Searching journal content for articles similar to van de Werken et al. 27 (6): 922.

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Research: Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins
- Larry D. Mesner,
- Veena Valsakumar,
- Marcin Cieślik,
- Rebecca Pickin,
- Joyce L. Hamlin,
- and Stefan Bekiranov
Genome Res. November 2013 23: 1774-1788; Published in Advance July 16, 2013, doi:10.1101/gr.155218.113
...within the 44 ENCODE pilot regions and to relate their positions to local transcriptional activity as well as to the few chromatin features then available through publicly available databases (Mesner et al. 2011). The results supported amodel inwhichmost origins correspond to zones of clustered...
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LETTER: H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome
- Florian M. Pauler,
- Mathew A. Sloane,
- Ru Huang,
- Kakkad Regha,
- Martha V. Koerner,
- Ido Tamir,
- Andreas Sommer,
- Andras Aszodi,
- Thomas Jenuwein,
- and Denise P. Barlow
Genome Res. February 2009 19: 221-233; Published in Advance December 1, 2008, doi:10.1101/gr.080861.108
...here show characteristic features in terms of size of modified region, total chromosome coverage and position relative to genes and gene activity. Peaks of active histone modification had an average width of 2.6 kb and covered 2%–4% of mouse chr 17, with H3K4me2 being two- to threefold more abundant...
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REVIEW: Structure of Chromosomal Duplicons and their Role in Mediating Human Genomic Disorders
- Yonggang Ji,
- Evan E. Eichler,
- Stuart Schwartz,
- and Robert D. Nicholls
Genome Res. May 1, 2000 10: 597-610; doi:10.1101/gr.10.5.597
..., double-strand breaks have been found primarily in promoter regions, suggesting a role for an open chromatin structure in homologous recombination ( Osman and Subramani 1998 ). The presence of a sequence in SMS–REP that is homologous to one with autonomously replicating activity also suggests a role...
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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...(Fig. 3H). Considering that the differential usage of PASs might change the number of RBP binding sites, we scanned the CD47 differential 3′ UTR using RBP motif position weight matrices. This analysis revealed that most RBP binding motifs within this region corresponded to ELAVL1 and ELAVL2 (Fig. 3I...
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Research: Birth, evolution, and transmission of satellite-free mammalian centromeric domains
- Solomon G. Nergadze,
- Francesca M. Piras,
- Riccardo Gamba,
- Marco Corbo,
- Federico Cerutti,
- Joseph G.W. McCarter,
- Eleonora Cappelletti,
- Francesco Gozzo,
- Rebecca M. Harman,
- Douglas F. Antczak,
- Donald Miller,
- Maren Scharfe,
- Giulio Pavesi,
- Elena Raimondi,
- Kevin F. Sullivan,
- and Elena Giulotto
Genome Res. June 2018 28: 789-799; Published in Advance April 30, 2018, doi:10.1101/gr.231159.117
.... Since we previously demonstrated the presence of a satellite-free centromere on horse Chromosome 11 by ChIP-on-chip (Wade et al. 2009; Purgato et al. 2015), as positive control, we carried out the same ChIP-seq experiment with chromatin from horse skin fibroblasts. The horse and donkey s share...
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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
...sequence (green). Inset images show magnifications of a CEN178-positive region (Lambing et al. 2020). Scale bar, 10 μm. (D) Representing monocentric satellite architecture, a physical map of A. thaliana Chromosome 3 is shown, with the location of the CENH3-occupied CEN178 array highlighted in blue (Naish...
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Research: Intrinsic DNA binding properties demonstrated for lineage-specifying basic helix-loop-helix transcription factors
- Bradford H. Casey,
- Rahul K. Kollipara,
- Karine Pozo,
- and Jane E. Johnson
Genome Res. April 2018 28: 484-496; Published in Advance March 2, 2018, doi:10.1101/gr.224360.117
...properties of the factors themselves. To distinguish between these mechanisms, we directly compared the chromatin binding properties of this subset of bHLH factors when ectopically expressed in embryonic stem cells, presenting them with a common chromatin landscape and cellular components. We find...
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Research: Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic
- Annelien Verfaillie,
- Dmitry Svetlichnyy,
- Hana Imrichova,
- Kristofer Davie,
- Mark Fiers,
- Zeynep Kalender Atak,
- Gert Hulselmans,
- Valerie Christiaens,
- and Stein Aerts
Genome Res. July 2016 26: 882-895; Published in Advance May 18, 2016, doi:10.1101/gr.204149.116
...data suggest that TP53 enhancers represent a class of unsophisticated cell-autonomous enhancers containing a single TP53 binding site, distinct from complex developmental enhancers that integrate signals from multiple transcription factors. Footnotes [Supplemental material is available...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...this region is large and thus may be driving some of the observed correlations between the density of TE classes, we repeated the analyses with Chromosome 4 omitted but observed no substantive changes in effect size or significance (Supplemental Fig. 3).Patterns in chromosomal TE distributions are shaped both...
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ARTICLE: The Small Chromosomes of Trypanosoma brucei Involved in Antigenic Variation Are Constructed Around Repetitive Palindromes
- Bill Wickstead,
- Klaus Ersfeld,
- and Keith Gull
Genome Res. June 2004 14: 1014-1024; doi:10.1101/gr.2227704
...central core of 177-bp repeats. Around the core are variable-length genic regions, the lengths of which define chromosomal class. We show the core region to be a repetitive palindrome with a single inversion point common to all the chromosomes of both classes, suggesting a mechanism of genesis...

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