Michiel’s paper on the effects of architectural protein depletion on promoter interactions is out in Cell Reports. It has been a stimulating collaboration with great people from IMP Vienna and Babraham Institute. Thanks also to Cell Reports for accommodating our inability to do wet lab experiments during revision!
A news article about this paper intended for a broad audience has been posted on MRC LMS website.
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Leave a Comment (0) →Jo Mitchelmore’s paper presenting her PhD work with us is finally out in Nucleic Acids Research:
Congratulations Jo and thanks Chris Wallace and Stasia Grinberg for invaluable help!
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Leave a Comment (0) →Monica’s and Mikhail’s News&Views article on two silencer papers is out in Nature Genetics. It was a very timely commission as a few relevant papers have been out recently elsewhere too!
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Leave a Comment (0) →Michiel’s preprint on the effects of cohesin depletion on rewiring of promoter-enhancer interactions and nascent transcription is out!
https://doi.org/10.1101/2020.02.10.941989
A fruitful collaboration with Gordana Wutz and Wen Tang at Jan-Michael Peters’s lab at the IMP, Matthias Muhar at the IMP’s Zuber lab, and Stefan Schoenfelder and Peter Fraser at Babraham.
Now fingers crossed for the story’s smooth sailing to a journal…
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Leave a Comment (0) →Michiel has successfully defended his viva on the role of architectural proteins and TADs in shaping promoter interactions and transcription.
Congratulations Michiel and thanks to examiners Sue Hadjur and Shamith Samarajiwa for their time and feedback!
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Leave a Comment (0) →Lina passed her Cambridge University viva with flying colours. Congratulations Dr Dobnikar!
Thanks to her examiners Sarah De Val (Oxford) and Martin Hemberg (Cambridge) for an engaging discussion and insightful comments.
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Leave a Comment (0) →Today sees the publication of not just one, but two preprints from our lab and our close collaborators.
The first preprint is work led by Jo Mitchelmore (our group’s first ever PhD student, now at Novartis), in which she has used changes in transcription factor binding affinity at promoter-connected regulatory regions as predictor variables to detect eQTLs. Using this method, she’s uncovered hundreds of novel associations – and a bunch of epromoters, regions that function both as distal enhancers and promoters of other genes. Great collaboration with Chris Wallace and her postdoc Stasiya Grinberg.
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Leave a Comment (0) →Helen Ray-Jones joins us as a postdoc, after a PhD with Stephen Eyre at Manchester University. Helen brings with her experimental and computational expertise in human genetics that is highly relevant to our work. Welcome Helen!
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Leave a Comment (0) →We have released Chicdiff, an R package for differential analysis of Capture Hi-C data. Joint work by the power team: Jonathan (now at AstraZeneca), William (now back at Cambridge) and Valeriya. The package is available on github, and the preprint describing it is on bioRxiv. If you work with Capture Hi-C data, please try it out and let us know what you think!
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Leave a Comment (0) →Our study of vascular smooth muscle cell heterogeneity using single-cell transcriptomics and lineage tracing is finally out! Co-led by our group’s Lina Dobnikar and Annabel Taylor fro Helle Jørgensen’s lab at Cambridge University.
Vascular smooth muscle cells (VSMCs) from are interesting for at least two reasons: (1) they originate from at least two different embryonic layers, depending on location and (2) in response to inflammation or injury, they lose their muscle cell phenotype and turn into migrating, proliferating fibroblast-like ‘synthetic’ cells.
We found that VSMCs homogeneously bear the footprints of their embryonic origins, but are heterogeneous with respect to other expressed genes. In particular, we found a rare VSMC subpopulation in healthy vessels that express a transcriptional signature (including progenitor marker Sca1) that is prevalent in vascular disease and potentially defines cells in the process of switching to the synthetic state.
Notably, Helle previously showed that only a small proportion of VSMCs expand in response to injury, so being able to catch cells ‘in the act’ of switching may help to understand ‘what makes them tick’.
Link to paper: https://www.nature.com/articles/s41467-018-06891-x.
Link to press release: https://www.babraham.ac.uk/news/2018/11/observation-of-blood-vessel-cells-changes-could-lead-to-early-detection-of-blocked-arteries.
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