Stefan Schoenfelder

Dr Schoenfelder holds a Babraham Institute Career Progression Fellowship which provides two years of support for his research.

Research Summary

Functional organisation of the genome in 3D
98% of the DNA in our body is non-coding, i.e. does not carry the information needed to build proteins. Non-coding has sometimes been equated with ‘non-functional’, or called ‘junk’ in the past; today we know that this is far from the truth. Scattered throughout non-coding DNA is a plethora of so-called regulatory elements, including enhancers, silencers and insulators. These regulatory elements function like molecular switches to control which genes are active (and thus produce proteins) in which cells. This process of gene expression control is vital to allow cells – which all contain the same genes – to specialise to carry out different tasks, and to help them respond to changes.

Enhancers are a type of regulatory element that control gene expression over long distances. They contact their target genes via chromosomal interactions, often bridging large distances in the genome, with the intervening DNA ‘looping out’. To understand how enhancers work, we study them in the context of the three-dimensional organisation of the genome.

Our aim is to find regulatory elements and to understand which genes they control. We also aim to uncover the molecular mechanisms by which regulatory elements find their target genes in the three-dimensional space of the cell nucleus, and to understand how altering the function of regulatory elements can lead to developmental malformations and disease.

We study these questions in pluripotent stem cells – cells that have the potential to create all cell types in the adult body. We use a combination of molecular, genetic, biochemical and imaging approaches to study pluripotent stem cells in their ‘ground state’, and when they start to form new cell types – a process called cell lineage specification.

Techniques and Methods

Through high-resolution mapping and experimental perturbation of the spatial genome architecture, we aim to reveal gene regulatory principles that underpin cell states and cell fate transitions. This may ultimately pave the way for us to experimentally engineer 3D genome folding to achieve predictable outcomes on gene expression and cell fate choice, with potential implications for gene therapy and regenerative medicine.

Latest Publications

Widespread reorganisation of pluripotent factor binding and gene regulatory interactions between human pluripotent states.
Chovanec P, Collier AJ, Krueger C, Várnai C, Semprich CI, Schoenfelder S, Corcoran AE, Rugg-Gunn PJ

The transition from naive to primed pluripotency is accompanied by an extensive reorganisation of transcriptional and epigenetic programmes. However, the role of transcriptional enhancers and three-dimensional chromatin organisation in coordinating these developmental programmes remains incompletely understood. Here, we generate a high-resolution atlas of gene regulatory interactions, chromatin profiles and transcription factor occupancy in naive and primed human pluripotent stem cells, and develop a network-graph approach to examine the atlas at multiple spatial scales. We uncover highly connected promoter hubs that change substantially in interaction frequency and in transcriptional co-regulation between pluripotent states. Small hubs frequently merge to form larger networks in primed cells, often linked by newly-formed Polycomb-associated interactions. We identify widespread state-specific differences in enhancer activity and interactivity that correspond with an extensive reconfiguration of OCT4, SOX2 and NANOG binding and target gene expression. These findings provide multilayered insights into the chromatin-based gene regulatory control of human pluripotent states.

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Nature communications, 12, 1, 07 04 2021

PMID: 33828098

Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence.
Olan I, Parry AJ, Schoenfelder S, Narita M, Ito Y, Chan ASL, Slater GSC, Bihary D, Bando M, Shirahige K, Kimura H, Samarajiwa SA, Fraser P, Narita M

Senescence is a state of stable proliferative arrest, generally accompanied by the senescence-associated secretory phenotype, which modulates tissue homeostasis. Enhancer-promoter interactions, facilitated by chromatin loops, play a key role in gene regulation but their relevance in senescence remains elusive. Here, we use Hi-C to show that oncogenic RAS-induced senescence in human diploid fibroblasts is accompanied by extensive enhancer-promoter rewiring, which is closely connected with dynamic cohesin binding to the genome. We find de novo cohesin peaks often at the 3' end of a subset of active genes. RAS-induced de novo cohesin peaks are transcription-dependent and enriched for senescence-associated genes, exemplified by IL1B, where de novo cohesin binding is involved in new loop formation. Similar IL1B induction with de novo cohesin appearance and new loop formation are observed in terminally differentiated macrophages, but not TNFα-treated cells. These results suggest that RAS-induced senescence represents a cell fate determination-like process characterised by a unique gene expression profile and 3D genome folding signature, mediated in part through cohesin redistribution on chromatin.

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Nature communications, 11, 1, 27 Nov 2020

PMID: 33247104

High-resolution three-dimensional chromatin profiling of the Chinese hamster ovary cell genome.
Bevan S, Schoenfelder S, Young RJ, Zhang L, Andrews S, Fraser P, O'Callaghan PM

Chinese hamster ovary (CHO) cell lines are the pillars of a multi-billion dollar biopharmaceutical industry producing recombinant therapeutic proteins. The effects of local chromatin organisation and epigenetic repression within these cell lines result in unpredictable and unstable transgene expression following random integration. Limited knowledge of the CHO genome and its higher-order chromatin organisation has thus far impeded functional genomics approaches required to tackle these issues. Here, we present an integrative three-dimensional (3D) map of genome organisation within the CHOK1SV® 10E9 cell line in conjunction with an improved, less fragmented CHOK1SV® 10E9 genome assembly. Using our high-resolution chromatin conformation datasets, we have assigned ≈ 90% of sequence to a chromosome-scale genome assembly. Our genome-wide 3D map identifies higher-order chromatin structures such as topologically associated domains, incorporates our chromatin accessibility data to enhance the identification of active cis-regulatory elements and importantly links these cis-regulatory elements to target promoters in a 3D promoter interactome. We demonstrate the power of our improved functional annotation by evaluating the 3D landscape of a transgene integration site and two phenotypically different cell lines. Our work opens up further novel genome engineering targets, has the potential to inform vital improvements for industrial biotherapeutic production, and represents a significant advancement for CHO cell line development. This article is protected by copyright. All rights reserved.

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Biotechnology and bioengineering, 1, 1, 23 Oct 2020

PMID: 33095445