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Welcome to Danuta

10/20/2022

 
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We are excited to welcome Danuta Forbes to the lab.

Following Denise' retirement, Danuta joins us as our new administrator.

Danuta joins us from MIT's Climate and Sustainability Consortium and before that from Tufts University.

Welcome Danuta!

Welcome to Christos and farewell to Denise

9/7/2022

 
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We are excited to welcome Christos Katsifis to the lab!

Christos is joining us as a Technical Associate having recently graduated from Magdalen College, University of Oxford with an MA degree in the Biological Sciences.

Christos will be working with Michele on understanding the dynamic mechanisms of gene regulation during neuronal differentiation and how this goes awry in FOXG1 Syndrome.

We are also sad to say goodbye to Denise MacPhail, our administrative assistant who is retiring after thirty-some years of work at MIT. Happy retirement, Denise!

Congratulations to Harvey and Viraat on receiving graduate fellowships

8/12/2022

 
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Congratulations to Viraat and Harvey for receiving graduate fellowships.
  • Viraat received the Koch Institute 2022/2023 graduate fellowship. Find his recent preprint here.
  • Harvey received the Mathworks 2022/2023 graduate fellowship. Find a recent Matlab article about his work here.

Congratulations to Viraat and Miles on their new Region Capture Micro-C preprint

7/19/2022

 
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We are thrilled to share our new preprint Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments. We develop a new chromosome conformation capture method that we call Region Capture Micro-C (RCMC). With RCMC we generate the deepest 3D genome maps thus far and reveal new insights into the mechanisms of enhancer-promoter and promoter-promoter interactions. These interactions can be seen as "dots" in the contact maps below:
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Please read the preprint for the full story. And huge congratulations to Viraat and Miles for putting this together.

Congratulations to Domenic on his new News & Views

7/19/2022

 
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Congratulations to Domenic on the publication of his News & Views article in Nature Structural and Molecular Biology.

Domenic wrote about an exciting new paper Condensin-driven loop extrusion on supercoiled DNA from Eugene Kim, Cees Dekker and co-workers on how loop extruding condensin complexes navigate supercoiled DNA.

2022 Photoshoot

7/19/2022

 
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Thanks to Michele, our resident photography expert, we now have new lab photos for 2022.
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Farewell to Emma and Asmita

7/19/2022

 
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We are very sad to say goodbye to Emma and Asmita.

Asmita joined the lab in Summer 2020 as the first Technical Associate and helped get the lab set up and organized. Asmita was a key contributer to the Fbn2 project on the dynamics of DNA looping and wrote a protocol on Single-Particle Tracking. Asmita is leaving this August and going to graduate school at Yale.

Emma joined the lab in Summer 2021 from Aviv Regev's group at the Broad Institute. Emma also kept the lab in order and led a project on developing new genome-editing methods for fluorescently labeling DNA loci using PRIME editing and derivatives. Emma has just left and is going to graduate school at Stanford.

We are very sad to see you go and wish you all the best in graduate school!

Welcome Andrea

7/19/2022

 
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We are very happy to welcome Andrea Perry to the lab,

Andrea joins us as a graduate student from MIT's Physics graduate program.

Andrea will be working on understanding long-range chromatin interactions using super-resolution live-cell imaging and much more.
Welcome Andrea!

Welcome Shorna

6/6/2022

 
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We are thrilled to welcome Shorna Alam to the lab.

Shorna is a Course 6 undergraduate student at MIT in Computer Science and Engineering and is joining us as a UROP.

Shorna will be working with Viraat on Micro-C and develop new computational methods for making sense of our Micro-C data.

Welcome Shorna!

Our preprint on the dynamics of CTCF/Cohesin loops has been published in Science

4/19/2022

 
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Congratulations to Michele, Hugo, and Asmita from the lab and Simon (Mirny lab) on the publication of their preprint in Science!

This was a wonderful collaboration with Christoph Zechner and Leonid Mirny's group as well as former colleagues  Claudia, Gina, and Stanley from Berkeley, where we developed a range of new experimental, microscopy, image analysis, Bayesian inference, and 3D polymer modeling approaches to directly visualize and quantify the dynamics of the structural chromatin loops that fold the human genome into domains.

We show that the chromatin loops formed by CTCF and cohesin are both dynamic and short-lived (~10-30 min median lifetime) and quite rare (only present ~3-6.5% of the time) using  Fbn2 as our model system. This has functional implications for how these loops may regulate downstream processes such as gene expression regulation.

For more information, please see:
  • The paper in Science
  • A news story written by Anne Trafton for MIT News
  • A news story from the Max Planck Institute

A representative movie and summary sketch are further shown below.
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Huge credit to Michele, Hugo, Simon, and Asmita for putting all of this together!
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