Life Sciences Research for Lifelong Health

Peter Fraser

Please note, Peter now also leads a research group at Florida State University. Visit his page there for full details of his current research.

Research Summary

Dynamic changes in chromatin and chromosome architecture regulates patterns of cellular gene expression during differentiation and development, or in response to environmental signals. Our research looks at various levels of chromatin, chromosome and nuclear structure, from individual nucleosome modifications to the dynamic 3D structure of chromosomes and their inter-relationships in the nucleus and how they affect genome functions.

Latest Publications

RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus.
Morf J, Wingett SW, Farabella I, Cairns J, Furlan-Magaril M, Jiménez-García LF, Liu X, Craig FF, Walker S, Segonds-Pichon A, Andrews S, Marti-Renom MA, Fraser P

The global, three-dimensional organization of RNA molecules in the nucleus is difficult to determine using existing methods. Here we introduce Proximity RNA-seq, which identifies colocalization preferences for pairs or groups of nascent and fully transcribed RNAs in the nucleus. Proximity RNA-seq is based on massive-throughput RNA barcoding of subnuclear particles in water-in-oil emulsion droplets, followed by cDNA sequencing. Our results show RNAs of varying tissue-specificity of expression, speed of RNA polymerase elongation and extent of alternative splicing positioned at varying distances from nucleoli. The simultaneous detection of multiple RNAs in proximity to each other distinguishes RNA-dense from sparse compartments. Application of Proximity RNA-seq will facilitate study of the spatial organization of transcripts in the nucleus, including non-coding RNAs, and its functional relevance.

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Nature biotechnology, 37, 1546-1696, 793-802, 2019

PMID: 31267103

Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes.
Miguel-Escalada I, Bonàs-Guarch S, Cebola I, Ponsa-Cobas J, Mendieta-Esteban J, Atla G, Javierre BM, Rolando DMY, Farabella I, Morgan CC, García-Hurtado J, Beucher A, Morán I, Pasquali L, Ramos-Rodríguez M, Appel EVR, Linneberg A, Gjesing AP, Witte DR, Pedersen O, Grarup N, Ravassard P, Torrents D, Mercader JM, Piemonti L, Berney T, de Koning EJP, Kerr-Conte J, Pattou F, Fedko IO, Groop L, Prokopenko I, Hansen T, Marti-Renom MA, Fraser P, Ferrer J

Genetic studies promise to provide insight into the molecular mechanisms underlying type 2 diabetes (T2D). Variants associated with T2D are often located in tissue-specific enhancer clusters or super-enhancers. So far, such domains have been defined through clustering of enhancers in linear genome maps rather than in three-dimensional (3D) space. Furthermore, their target genes are often unknown. We have created promoter capture Hi-C maps in human pancreatic islets. This linked diabetes-associated enhancers to their target genes, often located hundreds of kilobases away. It also revealed >1,300 groups of islet enhancers, super-enhancers and active promoters that form 3D hubs, some of which show coordinated glucose-dependent activity. We demonstrate that genetic variation in hubs impacts insulin secretion heritability, and show that hub annotations can be used for polygenic scores that predict T2D risk driven by islet regulatory variants. Human islet 3D chromatin architecture, therefore, provides a framework for interpretation of T2D genome-wide association study (GWAS) signals.

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Nature genetics, 51, 1546-1718, 1137-1148, 2019

PMID: 31253982

Long-range enhancer-promoter contacts in gene expression control.
Schoenfelder S, Fraser P

Spatiotemporal gene expression programmes are orchestrated by transcriptional enhancers, which are key regulatory DNA elements that engage in physical contacts with their target-gene promoters, often bridging considerable genomic distances. Recent progress in genomics, genome editing and microscopy methodologies have enabled the genome-wide mapping of enhancer-promoter contacts and their functional dissection. In this Review, we discuss novel concepts on how enhancer-promoter interactions are established and maintained, how the 3D architecture of mammalian genomes both facilitates and constrains enhancer-promoter contacts, and the role they play in gene expression control during normal development and disease.

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Nature reviews. Genetics, , 1471-0064, , 2019

PMID: 31086298

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Keywords

3d genome
genome function
 

Group Members

Latest Publications

RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus.

Morf J, Wingett SW, Farabella I

Nature biotechnology
37 1546-1696:793-802 (2019)

PMID: 31267103

Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes.

Miguel-Escalada I, Bonàs-Guarch S, Cebola I

Nature genetics
51 1546-1718:1137-1148 (2019)

PMID: 31253982

Long-range enhancer-promoter contacts in gene expression control.

Schoenfelder S, Fraser P

Nature reviews. Genetics
1471-0064: (2019)

PMID: 31086298

Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication.

Sima J, Chakraborty A, Dileep V

Cell
1097-4172: (2018)

PMID: 30595451

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions.

Schoenfelder S, Javierre BM, Furlan-Magaril M

Journal of visualized experiments : JoVE
1940-087X: (2018)

PMID: 30010637

Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks.

Choy MK, Javierre BM, Williams SG

Nature communications
9 2041-1723:2526 (2018)

PMID: 29955040

The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia.

Beekman R, Chapaprieta V, Russiñol N

Nature medicine
1546-170X: (2018)

PMID: 29785028