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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
...factors bind directly to the DNA to activate or repress transcription (Marr et al. 2021; Minnoye et al. 2021). Recent advances in sequencing technology have enabled the characterization of chromatin remodelers, nucleosome positioning, and chromatin accessibility using high-throughput assays like Ch...
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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
...in promoters but also in distal regulatory regions. Additional analyses reveal their colocalization with the chromatin remodelers CHD6, CHD8, and EP400. In summary, SEM provides an effective platform for exploration of nonstandard nucleosome subtypes.The nucleosome is the basic packaging unit of chromatin...
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Research: Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network
- Shelley Reich,
- Tobias Loschko,
- Julie Jung,
- Samantha Nestel,
- Ralf J. Sommer,
- and Michael S. Werner
Genome Res. July 2025 35: 1560-1573; Published in Advance June 9, 2025, doi:10.1101/gr.279783.124
...expectations for when differential gene expression should matter. Here, we collated existing data into a gene-regulatory network (GRN) and performed developmental transcriptomics across different environmental conditions, genetic backgrounds, and mutants to assess the regulatory logic of mouth-form plasticity...
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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
...was calculated as the log2FE (Log2[average mark signal/H3 (input) signal]) and then plotted at the TSS of genes categorized by their expression level. Arrowheads indicate the position of nucleosomes at which a difference in H3K27me3 enrichment is observed between the GSC-like and CySC-like chromatin profiles...
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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
...enriched with BRG1 (Fig. 2I). The regions that gained nucleosomes in both M-CLL and U-CLL versus NBCs had a more than threefold enrichment of BRG1 in comparison with neighboring regions (Fig. 2J). (2) The loci bound by another chromatin remodeler, CHD1, in lymphoblastoid B cells (The ENCODE Project...
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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
...this enhancer. These results demonstrate the power of caQTLs to characterize regulatory mechanisms at GWAS loci.Chromatin accessibility quantitative trait loci (caQTLs) have successfully identified functional variants and regulatory elements at a subset of gene expression QTLs (eQTLs) and -wide association...
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Research: ISWI1 complex proteins facilitate developmental genome editing in Paramecium
- Aditi Singh,
- Lilia Häußermann,
- Christiane Emmerich,
- Emily Nischwitz,
- Brandon K.B. Seah,
- Falk Butter,
- Mariusz Nowacki,
- and Estienne C. Swart
Genome Res. January 2025 35: 93-108; Published in Advance November 14, 2024, doi:10.1101/gr.278402.123
...lying within the IES might be more easily accessible than one outside.Besides nucleosome positioning, precise IES boundary targeting might also depend on the DNA topology, which influences protein binding and can be exploited in regulation (Baranello et al. 2012). Some ISWI family chromatin remodelers...
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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
...chromatin loops between convergent CTCF sites (van Ruiten and Rowland 2021). The genomic positions of boundaries and dots anchor all display enrichment for cohesin by ChIP-seq. Acute depletion of CTCF leads to -wide loss of TADs and dots in Hi-C contact maps as well as a loss of cohesin ChIP-seq enrichment...
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Research: Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites
- Patrick D. Wilson,
- Xinyang Yu,
- Christopher R. Handelmann,
- and Michael J. Buck
Genome Res. March 2025 35: 404-416; Published in Advance February 10, 2025, doi:10.1101/gr.279541.124
...by the TP53 (MA0106.3) or TP63 (MA0525.2) motif occurring within each ChIP-seq peak. Locations with multiple motifs were excluded from the analysis. Appropriate MNase-seq data were not available for TP73. To capture nucleosome positioning before TP53 or TP63 binding and any resultant chromatin remodeling...
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
..., modeling 3D chromatin organization, and predicting gene expression (Thibodeau et al. 2021; Karbalayghareh et al. 2022; Tan et al. 2023; Zhang et al. 2023; Grover et al. 2024). Although experimental assays such as FAIRE-seq (Giresi et al. 2007), DNase-seq (Song and Crawford 2010), and ATAC-seq (Buenrostro...
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