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The Bothma group investigates how noncoding regions of the genome control gene expression in development by imaging transcription with single molecule resolution in real time.
How a single embryonic cell interprets its genome to give rise to the many diverse cell types that build an animal is one of nature’s enduring mysteries. Unravelling it promises to not only yield new insights into disorders of development and cancer, but also reveal the organizing principles of life. Even though we have uncovered all the regulatory factors and noncoding regions of the genome involved in specifying cell identity, we still don’t understand how these all come together to build an animal. One of the main reasons why this knowledge gap persisted is because until now we could not visualize a key degree of freedom – time.
Thanks to a recent series of innovations in live imaging the time is ripe for the introduction of a new paradigm in the study of embryogenesis based on how cell fates are established in living animals as development is actually taking place. We can now measure transcription factor concentration dynamics in individual cells, visualize transcription as it’s actually happening and even watch the binding of a single transcription factor molecule to DNA in a living embryo. Our experimental workhorse is the early Drosophila melanogaster embryo because of the ease of imaging and powerful genetic tools available in the system, but we are excited to expand into artificial vertebrate embryos and organoids in the future.
The goal of the group is to understand how the noncoding parts of the genome drive cell fate decisions in development, by imaging the key molecular players mediating these decisions in their endogenous context in real time. This goal is underpinned by constantly developing new ground-breaking imaging and labelling technologies that empower us to visualize these processes in ways that have never been done before. These efforts will provide deep mechanistic insights into how regulatory DNA sequence encodes biological form and function, which will pave the way for us to understand how mutations in noncoding regions of the human genome cause disease.
Birnie A,* Plat A,* Korkmaz C, Bothma JP
Download|2023
Bothma JP, Norstad MR, Alamos S and Garcia HG
Download|2018
Bothma JP,* Garcia HG,* [...] Gregor T and Levine M
Download|2015
Download|2014
Download|2013
Bothma JP, Magliocco J and Levine M
Download|2011
Jacques Bothma started his scientific career in Australia, where he obtained a Bachelor of Science degree in Physics from the University of Queensland. He then decided to switch to Biology and pursued his PhD in Biophysics at the University of California, Berkeley, with Mike Levine. Here he uncovered genetic mechanisms for the robust and coordinated deployment of gene expression in development. He then stayed at Berkeley for his postdoc where he pioneered new quantitative live imaging approaches to visualize transcription and gene regulatory networks in embryos in the lab of Hernan Garcia. He started his group at the Hubrecht Institute at the end of 2019 where he now studies how noncoding parts of the genome control gene expression in development and disease using cutting edge live imaging techniques and quantitative approaches.
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We are currently recruiting enthusiastic, motivated people who are interested in working on exciting problems as part of a multidisciplinary team. We are interested in applicants from a broad range of backgrounds including, but not limited to, Biophysics, Developmental Biology, Cell Biology and Physics. If you are interested in learning more about the available position(s) in the lab, please send an email to Jacques Bothma, including a CV (with grades), a cover letter and names and contact information of 3 references.
