I’m excited to share my recent postdoc work. Here, we interrogate how different phage infection outcomes (productive vs. restrictive) affect the expression of phage defense systems. We find that a restricted infection not only inhibits the phage but also induces increased immune protein abundance.

PhD position in Gene Regulation Are you excited about studying the crucial process of transcription? Join our supportive, young and growing team!

The Vlaming lab is expanding! If you are or know a good prospective PhD student, excited about studying transcription, please (suggest them to) apply here: www.uu.nl/en/organisat...
My biased opinion: exciting topic, super nice colleagues, and great research environment in a lovely city.

Congrats to Azra, Sahil, and the rest of the team on their new study connecting viral infection to poly(A)-mediated stabilization of SINE transcripts!

Congrats to Apoorva and the rest of the team! This was a fun project to see progress over the last few years, and there's really something for everyone: early control of transcription elongation, transposons, stress, neurodevelopmental disease - the connections abound!

Reminder for the #RNA #RNAsky #GeneRegulation #Genetics #Genomics folks: the key deadlines for the @keystonesymposia.bsky.social "Epigenetics in Development and Disease" meeting in March 2025 are coming up fast (Jan 9 for short talks), and has a stellar lineup of speakers - tinyurl.com/4dwed92p

Circular Engineered Sortase for Interrogating Histone H3 in Chromatin Reversible modification of the histone H3 N-terminal tail is critical in regulating the chromatin structure, gene expression, and cell states, while its dysregulation contributes to disease pathogenesis. Understanding the crosstalk between H3 tail modifications in nucleosomes constitutes a central challenge in epigenetics. Here, we describe an engineered sortase transpeptidase, cW11, that displays highly favorable properties for introducing scarless H3 tails onto nucleosomes. This approach significantly accelerates the production of both symmetrically and asymmetrically modified nucleosomes. We demonstrate the utility of asymmetrically modified nucleosomes produced in this way in dissecting the impact of multiple modifications on eraser enzyme processing and molecular recognition by a reader protein. Moreover, we show that cW11 sortase is very effective at cutting and tagging histone H3 tails from endogenous histones, facilitating multiplex “cut-and-paste” middle-down proteomics with tandem mass tags. This cut-and-paste proteomics approach permits the quantitative analysis of histone H3 modification crosstalk after treatment with different histone deacetylase inhibitors. We propose that these chemoenzymatic tail isolation and modification strategies made possible with cW11 sortase will broadly power epigenetic discovery and therapeutic development.

A great collaboration with Phil Cole (Harvard) engineering Sortase to facilitate its transpeptidase activity on histone H3 has been published in JACS. This work developed multiplexed "cut-and-paste" middle-down proteomics with tandem mass tags for quantification.
pubs.acs.org/doi/full/10....