Searching journal content for articles similar to Chereji et al. 29 (12): 1985.

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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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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...author: ryan.lister@uwa.edu.auAbstractIn plants, cytosine DNA methylation (mC) is largely associated with transcriptional repression of transposable elements, but it can also be found in the body of expressed genes, referred to as gene body methylation (gbM). gbM is correlated with ubiquitously expressed...
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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
...and Fanning 2004; Aladjem 2007; Hamlin et al. 2008). Therefore, little is known about the distributions and natures of origins in mid- and late-replicating regions. Because physical access to these important elements/regions is paramount to successful orchestration of the DNA synthetic program, identifying...
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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
..., which enables changes to gene expression during development or disease or as a response to environmental stimuli. However, the regulation of DNA accessibility via the recruitment of transcription factors is difficult to study in the context of the native because every genomic site is distinct...
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Research: Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans
- Maude Strobino,
- Joanna M. Wenda,
- Laura Padayachy,
- and Florian A. Steiner
Genome Res. December 2020 30: 1740-1751; Published in Advance November 10, 2020, doi:10.1101/gr.260794.120
...to determine replication timing, map replication origins, and examine replication fork progression. Our analysis of the spatiotemporal regulation of DNA replication shows that despite the very rapid embryonic cell cycle, the is replicated from early and late firing origins and is partitioned into domains...
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Method: Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma
- Nancy H. Nabilsi,
- Loic P. Deleyrolle,
- Russell P. Darst,
- Alberto Riva,
- Brent A. Reynolds,
- and Michael P. Kladde
Genome Res. February 2014 24: 329-339; Published in Advance October 8, 2013, doi:10.1101/gr.161737.113
...that these epigenetic features are not random, but represent biologically relevant events. However, additional studies are required to determine the functional significance of DNA methylation, if any, at these genes. Our finding of differentially methylated/accessible genes previously shown to harbor mutations in GBM...
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Research: Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control
- Todd P. Michael,
- Evan Ernst,
- Nolan Hartwick,
- Philomena Chu,
- Douglas Bryant,
- Sarah Gilbert,
- Stefan Ortleb,
- Erin L. Baggs,
- K. Sowjanya Sree,
- Klaus J. Appenroth,
- Joerg Fuchs,
- Florian Jupe,
- Justin P. Sandoval,
- Ksenia V. Krasileva,
- Ljudmylla Borisjuk,
- Todd C. Mockler,
- Joseph R. Ecker,
- Robert A. Martienssen,
- and Eric Lam
Genome Res. February 2021 31: 225-238; Published in Advance December 23, 2020, doi:10.1101/gr.266429.120
...(v3) liliopsida odb10 database (Simão et al. 2015). Identification of high copy number repeats such as rDNA and centromere arrays in the two Wolffia accessions were performed as previously described (Hoang et al. 2018).Genome annotationCustom repeat libraries were constructed for each species...
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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
.... With this strategy we sought to obtain an understanding of (1) the molecular determinants of ORI specification and function, and (2) their relationships with cell proliferation and gene expression programs.View larger version: In this window In a new window Figure 1. DNA replication origin (ORI) identification...
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Method: Effect of minichromosome maintenance protein 2 deficiency on the locations of DNA replication origins
- Dimiter Kunnev,
- Amy Freeland,
- Maochun Qin,
- Robert W. Leach,
- Jianmin Wang,
- Rajani M. Shenoy,
- and Steven C. Pruitt
Genome Res. April 2015 25: 558-569; Published in Advance March 11, 2015, doi:10.1101/gr.176099.114
...deficiency reduces DNA replication initiation in gene-rich regions of the genome. DNA structural properties are shown to correlate with sequence motifs associated with replication origins and with locations that are preferentially affected by MCM2 deficiency. Reduced nascent strand density correlates...
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Research: Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification
- Robert K. Arthur,
- Lijia Ma,
- Matthew Slattery,
- Rebecca F. Spokony,
- Alexander Ostapenko,
- Nicolas Nègre,
- and Kevin P. White
Genome Res. July 2014 24: 1115-1124; Published in Advance July 1, 2014, doi:10.1101/gr.162008.113
...). These modifications can act directly or indirectly (through recruited enzymes) to alter DNA accessibility, thereby controlling other DNA–protein interactions (Campos and Reinberg 2009). Unlike TFBSs, however, histone modifications are not necessarily easily localizable to particular sequence elements, making...
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