Lera’s and Helen’s preprint is out!

Lera’s and Helen’s preprint describing a high-resolution promoter interaction profiling of a rare cell type, Type 3 Innate Lymphoid cells is out! In this collaborative project with labs in Cambridge and Ohio, we have taken advantage of these data to link GWAS variants associated with Crohn’s disease with target genes. Surprisingly, one of the prioritised genes, CLN3, is a causal gene for a rare neurodegenerative disorder Batten disease. With our collaborators in the US, we have then used a CLN3 mutant mouse model to show that this gene affects the immune function of Innate Lymphoid cells. We are very excited about this study!

Valeriya is starting her own lab!

Our senior postdoc Valeriya Malysheva is leaving us soon to start her own lab at the VIB Institute of Molecular Neurology in Antwerp, Belgium. We are extremely proud of her, but are sad to see her go!

Valeriya has described her experiences in our lab and institute in her post on the institute website here:

https://lms.mrc.ac.uk/the-lms-has-helped-me-take-my-first-step-towards-research-leadership/

A comprehensive review on enhancers and Covid gene prioritisation are published

Two papers from our lab in one news article:

* Helen’s and Mikhail’s long review about enhancers and their communication with promoters (>520 refs!) published in Cell Mol Life Sci.

* Our work with Covid HGI consortium, prioritising the genes using their Covid severity GWAS meta-analysis data and Capture Hi-C, published in Front Genet. Co-led by Michiel Thiecke (a former PhD student in the lab, now at Enhanc3D Genomics) and Emma Yang (a former MSc student in the lab, now at MRC HGU). Co-supervised by Helen and Mikhail.

Our guide to Capture Hi-C analysis is published

Our invited paper “Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools” is finally out at Nature Protocols (after 3 months in typesetting)!

Led by Paula (one of the lead authors of the original Chicago), Helen and Lera (postdocs in the lab), with invaluable contributions from other present and former lab members and collaborators.

For context, see also this Q&A on our institute’s website.

Bye Vanessa and Joe, welcome Namrata

Vanessa and Joe are leaving the lab to continue their studies. We are sorry that they are leaving and wish them all the best for their next steps. In the meantime, Namrata (another student in Joe’s masters course) is stepping in to continue the work started by Joe.

Joe joins the lab

Joe Ellaway has joined the lab for his (fully remote) MSc project in bioinformatics. He will be working on the computational prediction of enhancer-promoter contacts capitalising on existing models and Capture Hi-C data. Welcome Joe – sorry we don’t have a chance to meet you offline!

Collaborative work on Covid biology published

The results of a large collaborative effort to understand the epigenetic effects of Covid infection on lung cells and propose a repurposed treatment have been published in Cell. A press release presenting the key findings of the study is available here.

Congratulations Helen, Valeriya from the lab and Michiel from Enhanc3D Genomics!

Enhanc3D Genomics and our group contribute to COVID-19 GWAS interpretation

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.

Vanessa and Pavel join the lab

Pavel is starting his PhD with us, and Vanessa will be with us for her 3rd year BSc placement. Welcome Vanessa and Pavel!

Helen’s work on SARS-CoV-2 is featured on MRC LMS website

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.