Chromosomal coordination and differential structure of asynchronous replicating regions

Britny Blumenfeld,Oriya Vardi,Marganit Farago,Hagit Masika,Rachel Rapoport,Yishai Yehuda,Lamia Halaseh,Yehudit Bergman,Itamar Simon,Rena Levin-Klein,Howard Cedar

doi:10.1038/s41467-021-21348-4

Britny Blumenfeld, Oriya Vardi + Show 9 more

Open Access

https://doi.org/10.1038/s41467-021-21348-4

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Abstract

Stochastic asynchronous replication timing (AS-RT) is a phenomenon in which the time of replication of each allele is different, and the identity of the early allele varies between cells. By taking advantage of stable clonal pre-B cell populations derived from C57BL6/Castaneous mice, we have mapped the genome-wide AS-RT loci, independently of genetic differences. These regions are characterized by differential chromatin accessibility, mono-allelic expression and include new gene families involved in specifying cell identity. By combining population level mapping with single cell FISH, our data reveal the existence of a novel regulatory program that coordinates a fixed relationship between AS-RT regions on any given chromosome, with some loci set to replicate in a parallel and others set in the anti-parallel orientation. Our results show that AS-RT is a highly regulated epigenetic mark established during early embryogenesis that may be used for facilitating the programming of mono-allelic choice throughout development.

Highlights

Stochastic asynchronous replication timing (AS-RT) is a phenomenon in which the time of replication of each allele is different, and the identity of the early allele varies between cells
Previous studies have shown that AS-replication-time patterns present in somatic cells are maintained in a clonal manner, insuring that all cells behave with the same replication-time properties[6,7]
Comparing these patterns to those seen in pure between C57BL6 (B6) or Cast cell lines, we noted that a number of AS sites were due to a genetic difference between the strains (Supplementary Fig. 1a)

Summary

Introduction

Stochastic asynchronous replication timing (AS-RT) is a phenomenon in which the time of replication of each allele is different, and the identity of the early allele varies between cells. By taking advantage of stable clonal pre-B cell populations derived from C57BL6/Castaneous mice, we have mapped the genome-wide AS-RT loci, independently of genetic differences These regions are characterized by differential chromatin accessibility, mono-allelic expression and include new gene families involved in specifying cell identity. We solved this problem by employing clonal cells from a hybrid cross between C57BL6 (B6) and Castaneous (Cast) mice to chart replication timing over the entire genome, using polymorphisms to distinguish between the paternal and maternal alleles These experiments have revealed hundreds of previously undiscovered asynchronously replicating sites, allowing us to characterize these regions, gain insight into the regulation of this phenomenon and decipher the structurefunction relationship between replication timing and gene expression

Methods

Results

Conclusion