Repliscan: a tool for classifying replication timing regions

Zynda, Gregory J; Song, Jawon; Concia, Lorenzo; Wear, Emily E.; Hanley‐Bowdoin, Linda; Thompson, William F.; Vaughn, Matthew

doi:10.1101/094177

Cited by 7 publications

(16 citation statements)

References 28 publications

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“…Data were then analyzed as described by Zynda et al (2017). The scripts can be found at 732 https://github.com/zyndagj/repliscan.…”

Section: Genomic Dna Extraction and Immunoprecipitation Of Edu/af488-mentioning

confidence: 99%

“…The method used to assign a predominant time of replication to each 1-kb bin across the 746 genome is described by Zynda et al (2017). Each bin was classified as replicating at a given time 747 point if its normalized replication intensity was above a chromosome-specific threshold value, as 748 calculated by the following procedure.…”

Section: Classifying Predominant Replication Time 745mentioning

confidence: 99%

“…Arabidopsis genome, we used the Repliscan pipeline (Zynda et al, 2017) to assign a 516 predominant replication time based on the relative intensity of normalized signal in all three time 517…”

mentioning

confidence: 99%

“…Replication profiles were created using the Repliscan pipeline (Zynda et al, 2017). Read 164 counts were averaged over non-overlapping 1-kb bins, and the total number of reads per sample 165 (sequencing depth) was normalized to 1X genome coverage using the RPGC method (Ramírez et 166 al., 2016).…”

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confidence: 99%

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Genome-Wide Analysis of the Arabidopsis Replication Timing Program

et al. 2018

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33Eukaryotes use a temporally regulated process, known as the replication timing program, to 34 ensure that their genomes are fully and accurately duplicated during S phase. Replication timing 35 programs are predictive of genomic features and activity, and considered to be functional 36 readouts of chromatin organization. Although replication timing programs have been described 37 for yeast and animal systems, much less is known about the temporal regulation of plant DNA 38 replication or its relationship to genome sequence and chromatin structure. We used the 39 thymidine analog, 5-ethynyl-2'-deoxyuridine, in combination with flow sorting and Repli-Seq to 40 describe, at high-resolution, the genome-wide replication timing program for Arabidopsis 41 thaliana Col-0 suspension cells. We identified genomic regions that replicate predominantly 42 during early, mid and late S phase, and correlated these regions with genomic features and with 43 data for chromatin state, accessibility and long-distance interaction.

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“…Data were then analyzed as described by Zynda et al (2017). The scripts can be found at 732 https://github.com/zyndagj/repliscan.…”

Section: Genomic Dna Extraction and Immunoprecipitation Of Edu/af488-mentioning

confidence: 99%

Section: Classifying Predominant Replication Time 745mentioning

confidence: 99%

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confidence: 99%

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Genome-Wide Analysis of the Arabidopsis Replication Timing Program

et al. 2018

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“…We generated a profile of the replication activity in each S-phase stage across the genome using a custom computational pipeline called Repliscan described in detail by Zynda et al (2017). The read densities were aggregated into 1-kb windows, and after observing a strong Pearson correlation of 0.8 to 0.98 between the biological replicates (Supplemental Figure 2), the reads in each window of the replicates were summed ( Figure 1F).…”

Section: Whole-genome Profiling Of Dna Replication Timing In Maize Romentioning

confidence: 99%

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

Wear

Song²,

Zynda³

et al. 2017

Plant Cell

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All plants and animals must replicate their DNA, using a regulated process to ensure that their genomes are completely and accurately replicated. DNA replication timing programs have been extensively studied in yeast and animal systems, but much less is known about the replication programs of plants. We report a novel adaptation of the "Repli-seq" assay for use in intact root tips of maize (Zea mays) that includes several different cell lineages and present whole-genome replication timing profiles from cells in early, mid, and late S phase of the mitotic cell cycle. Maize root tips have a complex replication timing program, including regions of distinct early, mid, and late S replication that each constitute between 20 and 24% of the genome, as well as other loci corresponding to ;32% of the genome that exhibit replication activity in two different time windows. Analyses of genomic, transcriptional, and chromatin features of the euchromatic portion of the maize genome provide evidence for a gradient of early replicating, open chromatin that transitions gradually to less open and less transcriptionally active chromatin replicating in mid S phase. Our genomic level analysis also demonstrated that the centromere core replicates in mid S, before heavily compacted classical heterochromatin, including pericentromeres and knobs, which replicate during late S phase.

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LSD1 is required for euchromatic origin firing and replication timing

Wang

Huang

Cheng

et al. 2022

Sig Transduct Target Ther

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The chromatin-based rule governing the selection and activation of replication origins remains to be elucidated. It is believed that DNA replication initiates from open chromatin domains; thus, replication origins reside in open and active chromatin. However, we report here that lysine-specific demethylase 1 (LSD1), which biochemically catalyzes H3K4me1/2 demethylation favoring chromatin condensation, interacts with the DNA replication machinery in human cells. We find that LSD1 level peaks in early S phase, when it is required for DNA replication by facilitating origin firing in euchromatic regions. Indeed, euchromatic zones enriched in H3K4me2 are the preferred sites for the pre-replicative complex (pre-RC) binding. Remarkably, LSD1 deficiency leads to a genome-wide switch of replication from early to late. We show that LSD1-engaged DNA replication is mechanistically linked to the loading of TopBP1-Interacting Checkpoint and Replication Regulator (TICRR) onto the pre-RC and subsequent recruitment of CDC45 during origin firing. Together, these results reveal an unexpected role for LSD1 in euchromatic origin firing and replication timing, highlighting the importance of epigenetic regulation in the activation of replication origins. As selective inhibitors of LSD1 are being exploited as potential cancer therapeutics, our study supports the importance of leveraging an appropriate level of LSD1 to curb the side effects of anti-LSD1 therapy.

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Repliscan: a tool for classifying replication timing regions

Cited by 7 publications

References 28 publications

Genome-Wide Analysis of the Arabidopsis Replication Timing Program

Genome-Wide Analysis of the Arabidopsis Replication Timing Program

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

LSD1 is required for euchromatic origin firing and replication timing

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