Pizza Science and Beyond… with Vastenhouwlab

 

About once a month, DIPP PhD students gather to share & discuss their research with their peers in an informal atmosphere, along with pizza. Pizza Science and Beyond (PSB) is an initiative from the Student representatives of the DIPP predocs.

This year, both Mate (back in March) and Ksenia (this August) gave chalk talks featuring lab’s signature ZGA curve on a board.

How is transcription organised in the nucleus? How does the chromatin become open? Does Mate really have a wikipedia page?… and many other questions were discussed.

 

Photos by Shady El-Husseiny

eLife paper on ZGA timing: activator-repressor competition

Our study demonstrating how repressors (histones) and activators (transcription factors) jointly control transcription in the zebrafish embryo is now available online: Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos. Joseph et al. eLife (2016)

Competition Model

In this study, lead by Shai Joseph (Vastenhouw Lab) and carried out collaboratively with the Shevchenko and Zaburdaev lab, we could quantitatively address a long-standing question: how is the timing at which transcription starts in embryos controlled?

By a combination of quantitative, molecular, and functional techniques, we found that the two most prominent hypotheses, the "depleted repressor" and the "increasing activator" models, can be unified in a competition model. Here, repressing histones and activating transcription factors go head-to-head competing for access to DNA target sites.

Additionally, the nuclear-to-cytoplasmic ratio - often defined in the number of genomes in an embryo - resurfaced as a key concept, though in the form of a volume ratio between cell nuclei and overall cytoplasm. While the global concentration of not DNA-bound histones did not change at the time of transcription onset, we detected a marked decrease in the concentration of not DNA-bound histones specifically within cell nuclei.

 

BioRxiv: Histone and transcription factor binding competition

A preprint for our latest work is now on BioRxiv: “Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos”. The lead author of this study is Shai, with lots of support from within the Vastenhouw lab as well as the Zaburdaev (MPI-PKS) and Shevchenko labs (MPI-CBG).

You can go and read the preprint here: http://biorxiv.org/content/early/2017/04/13/125716