Congratulations to Achuthan Raja Venkatesh, who passed his biophysics qualifying exam today! The lab celebrated with bubblies. We are excited to see what you discover next on your PhD thesis journey.
Welcome Lynnette and Tianhong
Graduate students Lynnette Chan (Biophysics) and Tianhong “Tim” Wang (Chemical Systems Biology) have joined the Boettiger lab for their Ph.D. theses. Welcome!
TRACK-IT, now live
Our approach to tracking DNA loci in living cells at high resolution is now live on the BioRxiv:
https://www.biorxiv.org/content/10.1101/2025.03.27.645817v1
With this improved throughput and resolution, we quantify the contributions of cohesin to speed of cis-interactions across the genome.
Welcome Achuthan to the Boettiger Lab
Biophysics graduate student Achuthan has officially joined the lab as a co-mentored student with the Longzhi Tan Lab. He aims to determine the molecular mechanisms that specifically facilitate the expression of long-genes (1 Mb+ transcripts) in neuronal lineages, and the causes of their de-regulation in disease and aging.
Yike, Kavvya and Minhee’s paper published in G&D
https://genesdev.cshlp.org/content/39/5-6/348.long
Two unrelated distal genes activated by a shared enhancer benefit from localizing inside the same small topological domain.
In a collaboration between our team and the de Laat lab, led by de Laat lab graduate student Yike Huang, the team found that two genes, MYEOV, and CCND1 share a common enhancer. Genetic alterations that enlarge this TAD, such as deletion of the CTCF site upstream of MYEOV, not only increase inter-TAD interactions, but lead to a loss of interactions within the TAD. The resulting reduction in E-P contacts results in down-regulation of both genes. Confining the enhancer in a smaller TAD containing either gene results in an increase in contacts within the TAD, and a corresponding increase in gene expression. This is exciting, as intraTAD interactions are not expected to be effected by loss of boundary CTCFs according to the otherwise widely successful loop extrusion model.
Christina and Liang-Fu’s paper published!
Christina’s beautiful work, supported by Liang-Fu’s imaging, is now out in Molecular Cell – describing the differential responses of two promoters to long-range enhancers. Check it out here!
Congratulations Simon!
Simon passed his Genetics qualifying exam today. Congratulations!
Department Retreat
Some of the lab out for a hike along the Pacific Coast at Pt. Lobos, during our annual departmental retreat in early September. Also beautiful views over the water, and three sea otters.
Tide-pooling along the coast. There’s a nudibranch in there!
Alistair got tenure!
Thanks to all the wonderful lab members and collaborators who made it possible.
Welcome Abrar and Ivana!
New postdoctoral fellows Dr. Abrar Aljahani and Dr. Ivana Cavka join the lab.
“I’m a postdoc working with Alistair Boettiger. My work focuses on understanding gene regulation during early mammalian development, particularly how the three-dimensional organization of the genome influences gene expression. For my PhD at the Max Planck Institute for Multidisciplinary Sciences (MPI-NAT), I worked on developing a high-resolution Chromosome Conformation Capture (3C) method to map regulatory interactions and chromatin structures at the nanoscale. Currently, I’m employing super-resolution microscopy methods to further explore gene regulation mechanisms across various developmental stages.”
-Abrar
“My name is Ivana. I am starting as a new postdoc in Boettiger Lab. Previously, I was doing my doctoral studies at EMBL in Heidelberg (Germany). During that time, I worked on understanding the timing of crossover designation during Caenorhabditis elegans meiosis. I used various light-microscopy techniques, from super-resolution to more commonly used confocal microscopy techniques, to answer related biological questions. My primary research interest lies in chromatin organisation, and I am passionate about bioimage analysis and light microscopy.
I am originally from Croatia, a small European country on the coast of the Adriatic Sea. I am more of an indoor person. I enjoy reading, drawing, and cooking (especially Balkan pastries and sweets that go well with coffee). However, I also find joy in travel, going for occasional hikes and swims.”
-Ivana
