Genetics Training Grant Retreat to be held Friday, 9/26/14

The annual Genetics Training Grant seminar is being held on Friday, September 26th at the Shapiro Campus Center Auditorium at Brandeis University. Four cutting-edge synthetic biologists: Timothy Lu, Ron Weiss, William Shih and Ahmad Khalil will share their research for the Synthetic Biology: Insights and Applications” symposium.
Brandeis graduate students and post-docs will have the opportunity to meet the speakers and present their work in a poster session after the talks. We encourage researchers from all departments to contribute. If you are currently, or previously were on the Genetics Training Grant, presentation of a poster is expected. 

Schedule for GTG Retreat

9:30-10:30 Ron Weiss (MIT, Dept. of Biological Engineering)
“Synthetic biology: from parts to modules to therapeutic systems.”
10:30-11:00 Coffee Break
11:00-12:00 Timothy Lu (MIT, Dept. of Biology Engineering)
“Synthetic biology for human health applications.”
12:00-1:30 Break/Lunch
1:30-2:30 William Shih (Wyss Institute)
“DNA nanostructures as building blocks for molecular biophysics and future therapeutics.”
2:30-3:30 Ahmad Khalil (Boston University, Biomedical Engineering)
“Building molecular assemblies to control the flow of biological information.”
3:30-5:00 Poster session
Shapiro Science Center 2nd floor.
All life sciences students are invited to present.

Chromosome Tethering in Yeast

On July 14, 2014, PLOS ONE  published a paper from the Haber and Kondev labs. The paper, Effect of chromosome tethering on nuclear organization in yeast, was authored by Baris Avsaroglu, Gabriel Bronk, Susannah Gordon-Messer, Jungoh Ham, Debra A. Bressan, James E. Haber, and Jane Kondev.

by Baris Avsaroglu

Chromosopone.0102474_350mes are folded into the cell nucleus in a non-random fashion. In yeast cells the Rabl model is used to describe the folded state of interphase chromosomes in terms of tethering interactions of the centromeres and the telomeres with the nuclear periphery. By combining theory and experiments, we assess the importance of chromosome tethering in determining the spatial location of genes within the interphase yeast nucleus. Using a well-established polymer model of yeast chromosomes to compute the spatial distributions of several genetic loci, we demonstrate that telomere tethering strongly affects the positioning of genes within the first 10 kb of the telomere. Further increasing the distance of the gene from the telomere reduces the effect of the attachment at the nuclear envelope exponentially fast with a characteristic distance of 20 kb. We test these predictions experimentally using fluorescently labeled genetic loci on chromosome III in wild type and in two mutant yeast strains with altered tethering interactions. For all the cases examined we find good agreement between theory and experiment. This study provides a quantitative test of the polymer model of yeast chromosomes, which can be used to predict long-ranged interactions between genetic loci relevant in transcription regulation and DNA recombination.

Patching Up Broken Chromosomes

Olga Tsaponina and James Haber’s recent paper “Frequent Interchromosomal Template Switches during Gene Conversion in S. cerevisiae” was published online by Molecular Cell on July 24, 2014.

by James Haber

“The process of copying DNA every time our cells divide is exceptionally accurate, but in copying 6,000,000,000 base pairs of the genome mistakes do occur, including both mutations and the formation of chromosome breaks. These breaks must be repaired to maintain the integrity of our chromosomes.  In our recent paper we have demonstrated that the mechanism of patching up a broken chromosome is associated with a surprisingly high level of alterations of the sequence.  Many of these changes result from “slippage” of the DNA polymerases copying the DNA during the repair process; for example in copying a sequence of 4 Gs, the polymerase occasionally jumps over one, to lose a base from the sequence (a frameshift mutation).

graphical_abstract_350In this paper we focused on more dramatic slippage events in which the copying machinery jumped from one chromosome to a related but divergent sequence on another chromosome and then jumped back, creating a chimeric sequence.  These interchromosomal template switches (ICTS) occur at a low rate when the distant sequence is only 71% identical, but if we make that segment 100% identical we could find such jumps 10,000 times more frequently, in about 1 in 300 events.  This result reveals how unstable the copying machinery in DNA repair is compared to normal DNA replication. This was very surprising and provides an explanation for many complex rearrangements associated with cancers.  In carrying out this work we identified the first protein that is needed to permit these frequent jumps: a chromatin remodeling enzyme known as Rdh54 that previously did not have a well-defined role in DNA repair in somatic cells.

Finally, we learned a new role for the proteins that survey the genome for mismatched bases that arise during replication and found that one of these proteins, Msh6, is required to specify which strand of DNA containing a mismatch is the “good one” that should be used as the template to correct the mismatch.

This work was supported by the National Institutes of Health General Medical Institute”.

How regulatory sequences evolve in fruit flies

An IMP-Brandeis collaboration reveals the evolution of regulatory sequences in Drosophilids

By Yuliya Sytnikova and Nelson Lau

Enhancers are cis-regulatory DNA sequences that influence the promoters of genes, but identifying enhancers is not a straightforward process. Previously, the Stark lab developed a method for genome-wide enhancer detection called STARR-seq, (Arnold, Gerlach et al. 2013), that allowed them to identify thousands of enhancer sequences around the Drosophila melanogaster genome. In the most recent issue of Nature Genetics, a collaboration between the Stark lab of the IMP (Institute of Molecular Pathology) in Vienna, Austria, and the Lau lab at Brandeis University examines this hypothesis by studying the conservation of enhancer regulatory regions during Drosophilid fly evolution.

To ask if enhancers from D. melanogaster enhancers are also conserved in other Drosophila species in their sequences and locations, the Stark lab extended the STARR-Seq approach to D.yakuba and D.ananassae, which are separated from D.melanogaster by 11 and 40 million years ago, respectively (Arnold, Gerlach et al. 2014). Interestingly, this study also revealed hundreds of new sequences that gained enhancer function differentially between D.yakuba, D.ananassae, and D.melanogaster.

However, to test if these new sequences meaningfully direct different gene expression changes, the Lau lab conducted a targeted mRNA profiling experiment in purified endogenous follicle cells from D.yakuba and D.ananassae. The Stark lab had initiated the STARR-Seq analysis in an Ovarian Somatic Cell (OSC) line, which originated from the follicle cells of D.melanogaster, therefore the profiling of endogenous follicle cells from D.yakuba and D.ananassae was critical. The Lau lab achieved this using a methodology they developed for profiling Piwi-interacting RNAs from these cells (Matts, Synikova et al. 2013).

Figure 6: Evolution of enhancer activity in OSCs and gene expression in follicle cells in vivo.


Arnold CD, Gerlach D, Spies D, Matts JA, Sytnikova YA, Pagani M, Lau NC, Stark A. Nat Genet. 2014 Jun 8. doi: 10.1038/ng.3009. [Epub ahead of print] Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution.

Matts JA, Sytnikova Y, Chirn GW, Igloi GL, Lau NC. Methods Mol Biol. 2014;1093:123-36. doi: 10.1007/978-1-62703-694-8_10. Small RNA library construction from minute biological samples.


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