Sun Maybury-Lewis

Epigenetics Update - MethAgingDB: a comprehensive DNA methylation database for aging biology go.nature.com/4ltmg2T

Haixin Wang and Shengquan Chen reporting in Scientific Data

#Epigenetics #DNAm #DNAme #Aging
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Empower your research with high-res epigenetic insights at epigenometech.com

Non-canonical enhancers control gene expression and cell fate in human pluripotent stem cells Enhancers are key gene regulatory elements that ensure the precise spatiotemporal execution of developmental gene expression programmes. However recent findings indicate that approaches to identify en...

Delighted & excited to share our latest preprint on non-canonical enhancers in human pluripotent stem cells, the result of a fantastic and fun collaboration with @guenesdoganlab.bsky.social‬:
www.biorxiv.org/content/10.1...

🧵 below

ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...

Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...

Graphical abstract of the paper.

How long does an mRNA stay in the nucleus? How long does it stay in the cytoplasm? In an amazing collaboration with @landthalerm.bsky.social, we used metabolic labeling, cell fractionation and mathematical modeling to quantify mRNA flow through the cell. Finally out in MSB: doi.org/10.1038/s443...

I created a simple flow chart to help my lab trainees choose the most appropriate stats test in Prism (*for single-factor comparisons only). Feel free to share with your group if you think it could be helpful first start.

cBAF generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers - Nature Structural & Molecular Biology Here, the authors show that the canonical BRG/BRM-associated factor (SWI/SNF) chromatin remodeler generates subnucleosomes containing 50–80 bp of DNA associated with the four core histones. These hemi...

cBAF generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers.

www.nature.com/articles/s41...

Our recent study in Cell Metabolism provides compelling evidence that chromatin accessibility and transcription factor network remodeling in aging reflect the predictable degrading effects of a mechanism initially driving organismal maturation.
Link: doi.org/10.1016/j.cmet.2024.06.006
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A few years old, but worth a read (perhaps in particular to those who do ML in BIO or take biological databases for granted) 🧪🧬🖥️

"How Margaret Dayhoff Brought Modern Computing to Biology"

www.smithsonianmag.com/science-natu...

Leonid Mirny and I wrote this for all interested in chromosomes: "The chromosome folding problem and how cells solve it"

www.cell.com/action/showP...

I’ve just read this pre-print and it’s fantastic. A conserved element with no endogenous enhancer activity is nonetheless necessary and sufficient for extreme long range enhancer action. Recommend to anyone interested in gene regulation

Transcription regulation by biomolecular condensates - Nature Reviews Molecular Cell Biology Transcriptional condensates, which are formed through dynamic multivalent interactions between proteins, RNA and chromatin, regulate transcription by compartmentalizing its machinery in the crowded nu...

Regulation of transcription by condensates, great review by @bsabari.bsky.social and coll.

www.nature.com/articles/s41...

Created one! Let me know if you find anyone that is missing.
go.bsky.app/StHb8Ma

Hi folks on Bluesky! I'm a postdoc at Harvard Medical School, studying epigenomics underlying aging. Specifically, I am trying to understand the spatiotemporal dynamics of partial reprogramming by three of four Yamanaka factors (OSK). Happy to be here!

ok, I tried to make a starter pack on genome stability/DNA replication/DNA repair etc. Sorry if I couldn't find someone, please nominate yourself and your colleagues in comments or DMs, looking forward to connecting with everyone!
go.bsky.app/9jdDNxG

Hi BlueSky! It's great to be here. Here's a handy Starter Pack of DNA repair & genome stability groups that I found so far go.bsky.app/NvFWKvL

Hi Bluesky! I made a 3D chromatin starter pack.
Let me know if you would like to be added.
go.bsky.app/6tTQdqQ