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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
...proximity of the cross-linkable protein–DNA residues to each other.Additional RpoD cross-linking was detected up to ∼150 bp upstream of the TSS (based on the −35/−10 motif) (Fig. 2D, black arrow). Because in vitro structures of site-bound RpoD would not predict interactions this far upstream, this may...
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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
...repair (Cmya5 and Zcchc9), but it is unclear how those would contribute to an STR mutator phenotype.Msh3 is well known to be involved in regulating STR stability. Msh3 is one of multiple homologs of the Escherichia coli MutS MMR protein, which recognizes mismatched bases in DNA that arise during DNA...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...achieved AUC >0.7 in 80% cross-predictions and exhibited superior global transfer stability (standard deviation = 0.1269) compared with other species (average standard deviation = 0.1526). This property could be related to the global methylation pattern of DNA, and its sequences might capture more...
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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
...occur quite frequently in genomic DNA, not only in regulatory elements, but also in genes and elsewhere. Consensus sites often predict far more transcription factor binding sites than are actually bound in vivo. This observation has led to the proposal that consensus sites in nonregulatory regions...
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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
...Table 1). We grew each BAC separately in Escherichia coli and purified BAC DNA separately according to standard BAC preparation protocols. We sheared each BAC DNA (5 μg) separately using a Biorupter pico (Diagenode) to a 100- to 500-bp size, then ran on 1% agarose gel, manually selected 250- to 350-bp...
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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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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
...chromatin accessibility data from the liver and brain. Retroelements were both the dominant source of TE-CREs and had higher regulatory activity in MPRA experiments compared with DNA elements. A minority of TE subfamilies (16%) accounted for 46% of TE-CREs, but these “CRE superspreaders” were mostly active...
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Research: Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development
- Song Zhang,
- Chao Wang,
- Shenghua Qin,
- Choulin Chen,
- Yongzhou Bao,
- Yuanyuan Zhang,
- Lingna Xu,
- Qingyou Liu,
- Yunxiang Zhao,
- Kui Li,
- Zhonglin Tang,
- and Yuwen Liu
Genome Res. December 2024 34: 2190-2202; Published in Advance October 21, 2024, doi:10.1101/gr.278344.123
...by the change in allelic ratios between the output library, including replicate1 (C) and replicate2 (D), and the input library. Statistical significance (false discovery rate [FDR] < 0.05) was evaluated using Fisher's exact test. (E) DNA-binding motif-breaking scores were assessed for regulatory SNPs...
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Research: Genome-wide detection of novel regulatory RNAs in E. coli
- Rahul Raghavan,
- Eduardo A. Groisman,
- and Howard Ochman
Genome Res. September 2011 21: 1487-1497; Published in Advance June 10, 2011, doi:10.1101/gr.119370.110
...regulatory leader sequences and small RNAs (sRNAs), which both serve to modulate gene expression. Computational analyses have predicted the presence of hundreds of these noncoding regulatory RNAs in Escherichia coli ; however, only about 80 have been experimentally validated. By applying a deep...
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Research: Global loss of cellular m⁶A RNA methylation following infection with different SARS-CoV-2 variants
- Roshan Vaid,
- Akram Mendez,
- Ketan Thombare,
- Rebeca Burgos-Panadero,
- Rémy Robinot,
- Barbara F. Fonseca,
- Nikhil R. Gandasi,
- Johan Ringlander,
- Mohammad Hassan Baig,
- Jae-June Dong,
- Jae Yong Cho,
- Björn Reinius,
- Lisa A. Chakrabarti,
- Kristina Nystrom,
- and Tanmoy Mondal
Genome Res. March 2023 33: 299-313; Published in Advance March 1, 2023, doi:10.1101/gr.276407.121
...; Xiao et al. 2016). Finally, m6A modifications can also be erased by the dioxygenases FTO and ALKBH5, which specifically demethylate m6A RNA (Zhang et al. 2017; Wei et al. 2022).The m6A RNA modification has been identified in several viral genomic RNA, being first described for DNA viruses...
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