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Farewell Daria

4/5/2025

 
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We are sad to say goodbye to Daria Sels, who visited the lab for 9 months as a Master's student from Belgium, but we wish you all the best for your upcoming travel and your future PhD!

Congrats to Jamie on a great BATS presentation

4/5/2025

 
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Vicky Liu joins the lab

4/5/2025

 
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Vicky Liu joins the lab!

We are excited that Vicky Liu has joined the lab. Vicky received her undergraduate degree from Rice University before joining the MIT BE program and now the lab.

Welcome Vicky!

Congratulations to Viraat on his collaborative work with Nick Aboreden and Gerd Blobel on the looping factor LDB1

2/18/2025

 
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Congratulations to Viraat on his collaborative paper with Nick Aboreden and Gerd Blobel, where he used RCMC to show that LDB1 is a true looping factor. You can read the full paper in Molecular Cell.

Happy 5 year birthday to the lab

2/18/2025

 
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The lab turned 5 years old on Feb 1st, 2025. To celebrate, we went candlepin bowling in Southie!

Congratulations to James on his new preprint reporting genome-wide absolute quantification of chromatin looping

2/18/2025

 
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Congratulations to James on his new preprint in collaboration with Simon, Michele, Pia, and Ilya among our lab and the Zechner, Giorgetti, and Mirny labs. You can find the preprint on BioRxiv.
3D Genomics methods such as Hi-C and Micro-C can identify many thousands of loops across the genome, but all the quantifications are relative. By integrating super-resolution live-cell imaging with Micro-C and new computational methods, James now reports absolute quantification of chromatin loops for the first time (as in, e.g. this loop is present 3% of the time). Across the genome, James finds loops to be generally rare with implications for gene regulation and the mechanisms of enhancer-promoter interactions. Congratulations to James!

Congratulations to Domenic on his ZNF143 preprint getting published in Molecular Cell

2/18/2025

 
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Congratulations to Domenic, who's preprint on the TF ZNF143/ZFP143 has come out in Molecular Cell.
ZNF143 was reported to be a major looping factor that forms chromatin loops either by itself or with CTCF, but Domenic found that this is not the case. Instead, ZNF143 is a transcription factor that binds promoters to activate the expression of some ribosomal and mitochondrial genes. Domenic's paper was co-submitted and co-published with a paper from Elzo de Wit's lab who independently also found that ZNF143 is not a looping factor and was incorrectly assumed to be a looping factor due to a non-specific ZNF143 antibody that cross-reacts with CTCF. Congratulations to Domenic!

Lab holiday party

12/7/2024

 
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The lab receives a Transformative Research Award

10/16/2024

 
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We are fortunate to receive one of the 7 NIH Director's Transformative Research Awards awarded across the US in 2024 for High Risk High Reward research for "transformative projects that are inherently risky and untested but have the potential to create or overturn fundamental paradigms".
This award will support the lab until 2029. Thank you NIH.

Congratulations to Viraat on new preprint: Dynamics of microcompartment formation at the mitosis-to-G1 transition

10/16/2024

 
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Congratulations to Viraat on his new preprint in collaboration with Nick Aboreden and Gerd Blobel at UPenn, Ed Banigan and Leonid Mirny here at MIT and also to James Jusuf here in the lab.

Previously, it was thought that all 3D genome structure is erased during mitosis and must be re-established as cells enter G1 phase. Using RCMC to generate high-res 3D genome maps at the mitosis-to-G1 transition, we show for the first time that this is not the case.

We unexpected observe strong microcompartments that are present already in prometaphase and further strengthen in ana/telophase.

Using 3D polymer modeling, we show that chromosome compaction is a strong regulator of compartment strength and that the 2-3-fold higher compaction of mitotic chromosomes largely explains the existence of microcompartments in mitotic chromosomes.

Check out the full preprint here.

See also a related and co-submitted preprint from Job Dekker's lab here.

Below: a GIF showing how 3D genome structure changes from mitosis to G1 at the Klf1 locus, comparing RCMC to Hi-C.
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