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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. March 19, 2026 ; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
....5× coverage each) and compared the CNVs detected in PARTAGE to those identified in the ENCODE reference (Fig. 4A). Across the three PARTAGE replicates, we recovered between 92% and 100% of the ENCODE CNV events (Fig. 4B). The statistical significance of the overlap between ENCODE and PARTAGE CNVs was assessed...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells Jennifer A. Urban1, Daniel Ringwalt1, John M. Urban2,3, Wingel Xue1,5, Ryan Gleason1, Keji Zhao4 and Xin Chen1,2 1Department of Biology, The Johns Hopkins University...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
..., and the complete training protocol, enabling exact replication of the model architectures and experimental results.Feature encoding schemesMore than 24 common feature encoding schemes are widely used in epigenetic site prediction. In the work of EpiTEAmDNA, Li et al. (2023) demonstrated that 10 feature encoding...
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Research: Rtt109 promotes nucleosome replacement ahead of the replication fork
- Felix Jonas,
- Gilad Yaakov,
- and Naama Barkai
Genome Res. June 2022 32: 1089-1098; Published in Advance May 24, 2022, doi:10.1101/gr.276674.122
...cells undergoing slow synchronous replication in nucleotide-limiting conditions. We find that new histones are incorporated not only behind, but also ahead of the replication fork. We provide evidence that Rtt109, the S-phase-induced acetyltransferase, stabilizes nucleosomes behind the fork but promotes...
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Research: Rtt109 slows replication speed by histone N-terminal acetylation
- Nelly Frenkel,
- Felix Jonas,
- Miri Carmi,
- Gilad Yaakov,
- and Naama Barkai
Genome Res. March 2021 31: 426-435; Published in Advance February 9, 2021, doi:10.1101/gr.266510.120
...increases following deletion of RTT109, the gene encoding the enzyme required for the prereplication H3 acetylation wave. By using histone H3 mutants, we find that Rtt109-dependent N-terminal acetylation regulates fork velocity, whereas K56 acetylation contributes to replication dynamics only when N...
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Research: Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans
- Maude Strobino,
- Joanna M. Wenda,
- Laura Padayachy,
- and Florian A. Steiner
Genome Res. December 2020 30: 1740-1751; Published in Advance November 10, 2020, doi:10.1101/gr.260794.120
...the Repli-seq protocol. Instead of analyzing asynchronous cell populations, we used hydroxyurea (HU) to synchronize cells. Upon HU treatment, most cells are arrested at the entry of the S phase, and a large part of the cell population proceeds with DNA replication upon removal of HU (Supplemental Fig. S2...
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Research: Delayed DNA replication in haploid human embryonic stem cells
- Matthew M. Edwards,
- Michael V. Zuccaro,
- Ido Sagi,
- Qiliang Ding,
- Dan Vershkov,
- Nissim Benvenisty,
- Dieter Egli,
- and Amnon Koren
Genome Res. December 2021 31: 2155-2169; Published in Advance November 22, 2021, doi:10.1101/gr.275953.121
...-linked genes are possible candidates for mediating autosomal replication timing delays. For instance, ELK1 encodes an X-linked transcription factor primarily expressed in placenta and ovarian tissue (Uhlén et al. 2015) that was shown to cause transcriptional changes of autosomal genes in reactivated-X ESCs...
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Research: Replication timing networks reveal a link between transcription regulatory circuits and replication timing control
- Juan Carlos Rivera-Mulia,
- Sebo Kim,
- Haitham Gabr,
- Abhijit Chakraborty,
- Ferhat Ay,
- Tamer Kahveci,
- and David M. Gilbert
Genome Res. September 2019 29: 1415-1428; Published in Advance August 21, 2019, doi:10.1101/gr.247049.118
...State University, Tallahassee, Florida, 32306-4295, USA; 6Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, Florida 32306, USA Corresponding authors: gilbert@bio.fsu.edu, tamer@cise.ufl.eduAbstractDNA replication occurs in a defined temporal order known...
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Research: Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork
- Mónica P. Gutiérrez,
- Heather K. MacAlpine,
- and David M. MacAlpine
Genome Res. July 2019 29: 1123-1133; Published in Advance June 19, 2019, doi:10.1101/gr.243386.118
...Corresponding author: david.macalpine@duke.eduAbstractProper regulation and maintenance of the epi is necessary to preserve function. However, in every cell division, the epigenetic state is disassembled and then reassembled in the wake of the DNA replication fork. Chromatin restoration on nascent DNA...
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Research: Chromatin dynamics during DNA replication
- Raz Bar-Ziv,
- Yoav Voichek,
- and Naama Barkai
Genome Res. September 2016 26: 1245-1256; Published in Advance May 25, 2016, doi:10.1101/gr.201244.115
...in signal from earlier replicating loci (see Supplemental Note S1). All signals are log2-transformed, normalized by the signal in synchronized culture, and adjusted to show the same dynamic range. (B,C) Delayed post-replication recovery. Correlations were measured between changes in modification levels...

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