Allele-specific enhancer usage and genomic imprinting: a job for NOMe-seq

MONK_U23DTP2

Are you looking for a PhD position in the area of developmental (epi)genetics?  Our previous work has revealed that the human placenta has a unique epigenome.

In order to understand the consequence of the observed global hypomethylation on additional epigenetc layers, it is crucial to dissect chromatin accessibility profiles and compare them with DNA methylation.

This project will involve generating global expression and chromatin accessibility profiles in placenta cell lines and tissue biopsies using RNA-seq, NOMe-seq and ATAC-seq methods, as well as ultising the single-cell multi-omic NMT-seq approach.

Bioinformatic deconolution of transcriptome and Nanopore long-read accessibility datasets, combined with single-cell multi-omic analysis, will help resolve the heterogeneity that exists in this tissue across gestation and is crucial to appreciating tissue function in health and disease.

We are looking for an enthusiastic and ambitious student who is keen to unite both laboratory and computations skills to develop and apply NGS protocols to understand how chromatin accessibility influences allelic gene regulation in the human placenta.

The project is a joint NRP venture between the groups of Professor David Monk at UEA and Dr Wilfried Haerty at the Earlham Institute.

In addition to the generic skills training that is provided through the UEA/EI BBSRC NRPDTP programme, the student will be supported by an excellent infrastructure and will work closely with experts in the placental biology and epigenomics.

This diverse and stimulating environment allows for the development of key skills in preparation for a successful career in research or industry.

All candidates are strongly advised to contact the PI to discuss the projects prior to formal application.

References

Silver M, Saffari A, Kessler N, Chandak G, Fall C, Issarapu P, Dedaniya A, Betts M, Moore S, Routledge M, Herceg Z, Derkshan M, James P, Monk D, Prentice A. Environmentally sensitive hotspots in the methylome of the early human embryo. Elife. 2022 E72031.

Monteagudo-Sánchez A, Sánchez-Delgado M, Ramon Hernandez Mora J, Tubío Santamaría N, Gratacó E, Esteller M, López de Heredia M, Nunes V, Choux C, Fauque P, Perez de Nanclares G, Anton L, Elovitz A, Iglesias-Platas I, Monk D. Differences in expression rather than methylation at placenta-specific imprinted loci is associated with Intrauterine Growth Restriction. Clinical Epigenetics. 2019 11: 35.

Ramon Hernandez Mora J, Sanchez-Delgado M, Petazzi P, Moran S, Esteller M, Iglesias-Platas I, Monk D. Profiling of oxBS-450k 5-hydroxymethylcytosine in human placenta and brain reveals enrichment at imprinted loci. Epigenetics. 2018, 13:182-191.