Genome-wide measurement of DNA replication fork directionality and quantification of DNA replication initiation and termination with Okazaki fragment sequencing

Nataliya Petryk, Xia Wu, Yaqun Liu, Yves d’Aubenton-Carafa, Claude Thermes, Olivier Hyrien, Chun-Long Chen

Published: 2023-01-17 DOI: 10.1038/s41596-022-00793-5

Okazaki fragment sequencing

DNA replication

Replication fork directionality

Genome stability

Hidden Markov model

AI 解读

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Studying the dynamics of genome replication in mammalian cells has been historically challenging. To reveal the location of replication initiation and termination in the human genome, we developed Okazaki fragment sequencing (OK-seq), a quantitative appro
Introduction
Materials
Procedure
Timing
Troubleshooting
Anticipated results
References
ACKNOWLEDGMENTS

Tubbs, A. et al. Dual roles of poly(dA:dT) tracts in replication initiation and fork collapse. Cell 174, 1127–1142 (2018).
Kirstein, N. et al. Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zones. eLife 10, e62161 (2021).
Huberman, J. A. & Riggs, A. D. On the mechanism of DNA replication in mammalian chromosomes. J. Mol. Biol. 32, 327–341 (1968).
Hamlin, J. L., Mesner, L. D. & Dijkwel, P. A. A winding road to origin discovery. Chromosome Res. 18, 45–61 (2010).
Hyrien, O. Peaks cloaked in the mist: the landscape of mammalian replication origins. J. Cell Biol. 208, 147–160 (2015).
Hulke, M. L., Massey, D. J. & Koren, A. Genomic methods for measuring DNA replication dynamics. Chromosome Res. 28, 49–67 (2020).
Lebofsky, R., Heilig, R., Sonnleitner, M., Weissenbach, J. & Bensimon, A. DNA replication origin interference increases the spacing between initiation events in human cells. Mol. Biol. Cell 17, 5337–5345 (2006).
Demczuk, A. et al. Regulation of DNA replication within the immunoglobulin heavy-chain locus during B cell commitment. PLoS Biol. 10, e1001360 (2012).
Anglana, M., Apiou, F., Bensimon, A. & Debatisse, M. Dynamics of DNA replication in mammalian somatic cells: nucleotide pool modulates origin choice and interorigin spacing. Cell 114, 385–394 (2003).
Cadoret, J. C. et al. Genome-wide studies highlight indirect links between human replication origins and gene regulation. Proc. Natl Acad. Sci. USA 105, 15837–15842 (2008).
Besnard, E. et al. Unraveling cell type-specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs. Nat. Struct. Mol. Biol. 19, 837–844 (2012).
Karnani, N., Taylor, C. M., Malhotra, A. & Dutta, A. Genomic study of replication initiation in human chromosomes reveals the influence of transcription regulation and chromatin structure on origin selection. Mol. Biol. Cell 21, 393–404 (2010).
Mukhopadhyay, R. et al. Allele-specific genome-wide profiling in human primary erythroblasts reveal replication program organization. PLoS Genet. 10, e1004319 (2014).
Langley, A. R., Gräf, S., Smith, J. C. & Krude, T. Genome-wide identification and characterisation of human DNA replication origins by initiation site sequencing (ini-seq. Nucleic Acids Res. 44, 10230–10247 (2016).
Mesner, L. D. et al. Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription. Genome Res. 21, 377–389 (2011).
Mesner, L. D. et al. Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins. Genome Res. 23, 1774–1788 (2013).
Hansen, R. S. et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc. Natl Acad. Sci. USA 107, 139–144 (2010).
Chen, C. L. et al. Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes. Genome Res. 20, 447–457 (2010).
Zhao, P. A., Sasaki, T. & Gilbert, D. M. High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells. Genome Biol. 21, 76 (2020).
Koren, A. et al. Genetic variation in human DNA replication timing. Cell 159, 1015–1026 (2014).
Lobry, J. R. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol. 13, 660–665 (1996).
Touchon, M. et al. Replication-associated strand asymmetries in mammalian genomes: toward detection of replication origins. Proc. Natl Acad. Sci. USA 102, 9836–9841 (2005).
Huvet, M. et al. Human gene organization driven by the coordination of replication and transcription. Genome Res. 17, 1278–1285 (2007).
Chen, C. L. et al. Replication-associated mutational asymmetry in the human genome. Mol. Biol. Evol. 28, 2327–2337 (2011).
Audit, B. et al. Open chromatin encoded in DNA sequence is the signature of ‘master’ replication origins in human cells. Nucleic Acids Res. 37, 6064–6075 (2009).
Guilbaud, G. et al. Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome. PLoS Comput. Biol. 7, e1002322 (2011).
Baker, A. et al. Replication fork polarity gradients revealed by megabase-sized U-shaped replication timing domains in human cell lines. PLoS Comput. Biol. 8, e1002443 (2012).
Green, P., Ewing, B., Miller, W., Thomas, P. J. & Green, E. D. Transcription-associated mutational asymmetry in mammalian evolution. Nat. Genet. 33, 514–517 (2003).
Petryk, N. et al. Replication landscape of the human genome. Nat. Commun. 7, 10208 (2016).
Smith, D. J. & Whitehouse, I. Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434–438 (2012).
McGuffee, S. R., Smith, D. J. & Whitehouse, I. Quantitative, genome-wide analysis of eukaryotic replication initiation and termination. Mol. Cell 50, 123–135 (2013).
Hennion, M. et al. FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing. Genome Biol. 21, 125 (2020).
Liu, Y., Wu, X., D’aubenton-Carafa, Y., Thermes, C. & Chen, C.-L. OKseqHMM: a genome-wide replication fork directionality analysis toolkit. Nucleic Acids Res., https://doi.org/10.1093/nar/gkac1239 (2022).
Blin, M. et al. DNA molecular combing-based replication fork directionality profiling. Nucleic Acids Res. 49, e69 (2021).
Wang, W. et al. Genome-wide mapping of human DNA replication by optical replication mapping supports a stochastic model of eukaryotic replication. Mol. Cell 81, 2975–2988 (2021).
Wu, X. et al. Developmental and cancer-associated plasticity of DNA replication preferentially targets GC-poor, lowly expressed and late-replicating regions. Nucleic Acids Res. 46, 10157–10172 (2018).
Petryk, N. et al. MCM2 promotes symmetric inheritance of modified histones during DNA replication. Science 361, 1389–1392 (2018).
Chen, Y. H. et al. Transcription shapes DNA replication initiation and termination in human cells. Nat. Struct. Mol. Biol. 26, 67–77 (2019).
Li, Z. et al. DNA polymerase alpha interacts with H3-H4 and facilitates the transfer of parental histones to lagging strands. Sci. Adv. 6, eabb5820 (2020).
Hyrien, O., Maric, C. & Méchali, M. Transition in specification of embryonic metazoan DNA replication origins. Science 270, 994–997 (1995).
Dijkwel, P. A., Wang, S. & Hamlin, J. L. Initiation sites are distributed at frequent intervals in the Chinese hamster dihydrofolate reductase origin of replication but are used with very different efficiencies. Mol. Cell Biol. 22, 3053–3065 (2002).
Powell, S. K. et al. Dynamic loading and redistribution of the Mcm2-7 helicase complex through the cell cycle. EMBO J. 34, 531–543 (2015).
Gros, J. et al. Post-licensing specification of eukaryotic replication origins by facilitated Mcm2-7 sliding along DNA. Mol. Cell 60, 797–807 (2015).
Promonet, A. et al. Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites. Nat. Commun. 11, 3940 (2020).
Brison, O. et al. Transcription-mediated organization of the replication initiation program across large genes sets common fragile sites genome-wide. Nat. Commun. 10, 5693 (2019).
Letessier, A. et al. Cell-type-specific replication initiation programs set fragility of the FRA3B fragile site. Nature 470, 120–123 (2011).
Le Tallec, B. et al. Common fragile site profiling in epithelial and erythroid cells reveals that most recurrent cancer deletions lie in fragile sites hosting large genes. Cell Rep. 4, 420–428 (2013).
Hamperl, S., Bocek, M. J., Saldivar, J. C., Swigut, T. & Cimprich, K. A. Transcription–replication conflict orientation modulates R-loop levels and activates distinct DNA damage responses. Cell 170, 774–786 (2017).
Manzo, S. G. et al. DNA topoisomerase I differentially modulates R-loops across the human genome. Genome Biol. 19, 100 (2018).
Park, K. et al. Aicardi–Goutières syndrome-associated gene SAMHD1 preserves genome integrity by preventing R-loop formation at transcription-replication conflict regions. PLoS Genet. 17, e1009523 (2021).
Bayona-Feliu, A., Barroso, S., Muñoz, S. & Aguilera, A. The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription-replication conflicts. Nat. Genet. 53, 1050–1063 (2021).
Andrianova, M. A., Bazykin, G. A., Nikolaev, S. I. & Seplyarskiy, V. B. Human mismatch repair system balances mutation rates between strands by removing more mismatches from the lagging strand. Genome Res. 27, 1336–1343 (2017).
Jaksik, R., Wheeler, D. A. & Kimmel, M. Detection and characterization of replication origins defined by DNA polymerase epsilon. Preprint at https://doi.org/10.1101/2021.07.27.453931 (2021).
Shi, M. J. et al. APOBEC-mediated mutagenesis as a likely cause of FGFR3 S249C mutation over-representation in bladder cancer. Eur. Urol. 76, 9–13 (2019).
DeWeerd, R. A. et al. Prospectively defined patterns of APOBEC3A mutagenesis are prevalent in human cancers. Cell Rep. 38, 110555 (2022).
Flasch, D. A. et al. Genome-wide de novo L1 retrotransposition connects endonuclease activity with replication. Cell 177, 837–851 (2019).
Sultana, T. et al. The landscape of L1 retrotransposons in the human genome is shaped by pre-insertion sequence biases and post-insertion selection. Mol. Cell 74, 555–570 (2019).
Ming, X. et al. Kinetics and mechanisms of mitotic inheritance of DNA methylation and their roles in aging-associated methylome deterioration. Cell Res. 30, 980–996 (2020).
Reijns, M. A. et al. Lagging-strand replication shapes the mutational landscape of the genome. Nature 518, 502–506 (2015).
Daigaku, Y. et al. A global profile of replicative polymerase usage. Nat. Struct. Mol. Biol. 22, 192–198 (2015).
Clausen, A. R. et al. Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation. Nat. Struct. Mol. Biol. 22, 185–191 (2015).
Koh, K. D., Balachander, S., Hesselberth, J. R. & Storici, F. Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA. Nat. Methods 12, 251–257 (2015).
Zhou, Z. X., Lujan, S. A., Burkholder, A. B., Garbacz, M. A. & Kunkel, T. A. Roles for DNA polymerase δ in initiating and terminating leading strand DNA replication. Nat. Commun. 10, 3992 (2019).
Koyanagi, E. et al. Global landscape of replicative DNA polymerase usage in the human genome. Nat. Commun. 13, 7221 (2022).
Pratto, F. et al. Meiotic recombination mirrors patterns of germline replication in mice and humans. Cell 184, 4251–4267 (2021).
Sriramachandran, A. M. et al. Genome-wide nucleotide-resolution mapping of DNA replication patterns, single-strand breaks, and lesions by GLOE-seq. Mol. Cell 78, 975–985 (2020).
Kara, N., Krueger, F., Rugg-Gunn, P. & Houseley, J., Genome-wide analysis of DNA replication and DNA double-strand breaks using TrAEL-seq. PLoS Biol. 19, e3000886 (2020).
Kit Leng Lui, S. et al. Monitoring genome-wide replication fork directionality by Okazaki fragment sequencing in mammalian cells. Nat. Protoc. 16, 1193–1218 (2021).
Audit, B. et al. Multiscale analysis of genome-wide replication timing profiles using a wavelet-based signal-processing algorithm. Nat. Protoc. 8, 98–110 (2013).
Muller, C. A. et al. Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads. Nat. Methods 16, 429–436 (2019).
Gansauge, M. T. et al. Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. Nucleic Acids Res. 45, e79 (2017).
Salic, A. & Mitchison, T. J. A chemical method for fast and sensitive detection of DNA synthesis in vivo. Proc. Natl Acad. Sci. USA 105, 2415–2420 (2008).
Burgers, P. M. J. & Kunkel, T. A. Eukaryotic DNA replication fork. Annu. Rev. Biochem. 86, 417–438 (2017).
DePamphilis, M. L. Genome Duplication (Garland Science/Taylor & Francis Group, 2010).
Qu, D. et al. 5-Ethynyl-2′-deoxycytidine as a new agent for DNA labeling: detection of proliferating cells. Anal. Biochem. 417, 112–121 (2011).
Ligasova, A. et al. Dr Jekyll and Mr Hyde: a strange case of 5-ethynyl-2′-deoxyuridine and 5-ethynyl-2′-deoxycytidine. Open Biol. 6, 150172 (2016).
Manska, S., Octaviano, R. & Rossetto, C. C. 5-Ethynyl-2′-deoxycytidine and 5-ethynyl-2′-deoxyuridine are differentially incorporated in cells infected with HSV-1, HCMV, and KSHV viruses. J. Biol. Chem. 295, 5871–5890 (2020).
Green, M. R. & Sambrook, J. Molecular Cloning: A Laboratory Manual. 4th edn (Cold Spring Harbor Laboratory Press, 2012).
Giacca, M., Pelizon, C. & Falaschi, A. Mapping replication origins by quantifying relative abundance of nascent DNA strands using competitive polymerase chain reaction. Methods 13, 301–312 (1997).
Tornøe, C. W.; Christensen, C.; Meldal, M. (2002).e, C. W., Christensen, C. & Meldal, M. Peptidotriazoles on solid phase: [1,2,3]-triazoles by regiospecific copper(I)-catalyzed 1,3-dipolar cycloadditions of terminal alkynes to azides. J. Org. Chem. 67, 3057–3064 (2002).
Rostovtsev, V. V., Green, L. G., Fokin, V. V. & Sharpless, K. B. A stepwise Huisgen cycloaddition process: copper(I)-catalyzed regioselective “ligation” of azides and terminal alkynes. Angew. Chem. Int. Ed. 41, 2596–2599 (2002).
Presolski, S. I., Hong, V. P. & Finn, M. G. Copper-catalyzed azide-alkyne click chemistry for bioconjugation. Curr. Protoc. Chem. Biol. 3, 153–162 (2011).
Kwok, C. K., Ding, Y., Sherlock, M. E., Assmann, S. M. & Bevilacqua, P. C. A hybridization-based approach for quantitative and low-bias single-stranded DNA ligation. Anal. Biochem. 435, 181–186 (2013).
Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012).
Ramírez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160–W165 (2016).
Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).
R Core Team. R: a language and environment for statistical computing, https://www.r-project.org/ (R Foundation for Statistical Computing, 2020).
Himmelmann, L. HMM: HMM-Hidden Markov Models. R package version 1.0. (2016).
Morgan, M., Pages, H., Obenchain, V., and Hayden, N. Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import. R package version 1.30.0. (2017).
Lawrence, M. et al. Software for computing and annotating genomic ranges. PLoS Comput. Biol. 9, e1003118 (2013).
RStudio Team. RStudio: Integrated Development for R, http://www.rstudio.com/ (RStudio, PBC, 2020).
Andrews, S. FastQC: a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc (2010).
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17, 10–12 (2011).
TrimGalore https://doi.org/10.5281/zenodo.5127899 (2021).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
Picard Toolkit. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/ (2019).

Genome-wide measurement of DNA replication fork directionality and quantification of DNA replication initiation and termination with Okazaki fragment sequencing

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