TET-mediated Hydroxymethylation in Reprogramming to Induced Pluripotency Open Access
Wang, Tao (2013)
Published
Abstract
5-Hydroxymethylcytosine (5hmC) is a newly discovered modified form of cytosine that has been suspected to be an important epigenetic modification in stem cells and during neurodevelopment. Here, we report the roles of 5-hmC during reprogramming as well as neurodevelopment. Mammalian somatic cells can be directly reprogrammed into induced pluripotent stem cells (iPSCs) by introducing defined sets of transcription factors. Somatic cell reprogramming involves epigenomic reconfiguration, conferring iPSCs with characteristics similar to embryonic stem cells (ESCs). Human ES cells contain 5hmC, which is generated through the oxidation of 5-methylcytosine by the TET enzyme family. Here we show that 5hmC levels increase significantly during reprogramming to human iPSCs mainly owing to TET1 activation, and this hydroxymethylation change is critical for optimal epigenetic reprogramming, but does not compromise primed pluripotency. Compared with hES cells, we find iPS cells tend to form large-scale (100 kb-1.3 Mb) aberrant reprogramming hotspots in subtelomeric regions, most of which display incomplete hydroxymethylation on CG sites. Strikingly, these 5hmC aberrant hotspots largely coincide (~80%) with aberrant iPS-ES non-CG methylation regions. Our results suggest that TET1-mediated 5hmC modification could contribute the epigenetic variation of iPSCs and iPSC-hESC differences.
Table of Contents
Table of Contents
Chapter 1: Toward pluripotency by reprogramming: looking back, looking forward
Introduction 1
Abstract 2
Introduction 3
Reprogramming factors 5
Effect of stoichiometry 8
DNA methylation and de-methylation 10
Small molecule-mediated reprogramming 12
iPS and ES cells differences 14
Elite, stochastic, and deterministic models 16
MicroRNAs in somatic reprogramming 17
Disease modeling 19
Concluding remarks 22
References 25
Chapter 2: Subtelomeric hotspots of aberrant
5-hydroxymethylcytosine-mediated epigenetic modifications during
reprogramming to pluripotency
Abstract 34
Introduction 35
Results 37
TET1-mediated hydroxymethylation plays a critical role during reprogramming to pluripotency in human cells 37
5hmC epigenomic landscape during reprogramming 38
5hmC is bi-directionally correlated with DNA methylation changes and associated with pluripotency related gene networks 39
Sequence preferences of 5hmC modification during reprogramming 41
Aberrant 5hmC reprogramming hotspots cluster in telomere-proximal regions 41
Concordance of large-scale 5hmC hotspots and iPS-ES non-CG DMRs 43
Base-resolution 5hmC analyses reveal large-scale hotspots are mainly caused by aberrant CG hydroxymethylation 44
Discussion 47
Methods 51
References 99
Chapter 3: Genome-wide DNA hydroxymethylation changes are associated with neurodevelopmental genes in the developing human cerebellum
Abstract 106
Introduction 107
Results 110
Dynamics of DNA hydroxymethylation and its genomic features in human
cerebellum 110
5-hmC genomic features during cerebellum development 111
The fetus-specific DhMRs displays pluripotent epigenetic memories 112
DhMRs are associated with genes involved in neurodevelopmental disorders 113
Discussion 117
Material and Methods 122
References 141
Chapter 4: Discussion and future directions
Potential distinct roles between TET1 and TET2 147
DNA methylation and demethylation 149
Future direction for hydroxymethylation studies 150
References 153
About this Dissertation
| School | |
|---|---|
| Department | |
| Subfield / Discipline | |
| Degree | |
| Submission | |
| Language |
|
| Research Field | |
| Keyword | |
| Committee Chair / Thesis Advisor | |
| Committee Members |
Primary PDF
| Thumbnail | Title | Date Uploaded | Actions |
|---|---|---|---|
|
|
TET-mediated Hydroxymethylation in Reprogramming to Induced Pluripotency () | 2018-08-28 11:36:54 -0400 |
|
Supplemental Files
| Thumbnail | Title | Date Uploaded | Actions |
|---|