Searching journal content for articles similar to Lubelsky et al. 24 (7): 1102.

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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
...-translational modifications, play a crucial role in regulating programs integral to a cell's identity, like gene expression and DNA replication. However, the transcriptional, chromatin, and replication timing profiles of adult stem cells in vivo remain poorly understood. Containing germline stem cells (GSCs) and somatic cyst...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...of the complex relationship between chromatin organization and transcription.Every eukaryotic encodes the information necessary for cellular viability and growth. Although the underlying instructions embedded in the DNA are identical among the cells of an organism, complex regulatory mechanisms transform...
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Research: Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins
- Joana Sequeira-Mendes,
- Zaida Vergara,
- Ramon Peiró,
- Jordi Morata,
- Irene Aragüez,
- Celina Costas,
- Raul Mendez-Giraldez,
- Josep M. Casacuberta,
- Ugo Bastolla,
- and Crisanto Gutierrez
Genome Res. May 2019 29: 784-797; Published in Advance March 7, 2019, doi:10.1101/gr.240986.118
...). The association of pre-replication complexes (pre-RCs) with DNA specifies the genomic sites that can potentially act as ORIs. Some clues on the contribution of DNA sequence, chromatin marks, transcription factor binding sites, and GC content to ORI activity have been obtained (Méchali 2010; Costas et al. 2011...
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Research: Chromatin conformation and transcriptional activity are permissive regulators of DNA replication initiation in Drosophila
- Robin L. Armstrong,
- Taylor J.R. Penke,
- Brian D. Strahl,
- A. Gregory Matera,
- Daniel J. McKay,
- David M. MacAlpine,
- and Robert J. Duronio
Genome Res. November 2018 28: 1688-1700; Published in Advance October 2, 2018, doi:10.1101/gr.239913.118
...replication.Our data thus far indicate that increased chromatin accessibility and gene expression act upstream of advanced replication within pericentric heterochromatin in H3K9R mutants (Fig. 4D; Supplemental File S3). To further understand the relationship between transcription and DNA replication within...
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Method: Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes
- Deepani W. Poramba-Liyanage,
- Tessy Korthout,
- Christine E. Cucinotta,
- Ila van Kruijsbergen,
- Tibor van Welsem,
- Dris El Atmioui,
- Huib Ovaa,
- Toshio Tsukiyama,
- and Fred van Leeuwen
Genome Res. April 2020 30: 635-646; Published in Advance March 18, 2020, doi:10.1101/gr.256255.119
...to implement gene regulatory programs and ensure the expression of a subset of genes in agreement with the state and environmental cues of the cell. RNA polymerase II (Pol II) is an integral part of this assembly as it catalyzes the DNA-dependent synthesis of messenger RNA (mRNA). Regulation of Pol II occurs...
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Research: Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)
- Pengfei Lv,
- Xingzhuo Yang,
- Xianguo Zhao,
- Zhangwu Zhao,
- and Juan Du
Genome Res. May 2024 34: 725-739; Published in Advance June 12, 2024, doi:10.1101/gr.278661.123
...specifically enriched for H3K27me3 modification changes. DNA methylation changes were specifically associated with basal transcriptional factors, the Notch signaling pathway, and the spliceosome. Notably, the polycomb repressive complex was enriched for both H3K27me3 and H3K9me3 modification changes, whereas...
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Research: Dynamic DNA N⁶-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus
- Yongqiang Liu,
- Junhua Niu,
- Fei Ye,
- Therese Solberg,
- Borong Lu,
- Chundi Wang,
- Mariusz Nowacki,
- and Shan Gao
Genome Res. February 2024 34: 256-271; Published in Advance March 12, 2024, doi:10.1101/gr.278796.123
...that 6mA, a mark of active transcription, is involved in altering the expression of encystment-related genes through changes in 6mA levels and 6mA symmetric-to-asymmetric conversion. Most importantly, we show that reducing 6mA levels by knocking down the DNA 6mA methyltransferase PpAMT1 accelerates cyst...
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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
...ascribe functional roles to H3K56ac, showing that it promotes CAF-1-dependent chromatin assembly at the wake of the fork, reduces genomic instabilities, and ensures expression homeostasis by suppressing transcription from replicated DNA (Voichek et al. 2016b). Here, we reveal, for the first time, a role...
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Research: Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape
- J. Gray Camp,
- Christopher L. Frank,
- Colin R. Lickwar,
- Harendra Guturu,
- Tomas Rube,
- Aaron M. Wenger,
- Jenny Chen,
- Gill Bejerano,
- Gregory E. Crawford,
- and John F. Rawls
Genome Res. September 2014 24: 1504-1516; Published in Advance June 24, 2014, doi:10.1101/gr.165845.113
...coordinate interactions between transcription factors (TFs) and cis-regulatory DNA. Cis-regulatory regions (CRRs) harbor binding sites for multiple activating or repressing TFs and can be 2014 Camp et al. This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months...
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Research: Chromatin signatures of the Drosophila replication program
- Matthew L. Eaton,
- Joseph A. Prinz,
- Heather K. MacAlpine,
- George Tretyakov,
- Peter V. Kharchenko,
- and David M. MacAlpine
Genome Res. February 2011 21: 164-174; Published in Advance December 22, 2010, doi:10.1101/gr.116038.110
...factors, nucleosome positioning, and DNA accessibility that provide for the remarkable plasticity in gene expression derived from the . It is becoming increasingly clear that the replication program responds to many of the same epigenetic cues that regulate the transcription program. For example, X...
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