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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: An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride
- Inswasti Cahyani,
- John Tyson,
- Nadine Holmes,
- Josh Quick,
- Chris Moore,
- Nick Loman,
- and Matthew Loose
Genome Res. May 2025 35: 1154-1166; Published in Advance March 24, 2025, doi:10.1101/gr.279943.124
...to 5–6 µg of UHMW DNA for a 3.2 Gb (Table 3). We used this ratio for all GM12878 (Figs. 2⇑⇑–5) and HEK293 (Fig. 6) runs. Additionally, we tested different FRA to DNA ratios in Mongolian gerbil, tick Amblyomma variegatum, and yeast Saccharomyces cerevisiae (Table 3). These ratios produced UL sequencing...
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Research: Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin
- Hossein Salari,
- Marco Di Stefano,
- and Daniel Jost
Genome Res. January 2022 32: 28-43; Published in Advance December 28, 2021, doi:10.1101/gr.275827.121
...fundamental processes such as gene transcription and DNA repair. Experiments unveiled that chromatin motion is highly heterogeneous inside cell nuclei, ranging from a liquid-like, mobile state to a gel-like, rigid regime. Using polymer modeling, we investigate how these different physical states and dynamical...
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Research: Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation
- Răzvan V. Chereji,
- Peter R. Eriksson,
- Josefina Ocampo,
- Hemant K. Prajapati,
- and David J. Clark
Genome Res. December 2019 29: 1985-1995; Published in Advance September 11, 2019, doi:10.1101/gr.249326.119
...step is necessary because the AluI digest contains many long DNA fragments derived from protected chromatin, which are not suitable for Illumina sequencing.AluI cuts the sequence AG|CT to yield blunt ends. The yeast has approximately 40,000 AluI sites; the mouse has approximately 12.6 million sites...
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Research: Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast
- Gregory T. Booth,
- Isabel X. Wang,
- Vivian G. Cheung,
- and John T. Lis
Genome Res. June 2016 26: 799-811; Published in Advance May 12, 2016, doi:10.1101/gr.204578.116
...at the level of transcription.Unlike most well-studied metazoans, budding yeast displays a relatively uniform distribution of elongating Pol II across transcription units (Steinmetz et al. 2006). The lack of significant barriers to elongation in S. cerevisiae supports a model in which Pol II recruitment...
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Research: Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus
- Nikolaos Vakirlis,
- Véronique Sarilar,
- Guénola Drillon,
- Aubin Fleiss,
- Nicolas Agier,
- Jean-Philippe Meyniel,
- Lou Blanpain,
- Alessandra Carbone,
- Hugo Devillers,
- Kenny Dubois,
- Alexandre Gillet-Markowska,
- Stéphane Graziani,
- Nguyen Huu-Vang,
- Marion Poirel,
- Cyrielle Reisser,
- Jonathan Schott,
- Joseph Schacherer,
- Ingrid Lafontaine,
- Bertrand Llorente,
- Cécile Neuvéglise,
- and Gilles Fischer
Genome Res. July 2016 26: 918-932; Published in Advance May 31, 2016, doi:10.1101/gr.204420.116
...Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus Nikolaos Vakirlis 1 , 6 , Véronique Sarilar 2 , 6 , Guénola Drillon 1 , 6 , Aubin Fleiss 1 , Nicolas Agier...
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LETTER: Assessment of Compositional Heterogeneity Within and Between Eukaryotic Genomes
- Anton Nekrutenko and
- Wen-Hsiung Li
Genome Res. December 1, 2000 10: 1986-1995; doi:10.1101/gr.153400
...heterogeneity within, and uniformity between, DNA sequences of yeast chromosomes. Genome Res. 8 : 916 – 928 . ↵ Macaya G. , Thiery J.-P. , Bernardi G. ( 1976 ) An approach to the organization of eukaryotic s at a macromolecular level. J. Mol. Biol. 108 : 237 – 254 . ↵ Ostashevsky J. ( 1998 ) A plymer model...
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Method: Double insertion of transposable elements provides a substrate for the evolution of satellite DNA
- Michael P. McGurk and
- Daniel A. Barbash
Genome Res. May 2018 28: 714-725; Published in Advance March 27, 2018, doi:10.1101/gr.231472.117
...or Y heterochromatin based on the presence of rDNA and R-elements (Palazzo et al. 2016). We identify both expected junctions between Bari1 and Stalker4 in the all-female GDL sequences (Supplemental Table S4), indicating that it cannot reside on the Y Chromosome. Previous analyses identified the Bari1...
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Research: Global genome nucleotide excision repair is organized into domains that promote efficient DNA repair in chromatin
- Shirong Yu,
- Katie Evans,
- Patrick van Eijk,
- Mark Bennett,
- Richard M. Webster,
- Matthew Leadbitter,
- Yumin Teng,
- Raymond Waters,
- Stephen P. Jackson,
- and Simon H. Reed
Genome Res. October 2016 26: 1376-1387; Published in Advance July 28, 2016, doi:10.1101/gr.209106.116
...composite plots of relative DNA repair rates, including DNA sequences up to 2 kbp upstream and downstream. This represents ∼85% of the yeast . It is important to note that the profile-plotting function in Sandcastle ensures that no region of the is represented more than once in these plots. This feature...
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Research: RSC-dependent constructive and destructive interference between opposing arrays of phased nucleosomes in yeast
- Dwaipayan Ganguli,
- Răzvan V. Chereji,
- James R. Iben,
- Hope A. Cole,
- and David J. Clark
Genome Res. October 2014 24: 1637-1649; Published in Advance July 11, 2014, doi:10.1101/gr.177014.114
...; Hota and Bartholomew 2011; Narlikar et al. 2013). Genome-wide studies of nucleosomal DNA isolated from cells by digestion with micrococcal nuclease (MNase) and analyzed using tiling microarrays or massively parallel sequencing have revealed that most yeast genes have a nucleosome-depleted region (NDR...

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