My earlier notes

1. Histone methylation vs DNA methylation

DNMT3a3b vs PRC1/2.

http://www.biomedcentral.com/content/pdf/s12915-015-0118-4.pdf

DNA methylation degrades bivalent chromatin

Epigenetic drift

2. DNA methylation better predictor of chronological age than telomerase

  

http://www.genomebiology.com/2014/15/2/R24

3. DNMT3a

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4063825/

4. Bivalent chromatin

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3701188/

Bivalent promoters control hundreds or thousand genes, differentiation and tissue specific

5. Cancer DNA methylome

http://onlinelibrary.wiley.com/doi/10.1002/bies.201300130/full

6. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110498

PCR2 during embryonal stem cell differentiation

7. http://www.sciencedirect.com/science/article/pii/S1934590914000964

DNA methylation and histone meth in aging mouse HSCs, very thorough
p16INK4a not upregulated in old stem cell

8. http://www.pnas.org/content/111/7/2620.short

HSC renewal caused by DNMt3a mutation (effectively knock down)  induces leukemia

9. melatonin and aging

http://www.mdpi.com/1422-0067/15/9/16848/htm

10. Tissue maintenance

http://www.sciencedirect.com/science/article/pii/S193459091100484X

11. Epigenetic dysregulation, stem cells

http://www.stem-art.com/library/Basic/Epigenetic%20Control%20of%20Stem%20Cell%20Potential%20during%20Homeostasis,%20Aging,%20and%20Disease.pdf

12. Aging and epigenetic drift

http://www.jci.org/articles/view/69735?utm_campaign=impact_2014_january&utm_content=short_url&utm_medium=pdf&utm_source=impact

13.  review on dna methylation

http://download.bioon.com.cn/view/upload/201207/26095720_4487.pdf

14. review on histone methylation

http://thegreerlab.com/wp-content/uploads/2015/01/Histone-methylation-a-dynamic-mark-in-health-disease-and-inheritance.pdf

15. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0043840

Age-Associated Hyper-Methylated Regions in the Human Brain Overlap with Bivalent Chromatin Domains

16. hsc exhaustion by methylation of prc2 targets

http://www.idi.harvard.edu/uploads/investigators/Beerman_et_al_Cell_Stem_Cell_2013.pdf

17. Tumor microenvironment immune suppression is PTEN dependent

http://advances.sciencemag.org/content/1/10/e1500845.full

18. epigenetic deregulation is a common feature of aging in mammals

http://depts.washington.edu/lairdlab/pdfs/MaegawaEtAl2010.pdf

19. DNMT1 decreases with aging, citations

http://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed_citedin&from_uid=14577574

20. Aging and DNA methylation. Very good

http://bmcbiol.biomedcentral.com/articles/10.1186/s12915-015-0118-4#CR78

21. chromatin in aging and cancer (methylation, histones, ncRNA)

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4254271/

22. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3684276/

Transcriptome landscape in human genome

23. Partial hepatectomy, lncRNA regulates regeneration

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4514479/

24. Long non coding RNA really like to guide PRC2
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4514479/

25. surprise, aging can impair regeneration of liver

http://www.sjf.ch/wp-content/uploads/2012/10/Effect-of-age-on-liver-regeneration-following-partial-hepatectomy.pdf

26. http://www.nature.com/nrm/journal/v16/n10/full/nrm4048.html#affil-auth

Epigenetic regulation of ageing: linking environmental inputs to genomic stabilit

Very good

free on researchgate

it’s the chromatin, stupid!

26. Mouse strains survival curves

http://ilarjournal.oxfordjournals.org/content/52/1/4.full.pdf

27. Naked mole rate sequencing

http://www.nature.com/nature/journal/v479/n7372/full/nature10533.html

28. http://content-assets.jci.org/manuscripts/64000/64098/JCI64098.v1.pdf

Cellular senescence and the senescent
secretory phenotype: therapeutic opportunities

29. http://eprint.ncl.ac.uk/%2Ffile_store%2Fproduction%2F164151%2FB92B428A-EB7E-466D-9F68-022518C85BFE.pdf

Adult ‐ onset, short ‐ term dietary restriction reduces cell senescence in mice

30. https://www.researchgate.net/profile/Qintong_Li/publication/261990086_Insulin-like_growth_factor-1_regulates_the_SIRT1-p53_pathway_in_cellular_senescence._Aging_Cell/links/559ff42208ae967fb3e9675e.pdf

Insulin-like growth factor-1 regulates the SIRT1-p53 pathway in

cellular senescence

31.  https://www.researchgate.net/profile/David_Murray15/publication/230743547_Role_of_p16INK4A_in_Replicative_Senescence_and_DNA_Damage-Induced_Premature_Senescence_in_p53-Deficient_Human_Cells/links/53fb3fd90cf27c365cf08b38.pdf

Regulation of p16/INK4 (PRC2 and histone modification involved)

32. http://genesdev.cshlp.org/content/21/5/525.full

PRC2 meets senescence

33. p16 hypermethylation increases age related cancer incidence in mice

https://www.researchgate.net/publication/264247543_Targeted_p16Ink4a_epimutation_causes_tumorigenesis_and_reduces_survival_in_mice

seems like the epigenetic dysregulation of the genome, which upregulates many sequences, also upregulatesp16 thus inherently protecting against cancer -> lowering the threshold toward degenerating into senescencent phenotype

is there anything that drives epigenetic dysregulation or is it just enthropy?

34. or histone deacethylase??

https://www.researchgate.net/profile/Gunter_Kenis/publication/279517688_The_Epigenetics_of_Aging_and_Neurodegeneration/links/561cc19208ae78721fa250b7.pdf

35. Good thorough paper on time restricted feeding in mice. Unfortunately no lifespan or health span investigation, only biomarkers. Very good effects on serum insulin and cholersterol.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4255155/

36. mTOR regulates circadian rythm?

http://www.impactaging.com/papers/v6/n1/pdf/100633.pdf

37. Transposable elements drive ageing

https://www.researchgate.net/profile/Tibor_Vellai/publication/274395087_The_mechanism_of_ageing_primary_role_of_transposable_elements_in_genome_disintegration/links/552bb2da0cf21acb091e5df8.pdf

38. mtDNA mutations in oocytes are much less frequent than in somatic cells

http://www.sciencedirect.com/science/article/pii/S1934590916000679

39. http://www.cell.com/cell-reports/fulltext/S2211-1247%2815%2900792-5

While somatic cells depend mostly on mitochondrial oxidative phosphorylation (OxPhos), pluripotent stem cells possess immature mitochondria and preferentially use glycolysis as their major source of energy

40.https://www.researchgate.net/profile/Steen_Ooi/publication/5269344_The_colorful_history_of_active_DNA_demethylation/links/5411aae00cf264cee28b4ec4.pdf

DNA demethylation

41. Overexpression DNMR3b1 but not DNMT3a1 of cancer prone trangenic mice increases tumor incidence. Same pathway (igf2 overexpression by suppressing H19) as in DNMT1 overexpression study,

http://genesdev.cshlp.org/content/21/23/3110.full.html

Maybe DNMT3a can be overexpressed without adverse effects?

The article has a nice inrroduction where they state the cancer cells are generally hypomethylated byt hypermethylated at PRC2 binding sites. This is exactly the same as the findings about aging stem cell.

42. Adult stem cell epigenetics, very good

https://www.researchgate.net/profile/Lorenzo_Rinaldi2/publication/264199997_Epigenetic_regulation_of_adult_stem_cell_function/links/5629e16308ae22b1703159ad.pdf