Searching journal content for articles similar to Liu et al. 25 (8): 1182.

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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
...correlated with gene expression, we further explored connections among features to determine any additional relationships (Supplemental Fig. S11). Nucleosome occupancy within the start of the gene body (+1/+2/+3 positions) was correlated with nucleosome occupancy changes near the PAS (R = 0.46), which...
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Research: GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency in Paramecium
- Stefano Gnan,
- Mélody Matelot,
- Marion Weiman,
- Olivier Arnaiz,
- Frédéric Guérin,
- Linda Sperling,
- Mireille Bétermier,
- Claude Thermes,
- Chun-Long Chen,
- and Sandra Duharcourt
Genome Res. April 2022 32: 699-709; Published in Advance March 9, 2022, doi:10.1101/gr.276125.121
...been proposed that chromatin structure might influence splice site recognition. To investigate the roles of nucleosome positioning in intron recognition, we determined the nucleosome occupancy along the P. tetraurelia . We show that P. tetraurelia displays a regular nucleosome array with a nucleosome...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...relevance, integrating the origin of DNA and protein elements (cis and trans) to evaluate false-positive and false-negative risks across experimental systems. Moreover, we explore how perturbation strategies—gain and loss of function—can complement steady-state profiling to establish causality in gene...
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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...the positions with the highest read density, wave fronts reflect the distance traveled by the earliest RNAPII molecules released into productive elongation after DRB removal (Supplemental Fig. S1C). Therefore, wave fronts provide more accurate measurement of RNAPII elongation rates of individual genes. Moreover...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...). In the majority of eukaryotes, the key determinant for the site of kinetochore assembly is an epigenetic mark: the presence of at least one nucleosome containing a centromere-specific variant of histone 3, called CENH3 in plants and CENPA (also known as CENP-A) in mammals (Fig. 1A; Earnshaw and Rothfield 1985...
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Research: Regulation of nucleosome positioning by a CHD Type III chromatin remodeler and its relationship to developmental gene expression in Dictyostelium
- James L. Platt,
- Nicholas A. Kent,
- Alan R. Kimmel,
- and Adrian J. Harwood
Genome Res. April 2017 27: 591-600; Published in Advance March 22, 2017, doi:10.1101/gr.216309.116
...-stage mutant phenotypes via transcriptional changes. Although these data indicate that ChdC is required for developmental regulation of both nucleosome positioning (Fig. 4) and gene expression (Fig. 7; Supplemental Fig. S9), we wished to determine if these processes were functionally coupled. We examined...
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Method: Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay
- Jennifer Hammelman,
- Konstantin Krismer,
- Budhaditya Banerjee,
- David K. Gifford,
- and Richard I. Sherwood
Genome Res. October 2020 30: 1468-1480; Published in Advance September 24, 2020, doi:10.1101/gr.263228.120
...cells (Soenmezer et al. 2020), and recently, adenine methyltransferase has been used to map nucleosome positioning in human cell lines (Abdulhay et al. 2020; Stergachis et al. 2020). Here, we aim to develop an assay that takes advantage of adenine methyltransferase and restriction enzyme digestion...
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Research: Parent-of-origin-dependent nucleosome organization correlates with genomic imprinting in maize
- Xiaomei Dong,
- Jian Chen,
- Tong Li,
- En Li,
- Xiangbo Zhang,
- Mei Zhang,
- Weibin Song,
- Haiming Zhao,
- and Jinsheng Lai
Genome Res. July 2018 28: 1020-1028; Published in Advance June 14, 2018, doi:10.1101/gr.230201.117
...in Arabidopsis. Plant J 78: 706–714. ↵Liu MJ, Seddon AE, Tsai ZT, Major IT, Floer M, Howe GA, Shiu SH. 2015. Determinants of nucleosome positioning and their influence on plant gene expression. Genome Res 25: 1182–1195. ↵Lu F, Liu Y, Inoue A, Suzuki T, Zhao K, Zhang Y. 2016. Establishing chromatin regulatory...
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Research: Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans
- Tess E. Jeffers and
- Jason D. Lieb
Genome Res. January 2017 27: 75-86; Published in Advance November 14, 2016, doi:10.1101/gr.208173.116
...structural and regulatory functions in organizing the and restricting access of regulatory factors to the DNA sequence (Henikoff 2008). As such, the interactions between nucleosomes and DNA strongly influence the regulation of gene expression by determining DNA accessibility for transcription factors (TFs...
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Research: Independent evolution of transcript abundance and gene regulatory dynamics
- Gat Krieger,
- Offir Lupo,
- Avraham A. Levy,
- and Naama Barkai
Genome Res. July 2020 30: 1000-1011; Published in Advance July 22, 2020, doi:10.1101/gr.261537.120
...their cellular response. Therefore, expression levels measured at one condition provide limited information about expression levels at other conditions. Furthermore, determinants of expression level are often different from determinants of dynamic gene regulation. The former depends on the efficiency...

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