA segments in the genome, regardless of their mechanism of transposition.
Consists of ~50% of human genome.
Transpose is the movement of a genetic element from one location of the genome to another.
Retrotransposon and DNA transposons, autonomous and non-autonomous.

3. Retrotransposons Derived from viral genome.
R. Keith Slotkin & Robert Martienssen. Nature Reviews Genetics 8,   (April 2007) 
Derived from viral genome.
LTR: Long Terminal Repeats.
Needs to be reverse transcribed.
SINE (Short Interspersed Elements) and LINE (Long Interspersed Elements) are non-LTR retrotransposons.

4. DNA Transposons Transposase is responsible for transposition.
Transposase mutated
Miniature Inverted-Repeat Elements
New member of transposon
R. Keith Slotkin & Robert Martienssen. Nature Reviews Genetics 8,   (April 2007) 

5. Transposition
Henry L. Levin & John V. Moran. Nature Reviews Genetics 12,   (September 2011)

6. Consequences
Richard Cordaux & Mark A. Batzer. Nature Reviews Genetics 10,   (October 2009)
Transposons are highly mutagenic, cause insertion, chromosome breakage, recombination and genome rearrangement.

7. Transposon Needs Regulation
Number of transposable elements negatively correlated with fitness of the host.
Silenced by different mechanisms.

8. Silencing Mechanisms that Suppress TEs
Post-transcriptional silencing of TEs by RNAi
Chromatin modification
RNAi-mediated chromatin modification

9. Post-transcriptional Silencing of TEs by RNAi
dsRNA
cleaved by Dicer
siRNAs
RISC, Argonaute
siRNA-guided transcript -cleavage complex, RISC; Argonaute proteins is the cataclytic component. RdRP can additionally produce dsRNA from the cleaved RNA products.

10. Post-transcriptional Silencing of TEs by RNAi
RNAi is the main mechanism of TE silencing C. elegans, silencing Tc1 DNA transponson in germ line
Mutations in both argonaute- and dicer- family proteins cause the reactivation of TEs in eukaryotic species
TEs give rise to numerous siRNAs.
How TEs are specifically targeted by RNAi?
stuctures help to distinguish transcripts
3, in most species, including human.

11. Chromatin Modification
Modification of histone tails
Alert protein factors binding, send information to transcription factors
Methylation of histone H3K9 is a signal for transcriptionally repressive and inactive chromatin.
DNA methylation
Cytosine residue, in a symmetrical context (CpG)
Inheritable (mice, DNMT1 DNA methyltransferase)
Alterations in chromatin packing and condensation
SWI/SNF chromatin-remodelling proteins are required for TE silencing. (plant)
DDM1 in A. thaliana
CpG methylation is copied to new DNA strand upon DNA replication, providing a mechanism for inheritance of TE silencing.
DNMT1 DNA methyltransferase is reponsible for this maintenance of DNA methylation. Elevated IAP retrotransposon transcript levles in Dnmt-1-deficienct embryos.
SWI/SNF chromatin-remoldelling proteins use ATP hydrolysis to remodel nucleosomes, which are required for TE silencing.
DDM1 is a SWI/SNF2-like protein, which is specifically required for TE silencing and chromatin condesation.
If passed from a ddm1 mutant to wild-type background, TEs remains actived and do not regain DNA and H3K9 methylation.
Remodelling activity is specifically targeted to TEs: only TE transcripts are elevated in ddm1 mutants, most genes are unaffected.

12. RNAi-mediated Chromatin Modification
The maintenance of TE silencing at chromatin level involves both RNAi-independent and RNAi dependent pathway.
In S. pombe (fission yeast)
RNAi complex works on nascent RNAs
Argonaute proteins (Ago1) cleave nascent RNAs; the cleavage recruites the histone H3K9 methyltransferase Clr4 to the chromosome, mechanism unknown.
RNAi is specifically required for spreading H3K9 methylation from repeats into reporter genes. d
nascent RNAs are still bound to the chromosome and are processed co-transcriptionally into siRNAs.

13. RNAi-mediated Chromatin Modification
How do TEs that are silenced at the chromatin level produce transcripts that are to be cleaved into siRNAs?
In A. thaliana, plant-specific RNA polymerase Ⅳ
Loss of PolⅣ can transcriptionally reactive silenced TEs.
PolⅣa: generate siRNAs
PolⅣb: transfer siRNA signal
Symmetrical DNA methylation is heritable; Asymetrical methylation must be replaced at each cell division (less important).
Targetting mechanism perhaps involves RNAi.
polⅣb is probably guided to the correct location by its C-terminal domain, which is significantly longer than that of PolVa. C-terminal domain interacts directly with AGO4 in specific place( nuclear bodies) in an RNA-dependent manner, and might serve as a platform for different protein factors.

14. TEs influence the Genomes
TEs contribute to chromosome form and function
TE-induced epigenetic regulation of specific genes
Evolutionary implications

15. TEs contribute to chromosome form and function
Centromeres, telomeres and knobs
PEV and chromatin insulators
X inactivation

16. Centromeres and Telomeres
The centromeres are function as trafficking chromosomes at cell division. The DNA composition of centromeres differs widely in both length and primary nucleotide sequence between species, and it is the specific epigenetic context that confers their function. Thus the presence of TEs, and the epigenetic silencing apparatus that they recruit play a role in centromere function.
The telomeres work for preventing chromosome shortening following replication. Although whether TEs contribute to telomere- length regulation in mammals remains unknown, recent studies show that the epigenetic status (predominantly DNA methylation) of telomeric and sub-telomeric repeats has a role in regulating telomere elongation in mammalian cells.

17. KNOB
A chromosomal knob is a fragment of constitutive heterochromatin that has no known function.
Analysis of an A. thaliana knob, composed almost, entirely of full- length and fragmented TEs (many of which are inserted into each other), showed that heterochromatin was dependent on the epigenetic mechanisms of TE silencing.

18. Position Effect Variegation (PEV) and chromatin insulators
PEV: Heterochromatin can insert into adjacent genes and causes gene-silencing phenotype. TEs are nucleation centers for the formation of the type of facultative heterochromatin.
TEs themselves can function as insulators.

19. X inactivation
Female mammals must compensate for their double dosage of X- chromosome genes compared with XY males. This compensation is achieved by the inactivation and heterochromatinization of one of the two X chromosomes.
Inactivation is initiated at the X-chromosome inactivation center (XIC), and then spreads outwards from the XIC to the rest of the chromosome.
TEs function in both the initiation and spread of X inactivation. This is indirectly supported by a study on mice cells.

20. TE-induced epigenetic regulation of specific genes
Epiallele production and phenotypic variation
Paramutation
Imprinting
V(D)J Recombination

21. Epiallele production and phenotypic variation
TE promoters can influence the transcriptio of nearby genes.
In mice, the intracisternal A-particle (IAP) retrotransposon produces an outward-reading transcript that extends into the agouti coat-color gene. The level of agouti transcript, and the color of the coat, is subject to the epigenetic status of the retrotransposon and inheritable.

22. Paramutation
Paramutation is an interaction between alleles that results in a heritable expression change of one allele.
In maize, several genes in the anthocyanin pigmentation pathway have paramutable alleles, which are associated with and pendent on TEs.

23. Imprinting
On the mammalian X chromosome, TEs are specifically associated with monoallelic expressed genes that are located on autosomes, raising the possibility that TEs are involved in the regulation of imprinted genes.
The effect of TE-mediated imprinting in mammals might be mediated through the action of DNMT3L

24. Evolutionary implications
In the same specie, TEs have the ability to mutate genes, alter gene regulation and generate new genes, each providing fuel for evolution.
the stress-induced reactivation of TEs and the invasion of a new genome by TEs.
In different species, TEs can generate intraspecies variation. This happens in virus, plants, and animals.

25. Conclusions
TEs are all mobile DNA segments in the genome. Classified as retrotransposon, DNA transposon, autonomous and non-autonomous.
TEs silencing mechanisms: Post-transcriptional silencing by RNAi, chromatin modification(H3K9, CpG, SWI/SNF), RNAi-mediated chromatin modification.
TEs are involved in many epigenetic mechanisms, from chromosome form and function to specific genes, playing significant role in evolutionary history.