Sometimes we have a hard time figuring out where in the genome transcription factors prefer to bind. Cheeky little fellows. Our esteemed Hemangi Chaudhari was not having it. She took up her mighty pipette and worked to figure out what features reside in the flanking regions of TF binding sites that might define either high or low expression. Check out her publication that just came out in Genome Research, titled “Local sequence features that influence AP-1 cis-regulatory activity”. Great job, Hemangi!! (https://genome.cshlp.org/content/28/2/171.abstract)
In an effort to find something sweeter than the satisfaction of sequencing DNA, the lab trekked downtown to visit St. Louis’ own Bissinger’s Chocolate Factory. Led by a couple of chocolate fanatics, we sought to uncover the secrets behind this famous chocolate. But alas, our phones were confiscated and the chocolate-factory-dungeon was threatened if we strayed from the walkway and became too pesky of visitors.
On our tour, we learned of the hand-crafted nature of Bissinger’s chocolate. A few lab members couldn’t help but be reminded of how we too take care to make sure that every library we design receives high quality and individualized attention. After the tour, we were treated to a tasting. Barak liked the chocolate-covered cherries. Siqi preferred the milk chocolate over the dark chocolate. Clarice quipped that her mint chocolate tasted like toothpaste.
All in all, we had a wonderful time. Was it sweeter than that feeling of opening up your sequencing results to find a beautiful array of A’s, C’s, T’s and G’s? Maybe not, but alas the factory was neat and the chocolate was tasty.
Congratulations to Clarice Hong (Molecular Genetics and Genomics) and Siqi Zhao (Computational and Systems Biology) on passing their Qualifying Exams!!! They have their wagons hitched to a star and we can’t wait to see where their scientific adventures travel next.
Following the smashing success of our first big idea’s night, big ideas coated our benches just as Barak’s wool sweater once did. Ideas so big that we contemplated moving into a building with even higher ceilings. But alas, we shan’t desert our loyal coffee maker, so we stay put.
The second gathering of Big Idea’s Night took place at Retreat Gastropub. Amidst some fries and whiskey, we pitched ideas for how we can utilize our Center’s newest sequencing technologies. PacBio’s ultra-long sequencing reads and the 10x single-cell method both provide new avenues for innovative research. And to not exclude our friends in imaging, we discussed a new application of FISH, called clampFISH. This technology generates a FISH signal strong enough to be detected by FACS.
The idea most discussed utilizes ultra-long reads to query chromatin interactions. In our lab, we have identified strong regional effects on gene expression. How far do these regions stretch? With our landing pad in place, we can integrate reporter genes at variable distances and ask how the length relates to the coordinated expression between the reporter gene at the LP and at distance. If we see discordance at a certain distance, it may be possible to restore the similar expression with looping-related proteins, such as CTCF or YY1. As team landing pad ventures further into the mechanisms of this strong regional effect, we will draw from these discussions and this big idea.
Our intrepid landing pad explorer has successfully defended her thesis, titled “Integration of local and regional regulatory information in the human genome”!!!
Afterwards, we toasted champagne and had delicious Himalayan Yeti as we recounted Hemangi’s many wonderful accomplishments.
The inaugural Cohen Lab Big Idea’s Night! Barak loves to tell the story of the discovery of transfer RNA. Our scientific forefathers kicked around ideas over tea, scones, and maybe some beers too. Through this sort of brainstorming, the idea that there must be some molecule shuttling around amino acids was borne. Once our forefathers convinced themselves of the specifics of the idea, and how the experiment would work, actually conducting it became trivial. And thus tRNA was discovered. If such great biological discovery can be made over scones and ales, then lets indulge!
Settled into our lab’s old haunts, The Scottish Arms, we bounced around big ideas focused on master regulators. With new graduate students patrolling the benches, the lab has taken up new vocabulary as well: pioneer factors. Discussion flitted between definition, mechanism, and proof of these special transcription factors; perhaps we leave this discussion for our graduate students’ future presentations.
And so big idea #1 was not as much an idea but an open question: what would result from treating cells with two different master regulator cocktails? What type of cell would the transcriptome resemble? Would we see a random assortment of cell A and cell B, or would we see a monster, with the head of cell A and the body of cell B? With Halloween on the horizon, we’ll incubate this spooky idea until a rainy day comes along, ripe with time for a big idea experiment.
We are pleased to announce the Mike White PhD has been promoted to the rank of Assistant Professor of Genetics. This is well deserved. It is expected that Mike will continue his own research with the added distractions of worrying about grants, sitting on useless committees, and teaching classes to recalcitrant graduate students.
Graduate student and current BALSA president, Brett Maricque, and co-founder, Maxim Schillebeeckx, discuss how the BALSA group allows graduate students to gain business experience while providing quality, low cost consulting services for the growing St. Louis biotechnology sector and generating grant money for local entrepreneurs through the BALSA Foundation. Listen to the full conversation on the “St. Louis on the Air” website, http://news.stlpublicradio.org/post/balsa-foundation-awarding-grants-first-time-entrepreneurs.
The Olin Fellowships recognize accomplishments in biomedical research by doctoral students at Washington University. While thirty-two students were nominated, only eight awards were granted. Marc’s research focused on stochasticity in gene expression and the kinds of “noise” that are often disregarded when expression is measured. While he has moved on to his clinical rotations, Marc’s work in the Cohen lab can be found under our publications header.