A Tale of Two Strands: Decoding Chromatin Replication Through Strand-specific Sequencing

Overview

Journal Mol Cell

Publisher Cell Press

Date 2025 Jan 17

PMID 39824166

Authors

Zhiming Li

Zhiguo Zhang

Affiliations

Soon will be listed here.

Abstract

DNA replication, a fundamental process in all living organisms, proceeds with continuous synthesis of the leading strand by DNA polymerase ε (Pol ε) and discontinuous synthesis of the lagging strand by polymerase δ (Pol δ). This inherent asymmetry at each replication fork necessitates the development of methods to distinguish between these two nascent strands in vivo. Over the past decade, strand-specific sequencing strategies, such as enrichment and sequencing of protein-associated nascent DNA (eSPAN) and Okazaki fragment sequencing (OK-seq), have become essential tools for studying chromatin replication in eukaryotic cells. In this review, we outline the foundational principles underlying these methodologies and summarize key mechanistic insights into DNA replication, parental histone transfer, epigenetic inheritance, and beyond, gained through their applications. Finally, we discuss the limitations and challenges of current techniques, highlighting the need for further technological innovations to better understand the dynamics and regulation of chromatin replication in eukaryotic cells.

References

Xu X, Hua X, Brown K, Ren X, Zhang Z . Mcm2 promotes stem cell differentiation via its ability to bind H3-H4. Elife. 2022; 11. PMC: 9681210. DOI: 10.7554/eLife.80917. View

Zentner G, Henikoff S . Regulation of nucleosome dynamics by histone modifications. Nat Struct Mol Biol. 2013; 20(3):259-66. DOI: 10.1038/nsmb.2470. View

McClure A, Diffley J . Rad53 checkpoint kinase regulation of DNA replication fork rate via Mrc1 phosphorylation. Elife. 2021; 10. PMC: 8387023. DOI: 10.7554/eLife.69726. View

He Q, Wang F, ODonnell M, Li H . Cryo-EM reveals a nearly complete PCNA loading process and unique features of the human alternative clamp loader CTF18-RFC. Proc Natl Acad Sci U S A. 2024; 121(18):e2319727121. PMC: 11067034. DOI: 10.1073/pnas.2319727121. View

Ganier O, Prorok P, Akerman I, Mechali M . Metazoan DNA replication origins. Curr Opin Cell Biol. 2019; 58:134-141. DOI: 10.1016/j.ceb.2019.03.003. View

Waga S, Stillman B . The DNA replication fork in eukaryotic cells. Annu Rev Biochem. 1998; 67:721-51. DOI: 10.1146/annurev.biochem.67.1.721. View

Donnianni R, Zhou Z, Lujan S, Al-Zain A, Garcia V, Glancy E . DNA Polymerase Delta Synthesizes Both Strands during Break-Induced Replication. Mol Cell. 2019; 76(3):371-381.e4. PMC: 6862718. DOI: 10.1016/j.molcel.2019.07.033. View

Levin J, Yassour M, Adiconis X, Nusbaum C, Thompson D, Friedman N . Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods. 2010; 7(9):709-15. PMC: 3005310. DOI: 10.1038/nmeth.1491. View

Nava G, Grasso L, Sertic S, Pellicioli A, Muzi Falconi M, Lazzaro F . One, No One, and One Hundred Thousand: The Many Forms of Ribonucleotides in DNA. Int J Mol Sci. 2020; 21(5). PMC: 7084774. DOI: 10.3390/ijms21051706. View

10.

Nedelcheva M, Roguev A, Dolapchiev L, Shevchenko A, Taskov H, Shevchenko A . Uncoupling of unwinding from DNA synthesis implies regulation of MCM helicase by Tof1/Mrc1/Csm3 checkpoint complex. J Mol Biol. 2005; 347(3):509-21. DOI: 10.1016/j.jmb.2005.01.041. View

11.

Seczynska M, Lehner P . The sound of silence: mechanisms and implications of HUSH complex function. Trends Genet. 2023; 39(4):251-267. DOI: 10.1016/j.tig.2022.12.005. View

12.

He H, Li Y, Dong Q, Chang A, Gao F, Chi Z . Coordinated regulation of heterochromatin inheritance by Dpb3-Dpb4 complex. Proc Natl Acad Sci U S A. 2017; 114(47):12524-12529. PMC: 5703312. DOI: 10.1073/pnas.1712961114. View

13.

Jones P, Liang G . Rethinking how DNA methylation patterns are maintained. Nat Rev Genet. 2009; 10(11):805-11. PMC: 2848124. DOI: 10.1038/nrg2651. View

14.

Escobar T, Loyola A, Reinberg D . Parental nucleosome segregation and the inheritance of cellular identity. Nat Rev Genet. 2021; 22(6):379-392. PMC: 8609916. DOI: 10.1038/s41576-020-00312-w. View

15.

Tyler J, Adams C, Chen S, Kobayashi R, Kamakaka R, Kadonaga J . The RCAF complex mediates chromatin assembly during DNA replication and repair. Nature. 1999; 402(6761):555-60. DOI: 10.1038/990147. View

16.

Canela A, Sridharan S, Sciascia N, Tubbs A, Meltzer P, Sleckman B . DNA Breaks and End Resection Measured Genome-wide by End Sequencing. Mol Cell. 2016; 63(5):898-911. PMC: 6299834. DOI: 10.1016/j.molcel.2016.06.034. View

17.

Hu Y, Stillman B . Origins of DNA replication in eukaryotes. Mol Cell. 2023; 83(3):352-372. PMC: 9898300. DOI: 10.1016/j.molcel.2022.12.024. View

18.

Tian M, Wang Z, Su Z, Shibata E, Shibata Y, Dutta A . Integrative analysis of DNA replication origins and ORC-/MCM-binding sites in human cells reveals a lack of overlap. Elife. 2024; 12. PMC: 10990492. DOI: 10.7554/eLife.89548. View

19.

Logsdon G, Vollger M, Eichler E . Long-read human genome sequencing and its applications. Nat Rev Genet. 2020; 21(10):597-614. PMC: 7877196. DOI: 10.1038/s41576-020-0236-x. View

20.

Sharif J, Muto M, Takebayashi S, Suetake I, Iwamatsu A, Endo T . The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature. 2007; 450(7171):908-12. DOI: 10.1038/nature06397. View