Chromatin loops are involved in spatial organization of replication in budding yeast

by Kirill Ulianov | Irina Zhegalova | Ekaterina Khrameeva | Mikhail Gelfand | Skolkovo Institute of
Science and Technology, Moscow, Russia | Skolkovo Institute of Science and Technology, Moscow,
Russia; Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow,
Russia; Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia |
Skolkovo Institute of Science and Technology, Moscow, Russia | Skolkovo Institute of Science and
Technology, Moscow, Russia; Institute for Information Transmission Problems of the Russian Academy of
Sciences, Moscow, Russia;

 

The loop extrusion model explains well the formation of loop-like structures in the
mammalian species. According to the model, SMC complexes extrude DNA thread to form a
loop, while two CTCF molecules occupy loop boundaries and constrain the extrusion.
However, the CTCF-encoding gene appears only in Bilateria, while loop-like structures are
observed in the older taxa. Therefore, alternative mechanisms for the determination of the
loop boundaries must exist. We conducted an integrated analysis of multi-omic data to find
features underlying the loop formation in Saccharomyces cerevisiae. Our findings give
evidence that observing loops are related to the cellular replication machinery rather than
transcription regulation. Also, they support the model of the loop-mediated organization of
the replication factories which was proposed in previous studies of replication foci observed
in the nucleus during the S phase.

 

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