Evolution of DNA Replication Origin Specification and Gene Silencing Mechanisms

Hu, Y, Tareen, A, Sheu, Y-J, Ireland, WT, Speck, C, Li, H, Joshua-Tor, L, Kinney, JB, Stillman, B (July 2020) Evolution of DNA Replication Origin Specification and Gene Silencing Mechanisms. BioRxiv. (Unpublished)

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DOI: 10.1101/2020.07.04.187286

Abstract

DNA replication in eukaryotic cells initiates from chromosomal locations, called replication origins, that bind the Origin Recognition Complex (ORC) prior to S phase. Origin establishment is guided by well-defined DNA sequence motifs in Saccharomyces cerevisiae and some other budding yeasts, but most eukaryotes lack sequence-specific origins. At present, the mechanistic and evolutionary reasons for this difference are unclear. A 3.9 Å structure of S. cerevisiae ORC-Cdc6-Cdt1-Mcm2-7 (OCCM) bound to origin DNA revealed, among other things, that a loop within Orc2 inserts into a DNA minor groove and an α-helix within Orc4 inserts into a DNA major groove1. We show that this Orc4 α-helix mediates the sequence-specificity of origins in S. cerevisiae. Specifically, mutations were identified within this α-helix that alter the sequence-dependent activity of individual origins as well as change global genomic origin firing patterns. This was accomplished using a massively parallel origin selection assay analyzed using a custom mutual-information-based modeling approach and a separate analysis of whole-genome replication profiling and statistics. Interestingly, the sequence specificity of DNA replication initiation, as mediated by the Orc4 α-helix, has evolved in close conjunction with the gain of ORC-Sir4-mediated gene silencing and the loss of RNA interference.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA replication
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > origin recognition complex
CSHL Authors:
Communities: CSHL labs > Joshua-Tor lab
CSHL labs > Kinney lab
CSHL labs > Stillman lab
CSHL Cancer Center Program > Gene Regulation and Inheritance Program
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 4 July 2020
Date Deposited: 13 Jul 2021 17:33
Last Modified: 13 Jul 2021 17:33
URI: https://repository.cshl.edu/id/eprint/40279

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