Biology subjects

Molodtsov, M. I.

Publications and source records attributed to Molodtsov, M. I..

3 recordsLinked to original sources

bioRxiv2024

Replisome passage through the cohesin ring

Following eukaryotic genome replication, the two newly synthesised sister chromatids remain paired by the ring-shaped cohesin complex, enabling their faithful segregation to daughter cells during cell divisions1. Cohesin topologically embraces DNA already before DNA replication2-5, and replisome passage through the cohesin ring is thought of as a fail-safe mechanism ensuring that cohesin entraps both replication products6,7. Whether replisomes indeed pass through cohesin rings remains unknown. Here, we use biochemical reconstitution4,8,9 and single molecule fluorescence microscopy to directly visualise replisome-cohesin encounters. We find that the translocating eukaryotic replicative Cdc45-Mcm2-7-GINS (CMG) helicase is frequently an obstacle to cohesin, but that the likelihood with which CMG passes cohesin increases in the presence of replisome components with known sister chromatid cohesion functions7,10-14, or by preventing cohesin from freely sliding along the template DNA. Cohesin retains topological DNA entrapment during CMG passage, suggesting that the helicase passes through the ring. The passage frequency increases further when fully reconstituted replisomes encounter cohesin rings, resulting in successful establishment of cohesion between the two replication products. Our findings demonstrate the existence of a simple mechanism that links genome replication with chromosome segregation, replisome passage through cohesin rings.

molecular biology↗

bioRxiv2023

Cohesin chromatin loop formation by an extrinsic motor

The ring-shaped cohesin complex topologically entraps two DNAs to establish sister chromatid cohesion1-3. Cohesin also shapes the interphase chromatin landscape with wide-ranging implications for gene regulation4-7, which cohesin is thought to achieve by actively extruding DNA loops without topologically entrapping DNA8-11. The loop extrusion hypothesis finds motivation from in vitro observations12-14 - whether this process underlies in vivo chromatin loop formation remains untested. Here, using the budding yeast S. cerevisiae, we generate cohesin variants that have lost their ability to extrude DNA loops but retain their ability to topologically entrap DNA. Analysis of these variants suggests that in vivo chromatin loops form independently of loop extrusion. Instead, we find that transcription promotes loop formation, as well as acts as an extrinsic motor that expands these loops and defines their ultimate positions. Our results necessitate a re-evaluation of the loop extrusion model and point to an alternative mechanism for cohesin-dependent chromatin organisation. We propose that cohesin, akin to sister chromatid cohesion establishment at replication forks, forms chromatin loops by DNA-DNA capture at places of transcription, thus unifying cohesins two roles in chromosome segregation and interphase genome organisation.

molecular biology↗

bioRxiv2017

Video rate volumetric Ca2+ imaging across cortical layersusing Seeded Iterative Demixing (SID) microscopy

Light-field microscopy (LFM) is a scalable approach for volumetric Ca2+ imaging with the highest volumetric acquisition rates (up to 100 Hz). While this has enabled high-speed whole-brain Ca2+ imaging in small semi-transparent specimen, tissue scattering has limited its application in the rodent brain. Here we introduce Seeded Iterative Demixing (SID), a computational source extraction technique that extends LFM to the scattering mammalian cortex. Using GCaMP-expressing mice we demonstrate SIDs ability to capture neuronal dynamics in vivo within a volume of 900x900x260m located as deep as 380 m in the mouse cortex and hippocampus at 30 Hz volume rate while faithfully discriminating signals from neurons as close as 20 m, at three orders of magnitude reduced computational cost. The simplicity and scalability of LFM, coupled with the performance of SID opens up a range of new applications including closed-loop experiments and is expected to propel its wide dissemination within the neuroscience community.

neuroscience↗