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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 gr.281532.125; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...programs from the same samples. It is based on the sample collection for cell cycle analysis under 82 conditions that preserve both nucleic acids. First, cells are labeled with the nucleotide analog BrdU 83 to label nascent DNA and enable downstream purification by immunoprecipitation; then, single-84 cell...
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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
...are incubated with BrdU, followed by nuclei isolation. GFP-positive nuclei are then sorted by DNA content, separating into one of four S-phase fractions: early, early-mid, late-mid, or late replicating. Next, the BrdU-containing DNA is immunoprecipitated and prepared for sequencing to identify genomic locations...
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Resource: DEAD box RNA helicases are pervasive protein kinase interactors and activators
- Alexander Hirth,
- Edoardo Fatti,
- Eugen Netz,
- Sergio P. Acebron,
- Dimitris Papageorgiou,
- Andrea Švorinić,
- Cristina-Maria Cruciat,
- Emil Karaulanov,
- Alexandr Gopanenko,
- Tianheng Zhu,
- Irmgard Sinning,
- Jeroen Krijgsveld,
- Oliver Kohlbacher,
- and Christof Niehrs
Genome Res. June 2024 34: 952-966; Published in Advance July 10, 2024, doi:10.1101/gr.278264.123
...-tagged DDX/DHX helicases were immunoprecipitated in triplicates and subjected to quantitative mass spectrometry to identify bound proteins. As a negative control, we used FLAG-tagged GFP.Combined analysis of the triplicates of all transfected proteins together including GFP and using a peptide and protein...
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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
..., in budding yeast, binding of Fkh1 and Fkh2 TFs near a class of replication origins is necessary for early replication, but this function is separable from its transcription activity (Ostrow et al. 2017). Moreover, recently discovered cis elements that are necessary for control of RT in pluripotent cells have...
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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...QTL for TENM2, we validated regulatory activity for a variant within a predicted driver element that is coordinately regulated with 39 other elements. At another locus, we validate a predicted enhancer of RALGPS2 using CRISPR interference and demonstrate allelic effects on transcription for a haplotype within...
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Research: Replication timing is regulated by the number of MCMs loaded at origins
- Shankar P. Das,
- Tyler Borrman,
- Victor W.T. Liu,
- Scott C.-H. Yang,
- John Bechhoefer,
- and Nicholas Rhind
Genome Res. December 2015 25: 1886-1892; Published in Advance September 10, 2015, doi:10.1101/gr.195305.115
...(Gindin et al. 2014). Moreover, a model that uses DNase I hypersensitive sites as a proxy for licensed origins, which are fired by a hypothetical rate limiting activator thatmoveswith replication forks, accurately predicts developmentally regulated replication timing. Importantly, themodel does...
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Research: E4F1 and ZNF148 are transcriptional activators of the −57A > C and wild-type TERT promoter
- Boon Haow Chua,
- Nurkaiyisah Zaal Anuar,
- Laure Ferry,
- Cecilia Domrane,
- Anna Wittek,
- Vineeth T. Mukundan,
- Sudhakar Jha,
- Falk Butter,
- Daniel G. Tenen,
- Pierre-Antoine Defossez,
- and Dennis Kappei
Genome Res. November 2023 33: 1893-1905; Published in Advance November 2, 2023, doi:10.1101/gr.277724.123
...) binding sites and result in activation of the TERT gene, allowing cancer cells to achieve replicative immortality. Here, we used a systematic proteomics screen to identify transcription factors preferentially binding to the −146C > T, −124C > T, and −57A > C mutations. Although we confirmed binding...
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Method: ATAC-STARR-seq reveals transcription factor–bound activators and silencers within chromatin-accessible regions of the human genome
- Tyler J. Hansen and
- Emily Hodges
Genome Res. August 2022 32: 1529-1541; Published in Advance July 20, 2022, doi:10.1101/gr.276766.122
...plasmid design and the expected outcomes for neutral, active, and silent regulatory elements. Each ATAC-STARR-seq plasmid within a library contains a truncated GFP (trGFP) coding sequence, a polyadenylation signal sequence, an origin of replication (Ori) (which moonlights as a minimal core promoter...
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Research: The asymmetric distribution of RNA polymerase II and nucleosomes on replicated daughter genomes is caused by differences in replication timing between the lagging and the leading strand
- Rahima Ziane,
- Alain Camasses,
- and Marta Radman-Livaja
Genome Res. February 2022 32: 337-356; Published in Advance January 18, 2022, doi:10.1101/gr.275387.121
...in parallel, with which we identified clusters of secondary origins surrounding known origins. We found a difference in the timing of lagging and leading strand replication on the order of minutes at most yeast genes. We propose a model in which the majority of old histones and RNA polymerase II (RNAPII) bind...
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Method: A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation
- René A.M. Dirks,
- Peter C. Thomas,
- Haoyu Wu,
- Robert C. Jones,
- Hendrik G. Stunnenberg,
- and Hendrik Marks
Genome Res. May 2021 31: 919-933; Published in Advance March 11, 2021, doi:10.1101/gr.260745.120
...A): Preparation including pipetting of the plate takes at maximum 20 min, whereas harvesting of the 24 DNA samples of the ChIP takes another 10 min of hands-on time. The hands-free parallelized immunoprecipitation process that is performed on the bead columns takes ∼ 4.5 h (Supplemental Fig. S5...

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