Mathi Thiruppathy

Range extender mediates long-distance enhancer activity - Nature The REX element is associated with long-range enhancer–promoter interactions.

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

So cool! Congrats!! 🎉

How do non-coding variants in enhancers lead to disease? Happy to share our recent work, led by @ewholling.bsky.social, in which we discovered that poised chromatin sensitizes enhancers to aberrant activation by non-coding mutations, contributing to disease. www.biorxiv.org/content/10.1... 1/

Congrats Mathieu and coauthors!! As someone who tried (and more often than not failed) to take pictures of the incredibly fragile zebrafish gills, I am so floored by these perfect dissections and images at multiple stages of development. ⭐

😍 So much fascinating development in this system. These images and movies do justice to how beautiful and complex fish gills are.

-A Gill's Secret Sidekick -
A small, often-overlooked organ tucked behind the eye.
In zebrafish, the pseudobranch arises from mandibular arch mesenchyme — the same region that forms jaws — and shares gene expression and developmental programs with true gills.

🔬 #FluorescenceFriday #zebrafish

Wow! 😍 What an amazing dissection and so gorgeous! What is labeled?

Gills just wanna have #FluorescenceFriday 🎵

Phalloidin reveals the beauty of the filament's distal tip in cleared gills of adult 🦓🐟

#microscopy #devbio #sciart

Gorgeous gills. 😍

Really appreciated this opportunity from @the-node.bsky.social to write about the amazing journey I got to be on for 6 years and the people I met on the way.

Every day I feel fortunate to live in and work for a society that chooses to be curious. Now more than ever I hope it continues to do so. ✨

"Imagine a DAPI-like stain, but for the extracellular matrix." That's basically how this work was pitched to me by Kayvon and Antonio a year or so ago. Now the final product really delivers. Read about their versatile label for ECM in living tissues here: www.nature.com/articles/s41...

Figure 1 (A) Example images illustrating a major delay in initiation of bone mineralization in sox10 mutants between 3 and 7 dpf revealed by Alizarin Red staining. Some mineralization is present by 5 dpf but never achieves control levels before lethality at 8 dpf.

Sox10 is required for systemic initiation of bone mineralization

Read this #OpenAccess Research Article by Stefani Gjorcheska, Lindsey Barske & co. @cincyresearch.bsky.social :
https://journals.biologists.com/dev/article/152/2/dev204357/365396/Sox10-is-required-for-systemic-initiation-of-bone

Massively parallel characterization of transcriptional regulatory elements - Nature Lentivirus-based reporter assays for 680,000 regulatory sequences from three cell lines coupled to machine-learning models lead to insights into the grammar of cis-regulatory elements.

Massively parallel reporter assays (MPRAs) testing >680,000 sequences combined with machine learning to improve regulatory element & variant effect prediction. Amazing work by @vagar.bsky.social, Fumitaka Inoue, @jshendure.bsky.social and many others as part of ENCODE.
www.nature.com/articles/s41...

Thank you! :)

Thanks especially to @crumplab.bsky.social for providing the opportunity to do exciting, diverse experiments, as well as the necessary guidance and confidence!

Thank you to all co-authors! It's hard to emphasize how amazing it's been to work with people of such diverse expertise who still had an interest in various obscure aspects of this work.

Excited to share this story from my PhD revealing the surprising legacy of our gill-bearing ancestry in the form of our cartilaginous outer ears, summarized in this series of Tweets.