Searching journal content for articles similar to Lao and Forsdyke 10 (2): 228.

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  1. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...to chromatin compaction or PTMs as well as competition from other binding proteins. Consequently, EMSA can be applied to rule out DNA–protein interactions: If a protein is not able to bind the sequence of interest in an EMSA assay, it is unlikely that this interaction occurs in nature; however, positive...
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  2. Research: Semiconservative transmission of DNA N6-adenine methylation in a unicellular eukaryote
    • Yalan Sheng,
    • Yuanyuan Wang,
    • Wentao Yang,
    • Xue Qing Wang,
    • Jiuwei Lu,
    • Bo Pan,
    • Bei Nan,
    • Yongqiang Liu,
    • Fei Ye,
    • Chun Li,
    • Jikui Song,
    • Yali Dou,
    • Shan Gao,
    • and Yifan Liu
    Genome Res. May 2024 34: 740-756; Published in Advance May 14, 2024, doi:10.1101/gr.277843.123
    .... 2019; Wang et al. 2019). Tetrahymena contains within the same cytoplasmic compartment two types of nuclei, the somatic macronucleus (MAC) and the germline micronucleus (MIC) (Karrer 2012). Although missing in the transcriptionally silent MIC, 6mA is abundantly present in the transcriptionally active...
  3. Research: The chromatin landscape of the histone-possessing Bacteriovorax bacteria
    • Georgi K. Marinov,
    • Benjamin Doughty,
    • Anshul Kundaje,
    • and William J. Greenleaf
    Genome Res. January 2025 35: 109-123; Published in Advance November 21, 2024, doi:10.1101/gr.279418.124
    ...to eukaryotes and most archaea, with eukaryotic nucleosomal histones deriving from their archaeal ancestors. In contrast, bacteria lack histones as a rule. However, histone proteins have recently been identified in a few bacterial clades, most notably the phylum Bdellovibrionota, and these histones have been...
  4. Review: De novo gene birth and the conundrum of ORFan genes in bacteria
    • Md. Hassan uz-Zaman and
    • Howard Ochman
    Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
    ...-birth events traceable in extant s. Owing to their amenability to experimental evolutionary analysis and their strain-level variation in gene contents, bacteria offer the opportunity to identify forms of de novo gene birth that are not readily captured by conventional detection methods.De novo transcription...
  5. Research: Dynamic DNA N6-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus
    • Yongqiang Liu,
    • Junhua Niu,
    • Fei Ye,
    • Therese Solberg,
    • Borong Lu,
    • Chundi Wang,
    • Mariusz Nowacki,
    • and Shan Gao
    Genome Res. February 2024 34: 256-271; Published in Advance March 12, 2024, doi:10.1101/gr.278796.123
    ...was resuspended in 20 μL of DEPC-treated water and the quality assessed by 2% agarose gel electrophoresis.RNAi-mediated knockdownFresh control and RNAi feeding E. coli were cultured and induced by IPTG to express dsRNA of the target gene as described above. After induction, bacteria were washed and resuspended...
  6. 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
    ...organisms. Accumulating evidence suggests that, from bacteria to human, tsRNAs are not merely intermediates of the tRNA maturation process or residues of the tRNA degradation process as their biogenesis can show elaborate spatiotemporal patterns (Kumar et al. 2016; Sharma et al. 2016; Li et al. 2018; Dou et...
  7. Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
    • Kevin S. O'Leary,
    • Meng-Yen Li,
    • Kevyn Jackson,
    • Lijie Shi,
    • Elena Ezhkova,
    • Bernice E. Morrow,
    • and Deyou Zheng
    Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
    ...integrated analyses of single-cell RNA-seq data from multiple human tissues and organs. Single-cell epigenomic data further indicate that the expression is likely driven by an alternative promoter at the end of the first exon, resulting in at least one shorter transcript (referred to as sXIST) that is active...
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  8. Method: Accurate assembly of circular RNAs with TERRACE
    • Tasfia Zahin,
    • Qian Shi,
    • Xiaofei Carl Zang,
    • and Mingfu Shao
    Genome Res. September 2024 34: 1365-1370; Published in Advance July 26, 2024, doi:10.1101/gr.279106.124
    ....Splicing is a ubiquitous and essential post-transcriptional modification of precursor mRNAs. In this process, introns are excised and the two flanking exons are stitched together. Canonical splicing covalently connects the 3′ end of an upstream exon to the 5′ end of the immediate downstream exon. A class of noncanonical...
  9. Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
    • Haiyue Liu and
    • Lea H. Gregersen
    Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
    ...-scaled time point of nascent RNA labeling following DRB release provides a direct and quantitative view of this initial transcriptional slow phase. Between 5 and 10 min, elongation rates increased slightly and then accelerated in the 1015-min interval as RNAPII moved deeper into gene bodies (Fig. 4F...
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  10. 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
    ...also considered that the direction of regulation may not be the same across a regulatory cascade or pathway. For example, although activators typically promote gene expression by facilitating the recruitment of RNA polymerase and transcriptional machinery, their effects on downstream targets can...
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