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Congratulations to Asmita and Domenic on the publication of their collaborative paper on PARP particle tracking

1/9/2023

 
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Congratulations to Asmita and Domenic. Our collaborative work investigating the live single-molecule dynamics of PARP1 and PARP2 with and without DNA damage with Jyothi Mahadevan and Karolin Luger is now published in iScience.

Happy new year and congrats to Sarah and Domenic on finishing out the year with fantastic BATS presentations

1/2/2023

 
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A big congratulations to Sarah and Domenic who finished out the year with excellent BATS presentations, presenting their thesis research for the entire department. 

The Micro-C AID paper is now published

12/6/2022

 
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The Micro-C AID paper is now online in Nature Genetics.

Using Micro-C to profile 3D genome structure after acute loss of cohesin, CTCF, WAPL, and YY1, we found that enhancer-promoter interactions are surprisingly robust to these perturbations, at least at short timescales.

This is consistent with enhancer-promoter interactions forming through a (micro)-compartmentalization mechanism as we also found in our recent Region-Capture Micro-C preprint.

We suggest a time-buffering model where CTCF and cohesin may be more important for establishing enhancer-promoter interactions than for maintaining them. Read the full paper at Nature Genetics.

Congratulations to Sarah and Domenic on becoming PhD candidates!

12/6/2022

 
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A big congratulations to Sarah and Domenic who recently passed their Biological Engineering Qualifying Exams with flying colors and have now deservedly earned the titles of PhD candidates - Congrats Sarah & Domenic!

Congratulations to Jamie

10/20/2022

 
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Congratulations to Jamie on the publication of their preview in Molecular Cell.

Jamie previewed an interesting new article from Guo*, Al-Jibury*, Garcia-Millan*, ..., Pruessner, Merkenschlager Chromatin jets define the properties of cohesin-driven in vivo loop extrusion in Molecular Cell that reports the identification of "chromatin jets" - stripes orthogonal to the main diagonal in Hi-C maps, indicative of targeted loading of cohesin at sites.

Chromatin jets provide direct evidence of targeted cohesin loading and helps constrain possible extrusion parameters in vivo.

Check out Jamie's preview here.

And check out the article here.

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.
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