Next Generation Sequencing High Throughput Epigenomics

Lead Research Organisation: Babraham Institute
Department Name: Nuclear Dynamics

Abstract

Recent evidence suggests that an adult individual?s health and susceptibility to common diseases can sometimes be traced back to environmental and nutritional effects experienced by their mothers or grandmothers during pregnancy. The ?experiences? of the foetus during development in its mother?s womb appears to alter the way that an individuals genome is interpreted in later life leading to, in some cases, increase susceptibility to certain diseases. This altered genome interpretation can in some cases be passed passed on to the next generation as well, even in the absence of the original conditions. Though we have the sequence of the entire human genome, we know little about how it works, and how it is interpreted by cells. In this project we will take advantage of recent breakthroughs in DNA sequencing technologies that will permit us to collect hugely increased amounts of data from the genomes of cells before, during and after development. In addition to revealing important information about the workings of the genome these results will provide important insights into the fetal origins of adult disease and potentially lead to new strategies for prevention and new medicines or therapies for treatment of conditions that affect the quality of life.

Technical Summary

Development is the result of changes in gene expression programmes that give rise to different organs and tissues. With few exceptions, these changes occur without changes to DNA sequence. Changes in epigenetic modifications such as DNA methylation, histone modifications, histone variant deposition and the presence of non-nucleosomal chromatin-associated proteins are strongly linked to the transitions from totipotent to pluripotent stem cells, and precursor cells to fully differentiated somatic cells. Little is known about these interlaced systems work and interact. In this Collaboration Grant we propose to bring together a pre-eminent group of UK scientists working on epigenetics and chromatin during development. Our current funded research programmes are aimed at various and extensive epigenetic analyses of diverse ?developmental? cell-types; including primordial germ cells, developing oocytes, ES cells, blastocysts, TS cells, placenta, fetal liver and adult tissues. Presently these analyses are to be performed with real-time PCR, Sequenom massarray, or microarray based profiling, etc. Each of these techniques is limiting, either in terms of the number of samples or datapoints that can be assessed (PCR and Sequenom) or in the quality and quantitative value of data returned (array techniques). Rather than simply focussing on own little parts of the genome we propose to collaborate in the establishment of a new facility, to take advantage of improvements in DNA sequencing technology to create a database of genome-wide datasets representing an epigenetic time course through development. With the aid of an Illumina Genome Analyzer II (Solexa) massively parallel sequencing system we will generate genome-wide datasets for each experiment, rather than a tiny fragment of the genome. This will allow us to investigate the specific questions outlined in our present research programmes, while at the same time dramatically increasing the output and quality of each experiment. The data from each of the applicants will be deposited in a searchable database curated by the proposed postdoc. The net effect will be to create a programme that is substantially larger, more encompassing and providing much greater insight than the sum of the previous constituent parts. This collaborative database will foster interaction and sharing of expertise between applicants as well as create a shared resource for collaborative publications that would not have been possible without this grant.

Publications

10 25 50
 
Description International Human Epigenome Consortium
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
 
Description EU BLUEPRINT
Amount £500,000 (GBP)
Funding ID 282510 
Organisation European Commission 
Department Seventh Framework Programme (FP7)
Sector Public
Country European Union (EU)
Start  
 
Description EU NoE EpiGeneSys
Amount £400,000 (GBP)
Funding ID 257082 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start  
 
Description MRC Collaboration Grant (deep sequencing in Epigenomics)
Amount £960,000 (GBP)
Funding ID G0801156 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start  
 
Description Wellcome Trust Senior Investigator Award
Amount £2,900,000 (GBP)
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2011 
End 08/2018
 
Description Wellcome Trust Strategic Award
Amount £2,400,000 (GBP)
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2015 
End 12/2019
 
Title Hydroxymethylcytosine antibody 
Description We made an antibody to hydroxymethylcytosine which was commercialised by Diagenode 
Type Of Material Technology assay or reagent 
Year Produced 2011 
Provided To Others? Yes  
Impact Use in several publications. Development of hydroxymethylcytosine sequencing. 
URL http://www.diagenode.com/en/index.php
 
Title Oxidative bisulfite sequencing 
Description Chemical method for sequencing of hydroxymethylation commercialised by Cambridge Epigenetix. 
Type Of Material Technology assay or reagent 
Year Produced 2013 
Provided To Others? Yes  
Impact Use in several publications. 
URL http://www.cambridge-epigenetix.com
 
Title Whole genome bisulfite sequencing 
Description Whole genome bisulfite sequencing datasets from various mouse tissues 
Type Of Material Technology assay or reagent 
Year Produced 2010 
Provided To Others? Yes  
Impact None yet 
 
Description DNA methylation analysis in oocytes genetically deficient for Kdm1a (Lsd1) and Kdm1b (Aof1) 
Organisation University of Texas
Department M. D. Anderson Cancer Center
Country United States 
Sector Academic/University 
PI Contribution We were responsible for framing the project and experimental design and performed genome-wide DNA methylation analysis in oocytes genetically deficient in the H3K4me2 demethylases KDM1A or KDM1B, provided by the collaborating group.
Collaborator Contribution The partner provided oocytes from mice genetically deficient in Kdm1a or Kdm1b; provided RNA-seq datasets for these oocytes.
Impact Joint publications Stewart et al., 2015 Genes & Dev; Gahurova et al. 2017 Epigenetics & Chromatin. Deposited sequence datasets at NCBI GEO: GSE73803 and GSE74549.
Start Year 2011
 
Description Gastrulation team 
Organisation University of Cambridge
Country United Kingdom 
Sector Academic/University 
PI Contribution Conceived of the project and lead partner. Contributing single cell multi-omics and embryology.
Collaborator Contribution Helped to conceive of the project and several experimental and computational contributions.
Impact First publication Mohammed et al 2017. Experimental embryology, single cell biology, computation, modelling, epigenetics.
Start Year 2014
 
Description MRC EASIH 
Organisation University of Cambridge
Department Cambridge Institute for Medical Research (CIMR)
Country United Kingdom 
Sector Academic/University 
PI Contribution increased opportunities for deep sequencing using alternative platforms such as Roche 454 and ABI Solid
Collaborator Contribution MRC East Anglia Sequencing and Informatics Hub established in 2009
Impact see above
Start Year 2009
 
Description Sanger 
Organisation The Wellcome Trust Sanger Institute
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Leading to Associate Faculty Position at Sanger Institute
Collaborator Contribution Leading to Associate Faculty Position at Sanger Institute
Impact Leading to Associate Faculty Position at Sanger Institute
Start Year 2010
 
Description Sanger Single Cell Genomics Centre 
Organisation The Wellcome Trust Sanger Institute
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Helped to establish the Single Cell Genomics Centre at Sanger/EBI
Collaborator Contribution A number of Sanger and EBI PIs were involved
Impact Genomics, transcriptomics, epigenomics, computational biology
Start Year 2013
 
Company Name Cambridge Epigenetix 
Description Cambridge Epigenetix was spun out of Cambridge University in 2012 based on oxidative bisulfite sequencing IP 
Year Established 2012 
Impact CEG are in the process of developing an oxidative bisulfite sequencing kit
Website http://www.cegx.co.uk/
 
Description Cheltenham Science Festival 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? Yes
Type Of Presentation Keynote/Invited Speaker
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact A panel discussion and public debate on epigenetics at the Cheltenham Science Festival 2013

Several enquiries from members of the public who attended
Year(s) Of Engagement Activity 2013
URL http://www.cheltenhamfestivals.com/science/whats-on/2013/flexible-inheritance-epigenetic-effects-on-...
 
Description Royal Society Summer Exhibition 2012 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Type Of Presentation Workshop Facilitator
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Large public audience attendance over one week of all day exhibition

Much positive feedback from members of the public and scientists attending
Year(s) Of Engagement Activity 2012