Emma Farley 🇪🇺

A thread on some of the fascinating noncoding genetic discoveries from 2024. I've written long form posts and discussed on The Genetics Podcast about these stories. I'll share links to all below with a brief summary.

🧵1/7 Excited to share my paper "Optimization of the Irf8 +32-kb enhancer disrupts dendritic cell lineage segregation" out today @NatImmunol! Read it here: nature.com/articles/s4159….

And thats a wrap on our webinar series for the academic year. We are looking forward to starting the next series in September with a line up including @Yael_David__ , @EKFarley & @heard_lab. Please keep an eye out for our new website & linkedin that will be launching shortly!

Don't miss the deadline, this coming Monday (June 3rd) to submit an abstract for the Transcription & Chromatin meeting @embl. 50% of speakers are selected from the abstracts. This is always a very lively conference, on site @EMBLHeidelberg Check out the great line up of speakers

Wrote a 1-pager for @NatureRevGenet on how we should stop pretending transcription factor binding sites are a discrete entity. Just like a cup exists in many states between "full" and "empty", TFBSs are continuous. rdcu.be/dzL8o - feat. sweet new paper from @EKFarley

@CarldeBoerPhD @NatureRevGenet Great point Carl. So glad you wrote this!

@BrayLabCam @JoeSolvason @granton_jindal Thanks, so happy it’s out.

@EKFarley @JoeSolvason @granton_jindal Congratulations to you all. Super to see this cool story in print now!

Pinpointing causal variants that disrupt development. So proud of the amazing team on this epic enhancer genotype-to-phenotype study. Well Done, Fabian Lim, @JoeSolvason, Genevieve Ryan, Sophia Le, @granton_jindal, Paige Steffen and Simran Jandu!!! doi.org/10.1038/s41586…

@benoitbruneau @JoeSolvason @granton_jindal Thanks Benoit!

@EKFarley @JoeSolvason @granton_jindal Superb!

The prevalence of suboptimal affinity binding sites within enhancers creates a vulnerability in genomes whereby single-nucleotide changes that optimize affinity, even slightly, can be pathogenic. doi.org/10.1038/s41586…

@LabWaggoner @Nature @joe_solvason Even the IFN enhanceosome contains suboptimal affinity sites, affinity optimizing single nucleotide variants in this enhancer cause GOF expression.

Prevalence of binding sites with suboptimal affinity in enhancers (for ETS) creates a vulnerability in genomes whereby single-nucleotide variants that optimize affinity, even slightly, can be pathogenic @Nature @EKFarley @joe_solvason nature.com/articles/s4158…

@LabWaggoner @Nature @joe_solvason Great summary of our work! We show a very subtle increase in suboptimal-affinity ETS sites leads to extra digits, but we also find that this applies to other TFs, including Hox, AP-1, and IRF.

Please spread the word: a PhD position to dig into the origin of neurons by characterising ctenophore neuropeptides! Involves work with cool marine animals😉! Deadline - January 8. @BristolBioSci findaphd.com/phds/project/f…

From Fish to Mammals: Unraveling Brachyury Control in the Notochord by @aburger2009 & @KozmikLab, w/@EKFarley @MaxYunLab @AxelVisel @m_osterwalder @LiciaSelleri @FishEvoDevoGeno & teams is now out in nature.com/articles/s4146… Wonderful collaboration. Happy to be part of it!

@chrmosimann @aburger2009 @KozmikLab @MaxYunLab @AxelVisel @m_osterwalder @LiciaSelleri @FishEvoDevoGeno So much fun to be part of this multi species collaboration

@chrmosimann @MaxYunLab ✌🏼 this is the closest to a sea squirt emoji I can find.

@TriggerLoop Thanks @TriggerLoop glad you like it! Was great to catch up last week.

Early-career researchers can apply for a funded place at our Workshop 'Building to Understand: The Constructionist Approach to Studying Gene Regulation' organised by Jef Boeke @JefBoeke, Sudarshan Pinglay @sudpinglay & Stefan Mundlos @StefanMundlos. biologists.com/workshops/july…

Big thanks to @EKfarley and authors @itsalexistb @joe_solvason @KlieAdam @kellyafrazer and those not on Twitter. Also, thanks to funding support from Hartwell Postdoctoral Fellowship, AHA Postdoctoral fellowship, UCSD Cardiology NIH T32, and UCSD CRES.

@benoitbruneau @granton_jindal It was a great team! Thanks @itsalexistb for the beautiful movies, and for working with Aga & @kellyafrazer on our human cardiomyocyte studies. Thanks @joe_solvason @KlieAdam, Reid Larson and Michelle for bioinformatics. And Ben, Sophia and Jessica for experimental support.

@benoitbruneau @granton_jindal Thanks Benoit. It was a really fun project and huge surprise such small changes to an enhancer could have such dramatic effects. All led by @granton_jindal an amazing Postdoc on the job market this year.

Great work on enhancer mutations from @EKFarley's lab, led by @granton_jindal. Great use of model organisms! cell.com/developmental-…