Searching journal content for articles similar to Raghavan et al. 21 (9): 1487.

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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...-in orientations in vitro (Song et al. 2011, 2014). However, to what extent nucleosomes modulate CPD deamination in other sequence contexts and across the of intact cells remains unclear.Genome-wide sequencing methods have emerged as powerful tools to understand how different genomic and chromatin contexts impact...
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Research: Genome-wide promoter assembly in E. coli measured at single-base resolution
- Jordan John,
- Javaid Jabbar,
- Nitika Badjatia,
- Matthew J. Rossi,
- William K.M. Lai,
- and B. Franklin Pugh
Genome Res. May 2022 32: 878-892; Published in Advance April 28, 2022, doi:10.1101/gr.276544.121
...are enriched with YR nucleotides (IUPAC nomenclature), this determination was based on only 88 promoters (Hawley and McClure 1983). Genome-wide studies based on mapping RNA 5′ ends have found the YR motif to be enriched, with 79% of the +1 nucleotide being an R (Kim et al. 2012), whereas another study had R...
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Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
- Mikhail O. Maksimov,
- Cynthia Wu,
- David G. Ashbrook,
- Flavia Villani,
- Vincenza Colonna,
- Nima Mousavi,
- Nichole Ma,
- Lu Lu,
- Jonathan K. Pritchard,
- Alon Goren,
- Robert W. Williams,
- Abraham A. Palmer,
- and Melissa Gymrek
Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
...a zinc finger–containing protein that can bind DNA or RNA (Zhou et al. 2008). Although we cannot rule out the impact of this mutation, there is currently no known link between this gene and STR stability.Expansion propensity QTL colocalizes with multiple cis-eQTLsWe next wondered if the QTL for expansion...
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Research: Genetic exchange with an outcrossing sister species causes severe genome-wide dysregulation in a selfing Caenorhabditis nematode
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- Yongbin Li,
- Xiao Liu,
- Peter Sarkies,
- and Zhongying Zhao
Genome Res. November/December 2022 32: 2015-2027; Published in Advance November 9, 2022, doi:10.1101/gr.277205.122
.... Misregulation of transposable elements, coding genes, and small regulatory RNAs was more widespread in the bB2 compared with the nB2 hybrids, which is a plausible explanation for the differential phenotypes between the two hybrids. Our results show that regulation of the C. briggsae is strongly affected...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
...are tightly controlled, raising the possibility that their breakdown products, tsRNAs, may provide a link between the overall translational status of a cell to specific changes in gene regulatory network. We hypothesize that Drosophila pupation, being a special developmental stage during which...
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Method: A systematic genome-wide account of binding sites for the model transcription factor Gcn4
- Christopher T. Coey and
- David J. Clark
Genome Res. February 2022 32: 367-377; Published in Advance December 16, 2021, doi:10.1101/gr.276080.121
..., such that only sites in nucleosome-depleted regulatory regions are bound. We compared the binding of the yeast transcription factor Gcn4 in vivo using published ChIP-seq data (546 sites) and in vitro, using a modified SELEX method (“G-SELEX”), which utilizes short genomic DNA fragments to quantify binding at all...
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Research: Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands
- Brian S. Roberts,
- E. Christopher Partridge,
- Bryan A. Moyers,
- Vikram Agarwal,
- Kimberly M. Newberry,
- Beth K. Martin,
- Jay Shendure,
- Richard M. Myers,
- and Gregory M. Cooper
Genome Res. May 2021 31: 866-876; Published in Advance April 20, 2021, doi:10.1101/gr.270751.120
...contributes to its own abundance within the pool of plasmid-derived RNA. Another mode of MPRA, “survey of regulatory elements” (SuRE), involves placement of sequence elements in an upstream location relative to a gene in a promoter-free plasmid (Van Arensbergen et al. 2019). These elements are linked...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...-specific regulatory effects (Karttunen et al. 2023). We therefore conducted the same analyses using RNA-seq data from 13 different tissues (Lien et al. 2016). Using TE-CREs from both the liver and brain, 71 TE subfamilies (71 of 1465 = 4.8%) were associated with significant coexpression (Fig. 5D), of which 29 (41...
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Research: Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
- Kristina Krassovsky,
- Rajarshi P. Ghosh,
- and Barbara J. Meyer
Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120
...overwind or underwind DNA, creating DNA supercoils (Kouzine and Levens 2007). Supercoils can, in turn, induce formation of single-stranded DNA (ssDNA, hereafter SS DNA) or other non-B DNA structures.Genome-wide mapping of alternative DNA structures in cell lines and computational predictions in s suggested...
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Method: Genome-wide reconstitution of chromatin transactions reveals that RSC preferentially disrupts H2AZ-containing nucleosomes
- Aylin Cakiroglu,
- Cedric R. Clapier,
- Andreas H. Ehrensberger,
- Elodie Darbo,
- Bradley R. Cairns,
- Nicholas M. Luscombe,
- and Jesper Q. Svejstrup
Genome Res. June 2019 29: 988-998; Published in Advance May 16, 2019, doi:10.1101/gr.243139.118
.... Nucleosomes influence reactions on DNA in at least two ways: By occluding access to the DNA, they can exert an inhibitory function; and by recruiting enzymes and regulatory factors, they may stimulate catalysis. The regulatory capacity of nucleosomes is amplified vastly through regional incorporation...
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