In collaboration with Enhanc3D Genomics Ltd, we have linked non-coding GWAS SNPs associated with COVID-19 susceptibility and severity with their putative target gene based on 3D chromosomal conformation in blood cells.
For this analysis, we have used the COGS approach and Promoter Capture Hi-C data from our earlier study (Javierre et al., Cell 2016). The GWAS data are coming from the COVID-19 Host Genetics Initiative that we have joined for this task.
Our data are currently available at https://osf.io/k2mxe/ and will evolve with the next releases of the GWAS meta-analysis dataset. Our results will also be posted on the www.covid19hg.org website in due course.
Pavel is starting his PhD with us, and Vanessa will be with us for her 3rd year BSc placement. Welcome Vanessa and Pavel!
A few people in our lab – including Helen, Valeriya and Emma, helped by Michiel who is now employed by our spinout company – have joined forces to help out in Covid-related research.
An article about Helen’s contribution has been posted on MRC LMS website.
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.
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!
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!
Michiel’s preprint on the effects of cohesin depletion on rewiring of promoter-enhancer interactions and nascent transcription is out!
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…
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!
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.
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.