Table 3. Origin mapping methods.

Table and figure motifs show many methods to map origins of DNA replication in cell populations and in single cells or molecules⁹⁶.

Method	Description	Cite	Comments	Illustration
2D gel assays and fork direction analysis	Uses distinct gel migration patterns to characterize replication intermediates and detect origin firing efficiency	Brewer and Fangman117 Huberman et al., 118	Pooled data using population cells
Density transfer	Uses density isotypes to distinguish newly synthesized DNA form parental DNA followed by DNA sequencing and quantitative copy number profiling to map general patterns of replication timing	Gilbert,84; Pope et al., 14; Rhind and Gilbert6.
ChlP-seq (chromatin immunoprecipitation followed by DNA sequencing)	Identify locations of ORC and MCM binding sites to predict the location of replication origins	Belsky et al., 256; Long et al., 214; Lucas and Raghuraman,257; MacAlpine et al190,258
Bubble-seq	Trap replication bubbles and sequence DNA	Mesner et al., 259
Ini-seq (initiation site sequencing)	Label nascent DNA with DNA analogs and either immuno-precipitate the labeled nascent DNA or separate the labeled nascent DNA from unreplicated DNA using density difference	Guilbaud et al., 107; Langley et al., 260.
OK-seq (Okazaki-fragment sequencing)	Isolate and sequence Okazaki fragments to map replication fork direction in asynchronous population of cells	Petryk et al., 82.
Repli-seq	Label nascent DNA with BrdU; look for the enrichment of BrdU-immunoprecipitated DNA in late S phase cells compared to early S phase cells	Zhao et al., 158.
SNS-seq (Short Nascent Strand-sequencing)	Identify nascent RNA-primed DNA synthesized at origins by the primase DNA polymerase a (Pol a)	Besnard et al., 261; Cadoret et al., 157; Cayrou et al., 262; Picard et al., 263
S-jump based computational origin prediction	S-jump based method which computes the excess G over C and T over A along one DNA strand where abrupt changes correlate with the location of replication origins (N-domains and U-shaped domains of skew jumps), however the location of actual origins needs experimental validation	Brodie et al., 264.	Computational prediction data using population cells
Electron microscopy and fiber autoradiography	Visually observation of replication origins on radiolabeled DNA		Single molecule data using population cells
DNA combing	Fluorescently label nascent DNA. DNA molecules stretched and aligned along a slide and visualized by various fluorescence microscopy techniques	Bensimon et al., 265; Michalet et al., 266; Pasero et al.267.
DNAscent; FORK-seq etc.	Nanopore sequencing based methods that detect DNA analog labeled nascent DxwNA	Hennion et al., 268; Muller et al., 269; Georgieva et al., 270; Boemo271
ORM (optical replication mapping)	Fluorescent nucleotide analog pulse-labeled nascent DNA in combination with the optical mapping method (Bionano Genomics) to map long individual DNA molecules	Wang et al., 109
scRepli-seq	Uses a commercial whole genome amplification kit, SeqPlex from Sigma, to prepare sequencing libraries	Miura et al., 272; Takahashi et al., 273.	Single cell data
LIANTI (Linear Amplification via Transposon Insertion)	Combines the T7 in vitro transcription to the Tn5 transposition to avoid the intrinsic limitations of Tn5 transposition being symmetric and reduce biases and errors during the amplification steps	Chen et al., 274
DLP (direct library preparation)	Uses nanoliter-volume reactions to adapt the conventional transposase-based library construction to single cells	Laks et al., 275; Zahn et al., 276.