Life Sciences Research for Lifelong Health

Gavin Kelsey

Research Summary

It is thought that epigenetic information can be programmed by environmental factors, such as diet and early life experiences, and such changes can be perpetuated long after these exposures and potentially to future generations.  Such epigenetic programming may contribute to our risk of developing disease in later life.  Imprinted genes (whose expression is determined by the parent that contributed them) are a model for how epigenetic events in gametes of one generation dictate gene activity in the next.

Our mapping of methylation of DNA in the egg, sperm and embryo suggests that this epigenetic influence may extend well beyond the small number of known imprinted genes.  Using genome-wide approaches, we are tracking the fate of DNA methylation patterns inherited from the egg and sperm, the stability of these marks throughout the lifetime and ageing, and how they affect activity of associated genes.  In particular, we are investigating whether DNA methylation in particular populations of neurons in the hypothalamus, the part of the brain that senses nutritional status to control metabolism and appetite, is altered by exposure to altered diets and may modify response to nutritional status.

The discovery that gene transcription is essential for DNA methylation and imprint establishment may help to explain how the methylation modifications in the genome of the egg may be modified by adverse environments or how imprinting is disrupted in some imprinted gene disorders.

Latest Publication:
Hira is essential for normal transcriptional regulation and efficient de novo DNA methylation during mouse oogenesis.
Nashun B, Hill PWS, Smallwood SA, Dharmalingam G, Amouroux R, Clark SJ, Sharma V, Ndjetehe E, Pelczar P, Festenstein R‎, Kelsey G, Hajkova P.
Mol Cell. 2015 AOP 5th Nov. 2015, doi:10.1016/j.molcel.2015.10.010.

Latest Publications

The histone 3 lysine 4 methyltransferase Setd1b is a maternal effect gene required for the oogenic gene expression program.
Brici D, Zhang Q, Reinhardt S, Dahl A, Hartmann H, Schmidt K, Goveas N, Huang J, Gahurova L, Kelsey G, Anastassiadis K, Stewart AF, Kranz A

Germ cell development involves major reprogramming of the epigenome to prime the zygote for totipotency. Histone 3 lysine 4 (H3K4) methylations are universal epigenetic marks mediated in mammals by six H3K4 methyltransferases related to fly Trithorax, including two yeast Set1 orthologs: Setd1a and Setd1b. Whereas Setd1a plays no role in oogenesis, we report that Setd1b deficiency causes female sterility. Oocyte specific Gdf9iCre conditional knockout (Setd1b(Gdf9) cKO) ovaries develop through all stages however follicular loss accumulated with age and unfertilized metaphase II (MII) oocytes exhibited irregularities of the zona pellucida and meiotic spindle. Most Setd1b(Gdf9) cKO zygotes remained in the pronuclear stage and displayed polyspermy in the perivitelline space. Expression profiling of Setd1b(Gdf9) cKO MII oocytes revealed (i) that Setd1b promotes the expression of the major oocyte transcription factors including Obox1, 2, 5, 7, Meis2 and Sall4; and (ii) two-times more up- than downregulated mRNAs suggesting that Setd1b also promotes the expression of negative regulators of oocyte development with multiple Zfp-KRAB factors implicated. Together, these findings indicate that Setd1b serves as maternal effect gene through regulation of the oocyte gene expression program.

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Development (Cambridge, England), , 1477-9129, , 2017

PMID: 28619824

Transcription and chromatin determinants of de novo DNA methylation timing in oocytes.
Gahurova L, Tomizawa SI, Smallwood SA, Stewart-Morgan KR, Saadeh H, Kim J, Andrews SR, Chen T, Kelsey G

Gametogenesis in mammals entails profound re-patterning of the epigenome. In the female germline, DNA methylation is acquired late in oogenesis from an essentially unmethylated baseline and is established largely as a consequence of transcription events. Molecular and functional studies have shown that imprinted genes become methylated at different times during oocyte growth; however, little is known about the kinetics of methylation gain genome wide and the reasons for asynchrony in methylation at imprinted loci.

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Epigenetics & chromatin, 10, 1756-8935, 25, 2017

PMID: 28507606

Genome-wide base-resolution mapping of DNA methylation in single cells using single-cell bisulfite sequencing (scBS-seq).
Clark SJ, Smallwood SA, Lee HJ, Krueger F, Reik W, Kelsey G

DNA methylation (DNAme) is an important epigenetic mark in diverse species. Our current understanding of DNAme is based on measurements from bulk cell samples, which obscures intercellular differences and prevents analyses of rare cell types. Thus, the ability to measure DNAme in single cells has the potential to make important contributions to the understanding of several key biological processes, such as embryonic development, disease progression and aging. We have recently reported a method for generating genome-wide DNAme maps from single cells, using single-cell bisulfite sequencing (scBS-seq), allowing the quantitative measurement of DNAme at up to 50% of CpG dinucleotides throughout the mouse genome. Here we present a detailed protocol for scBS-seq that includes our most recent developments to optimize recovery of CpGs, mapping efficiency and success rate; reduce hands-on time; and increase sample throughput with the option of using an automated liquid handler. We provide step-by-step instructions for each stage of the method, comprising cell lysis and bisulfite (BS) conversion, preamplification and adaptor tagging, library amplification, sequencing and, lastly, alignment and methylation calling. An individual with relevant molecular biology expertise can complete library preparation within 3 d. Subsequent computational steps require 1-3 d for someone with bioinformatics expertise.

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Nature protocols, 12, 1750-2799, 534-547, 2017

PMID: 28182018

01223 496332

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Keywords

developmental biology
dna
epigenetics
methylation
single-cell

Group Members

Latest Publications

The histone 3 lysine 4 methyltransferase Setd1b is a maternal effect gene required for the oogenic gene expression program.

Brici D, Zhang Q, Reinhardt S

Development (Cambridge, England)
1477-9129: (2017)

PMID: 28619824

Transcription and chromatin determinants of de novo DNA methylation timing in oocytes.

Gahurova L, Tomizawa SI, Smallwood SA

Epigenetics & chromatin
10 1756-8935:25 (2017)

PMID: 28507606

Establishment and functions of DNA methylation in the germline.

Stewart KR, Veselovska L, Kelsey G

Epigenomics
1750-192X: (2016)

PMID: 27659720

Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity.

Clark SJ, Lee HJ, Smallwood SA

Genome biology
17 1474-760X:72 (2016)

PMID: 27091476

Pervasive polymorphic imprinted methylation in the human placenta.

Hanna CW, Peñaherrera MS, Saadeh H

Genome research
1549-5469: (2016)

PMID: 26769960

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity.

Angermueller C, Clark SJ, Lee HJ

Nature methods
1548-7105: (2016)

PMID: 26752769