Blog Posts

Congratulations to Viraat, Michele, and Denise

4/9/2020

In these uncertain times, it is especially nice to receive good news.

Viraat received honorable mention for his NSF Graduate Research Fellowship Program (GFRP) application. He can be found here. Congratulations to Viraat!

Michele received a post-doctoral fellowship "award without funding" from the Autism Science Foundation. Due to COVID-19 they are not currently providing funded awards, but the "project was considered to be so meritorious that it would have received funding". Congratulations to Michele!

Denise is celebrating 30 years with MIT today. What a milestone. Congratulations to Denise!

The high-resolution Micro-C paper is published

3/25/2020

The ultra-high resolution Micro-C paper in mouse embryonic stem cells is published in Molecular Cell. Besides capturing Compartments, TADs, Loops, Stripes/Flames, Micro-C is uniquely capable of capturing transcription-associated chromatin interactions such as Enhancer-Promoter (E-P) and Promoter-Promoter (P-P) interactions.
This paper was led by Stanley Tsung-Han Hsieh and please read the full story here. A complementary Micro-C paper back-to-back can be found here.

Lab donation to help fight COVID-19

3/25/2020

We are proud to be donating 57,000 nitrile gloves to local Cambridge/Boston area hospitals!

lab trip to Bota Borg

3/12/2020

Firm believers in the importance of collegiality, the Hansen lab decided to inaugurate its first lab outing by trading the lab bench for Boston's Boda Borg. After an evening of jumping around, solving puzzles, and learning from our mistakes, we triumphantly completed 3 rooms and returned home. Who knows where we'll head to next...

Asmita Jha will join the lab as our new Technical Associate

3/12/2020

We are incredibly excited that Asmita Jha will join us as a Technical Associate this June 2020.

Asmita will join us from the University of Colorado, Boulder where she has been studying Molecular and Cellular Developmental Biology and working with Karolin Luger on using live-cell imaging to understand DNA damage dynamics.

We look forward to welcoming Asmita!

Two new protocols published: Convenient absolute protein abundance quantification and robust co-IPs

2/22/2020

Two new protocols led by Claudia Cattoglio are now published with detailed step-by-step guidelines.
The first provides a detailed protocol for how to measure the absolute abundance (#proteins per cell) of any Halo-Tagged protein in a couple of afternoons using just Flow Cytometry based on our 2019 paper and can be found here: https://bio-protocol.org/e3527
The second protocol provides detailed step-by-step guidance for to carry out robust co-IP experiments, for example of the same protein with two different epitope tags and can be found here: https://bio-protocol.org/e3526

The lab is officially a lab

2/12/2020

We are officially a lab. Michele Gabriele has joined as the lab's first post-doc and Viraat Goel and Jin (Harvey) Yang have joined as the first two graduate students from MIT's Biological Engineering program. Science is happening!

New paper: The target search mechanism of CTCF is published in Nature Chemical Biology

12/2/2019

Our BioRxiv preprint on CTCF's target search mechanism is now published in Nature Chemical Biology:

We show that CTCF exhibits anisotropic diffusion
We devise the Anisotropic Diffusion through transient Trapping in Zones model (ADTZ-model) to theoretically explain the data
We show that the zones likely correspond to CTCF clusters
Deleting the internal RNA-Binding Region (RBRi) in CTCF strongly reduces both trapping and CTCF clustering

Our results suggest two sources of CTCF anisotropy: DNA-mediated interactions that causes anisotropy without a defined scale and RNA-mediated interactions which result in local trapping
Functionally, transient RBRi-mediated trapping serves to accelerate the cognate DNA-target search. The presence of the RBRi-domain does not affect DNA-binding, but increases the rate at which CTCF finds a cognate DNA target site by ~2.5-fold!!!.
Thus, the DNA-target search mechanism of CTCF appears to be 'guided' by RNA

Shdema Filler-Hayut joins the lab

9/28/2019

Shdema Filler-Hayut is joining the lab as a post-doc starting in early 2020. Shdema is joining the lab from the Weizmann Institute in Israel, where she worked with Avraham Levy on how double-strand breaks (DSBs) are repaired in plants. In particular, Shdema showed that DSBs in somatic plant cells can be repaired using homologous chromosomes by exploiting Cas9 and a clever genetic approach in tomatoes, with deeps applications for improving agriculture.
We are thrilled that Shdema is joining the lab and look forward to welcoming her.

Preprint on how an RNA-Binding Region (RBRi) in CTCF regulates clustering and chromatin looping is now published in Molecular Cell

9/12/2019

Our preprint describing our functional characterization of an internal RNA-Binding Region (RBRi) in CTCF is online today in Molecular Cell.

We show that CTCF self-associates in a largely RNA-dependent and DNA-independent manner
When we delete the RBRi in CTCF endogenously in mESCs, the cells get very sick, suggesting its functional important.
RBRi-del-CTCF shows substantially lower clustering in cells
RBRi-del-mESCs have lost about 1/3-1/2 of all chromatin loops
CTCF binding sites and CTCF loops fall into at least 2 distinct classes: RBRi-dependent or RBRi-independent

Overall, we believe our discovery of distinct classes of chromatin loops highlights a key future question: what are the mechanistic differences between these sites?
Also check out a similar story published back-to-back.

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