Searching journal content for articles similar to Rodriguez et al. 27 (2): 269.

Displaying results 1-10 of 165

For checked items

view abstracts
download to citation manager

Select this article
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
...@cs.duke.eduAbstractEpigenetic mechanisms contribute to gene regulation by altering chromatin accessibility through changes in transcription factor (TF) and nucleosome occupancy across the . Despite numerous studies focusing on changes in gene expression, the intricate chromatin-mediated regulatory code remains largely uncharted...
Select this article
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
..., and four origin recognition complex (ORC) components are all enriched in GSC-like cells compared with CySC-like cells (Table 1).View this table: In this window In a new window Table 1. Composition and function of select DNA replication and chromatin regulation complexesTo control for potential biases...
OPEN ACCESS ARTICLE
Select this article
Research: Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy
- Hadi Rahmaninejad,
- Yao Xiao,
- Maxime M.C. Tortora,
- and Geoffrey Fudenberg
Genome Res. August 2025 35: 1745-1757; Published in Advance July 8, 2025, doi:10.1101/gr.280108.124
...by acting as a barrier to loop extrusion by the cohesin complex (Fudenberg et al. 2017; van Ruiten and Rowland 2021). During loop extrusion, cohesin binds to chromatin and acts as a motor to progressively create larger chromatin loops until it dissociates. Cohesin accessory proteins modulate parameters...
OPEN ACCESS ARTICLE
Select this article
Method: Size-based expectation maximization for characterizing nucleosome positions and subtypes
- Jianyu Yang,
- Kuangyu Yen,
- and Shaun Mahony
Genome Res. September 2024 34: 1334-1343; Published in Advance June 17, 2024, doi:10.1101/gr.279138.124
...is then (3) We incorporate several biological assumptions in the form of priors on the parameters. We place a sparseness-promoting negative Dirichlet prior α on the nucleosome-weighted occupancy π, based on the assumption that each nucleosome should have sufficient numbers of assigned fragments to support...
Select this article
Research: Nucleosome repositioning in chronic lymphocytic leukemia
- Kristan V. Piroeva,
- Charlotte McDonald,
- Charalampos Xanthopoulos,
- Chelsea Fox,
- Christopher T. Clarkson,
- Jan-Philipp Mallm,
- Yevhen Vainshtein,
- Luminita Ruje,
- Lara C. Klett,
- Stephan Stilgenbauer,
- Daniel Mertens,
- Efterpi Kostareli,
- Karsten Rippe,
- and Vladimir B. Teif
Genome Res. October 2023 33: 1649-1661; Published in Advance September 12, 2023, doi:10.1101/gr.277298.122
...NBCs. The violin plots correspond to the distribution based on three ChIP-seq replicates. Fisher's test, P < 10 × 10−3 for all points.Nucleosome relocation correlates with chromatin remodeling activityTo characterize regions with increased or decreased nucleosome occupancy in CLL in further detail, we...
OPEN ACCESS ARTICLE
Select this article
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
.... A schematic model describing the main findings: Rtt109-dependent acetylation of K56 stabilizes nucleosomes behind the replication fork, whereas acetylation of K9 promotes nucleosome replacement ahead of the fork. See Discussion.DiscussionThe packaging of eukaryotic s within chromatin poses a major obstacle...
Select this article
Research: Linking the dynamics of chromatin occupancy and transcription with predictive models
- Trung Q. Tran,
- Heather K. MacAlpine,
- Vinay Tripuraneni,
- Sneha Mitra,
- David M. MacAlpine,
- and Alexander J. Hartemink
Genome Res. June 2021 31: 1035-1046; Published in Advance April 23, 2021, doi:10.1101/gr.267237.120
...digestion. Digestion by a nuclease, such as micrococcal nuclease (MNase), provides a complementary perspective to understanding chromatin occupancy by probing accessibility at base-pair precision. Recent -wide mapping studies have used nucleosome-sized MNase-seq fragments to characterize the dynamics...
Select this article
Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
- Samuel H. Kim,
- Georgi K. Marinov,
- and William J. Greenleaf
Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
...-ATAC to continue to derive useful insights into chromatin organization and transcriptional regulation in other contexts in the future.Active cis-regulatory elements in most eukaryotes are usually characterized by low levels of nucleosome occupancy, a unique property first appreciated more than four decades ago (Wu...
Select this article
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
..., DNA is wrapped around histone octamers to form nucleosomes, the basic building blocks of the chromatin structure. This packing presents a unified platform for regulating processes that require DNA accessibility (Gossett and Lieb 2012), including gene transcription and DNA replication (Bannister...
Select this article
Research: The chromatin environment shapes DNA replication origin organization and defines origin classes
- Christelle Cayrou,
- Benoit Ballester,
- Isabelle Peiffer,
- Romain Fenouil,
- Philippe Coulombe,
- Jean-Christophe Andrau,
- Jacques van Helden,
- and Marcel Méchali
Genome Res. December 2015 25: 1873-1885; Published in Advance November 11, 2015, doi:10.1101/gr.192799.115
...is positioned at the replication start and is surrounded by a NDR of ∼200 bp. This is in agreement with results based on the computational prediction of nucleosome occupancy at origins (Cayrou et al. 2012a) and with the MNase-seq results at six mammalian origins (Lombraña et al. 2013). The positioned nucleosome...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Rodriguez et al. 27 (2): 269.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: