EUSynBioSeminar: “Biosaftey in Synthetic Biology: A Genetic Firewall Metric”

Rahmi Lale is an academic at the Department of Biotechnology and Food Science at the Norwegian University of Science and Technology (NTNU) in Trondheim, Norway. He is also the co-founder and CEO of Syngens, an NTNU spin-off operating at the intersection of Artificial Intelligence (AI) and Synthetic Biology.

At NTNU, he leads an interdisciplinary lab that integrates biophysics, computational, and synthetic biology. His primary research focus is on understanding and controlling transcriptional and translational regulation in various microorganisms, ranging from bacteria to higher eukaryotes.

At Syngens, he leverages the predictive power of AI to engineer biological systems for biomanufacturing applicati

Dr. Kathakali Sarkar from Imperial College London shared with us a talk titled "Distributed computing with engineered bacteria performing complex computing functions".

Dr. Sud Pinglay, Postdoctoral fellow from NYU, shared with us a talk titled “Synthetic Regulatory Genomics: genome writing to understand gene expression control“.

Abstract
The genomics revolution has resulted in the generation of a large catalogue of non-coding elements that are implicated in the control of gene expression. A synergistic understanding of how the inputs from many different such elements are integrated to result in a particular gene expression pattern has remained elusive. This is largely due to a technological gap in our ability to manipulate DNA on a scale that accurately models the size and complexity of native loci (>100kb). Despite the emergence of CRISPR/Cas9 based genome editing, it is challenging to generate multiple, precise edits on the same haplotype or large-scale intricate rearrangements in order to functionally interrogate the multi-way connections between regulatory elements.
In my talk, I will describe the development of a ‘synthetic regulatory reconstitution’ approach and its initial application to the study of the mammalian HoxA cluster. Bottom-up synthesis of large DNA segments (>100kb) allows for the arbitrary modification, removal and inclusion of elements on the scale that is required to probe gene regulation. We coupled the bottom-up synthesis of mammalian HoxA clusters (130-170kb) containing subsets of locus constituents, with their site-specific delivery to an ectopic location in the mouse genome. To date, this represents well over four megabases of DNA written into the mouse genome. This enabled us to identify a minimal set of elements that were sufficient, and not just necessary, to specify the dynamic regulation of HoxA genes. I will also outline plans to apply this approach towards understanding the regulation of the mammalian X inactivation center, the emergence of phenotypic novelty in moles and to construct regulatory landscapes from first principles in Drosophila.
We expect such ‘Synthetic Regulatory Genomics’ studies to be broadly generalizable allowing us to understand principles of gene regulation in complex genomes.