Searching journal content for articles similar to Wang et al. 17 (8): 000.

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  1. Method: Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins
    • Haoyi Wang,
    • David Mayhew,
    • Xuhua Chen,
    • Mark Johnston,
    • and Robi David Mitra
    Genome Res. May 2011 21: 748-755; Published in Advance April 6, 2011, doi:10.1101/gr.114850.110
    ...Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins Haoyi Wang 1 , 3 , 4 , David Mayhew 1 , 3 , Xuhua Chen 1 , Mark Johnston 2 , 5 and Robi David Mitra 1 , 5 1 Department...
  2. 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
    ..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
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  3. Resource: Multiparameter functional diversity of human C2H2 zinc finger proteins
    • Frank W. Schmitges,
    • Ernest Radovani,
    • Hamed S. Najafabadi,
    • Marjan Barazandeh,
    • Laura F. Campitelli,
    • Yimeng Yin,
    • Arttu Jolma,
    • Guoqing Zhong,
    • Hongbo Guo,
    • Tharsan Kanagalingam,
    • Wei F. Dai,
    • Jussi Taipale,
    • Andrew Emili,
    • Jack F. Greenblatt,
    • and Timothy R. Hughes
    Genome Res. December 2016 26: 1742-1752; Published in Advance November 16, 2016, doi:10.1101/gr.209643.116
    ...the largest and most enigmatic class of human transcription factors. Their C2H2-ZF arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. In addition, little is known about whether or how these proteins...
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  4. Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
    • Mari B. Gornitzka,
    • Egil Røsjø,
    • Uddalok Jana,
    • Easton E. Ford,
    • Alan Tourancheau,
    • William D. Lees,
    • Zachary Vanwinkle,
    • Melissa L. Smith,
    • Corey T. Watson,
    • and Andreas Lossius
    Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
    ...the protocol “High Molecular Weight DNA (HMW DNA) Extraction from Cells” (NEB T3050) with the following alterations: (1) the agitation speed during cell lysis was set to 1400 rpm for 10 min; (2) the incubation time with beads during gDNA binding to beads was increased to 8 min; (3) the elution buffer...
  5. Method: Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses
    • Yiming Kang,
    • Nikhil R. Patel,
    • Christian Shively,
    • Pamela Samantha Recio,
    • Xuhua Chen,
    • Bernd J. Wranik,
    • Griffin Kim,
    • R. Scott McIsaac,
    • Robi Mitra,
    • and Michael R. Brent
    Genome Res. March 2020 30: 459-471; Published in Advance February 14, 2020, doi:10.1101/gr.259655.119
    ...cards. One such technology is DamID, in which a DNA-methyltransferase is tethered to a DNA-binding protein and changes in DNA methylation relative to a control are assayed to determine binding location (van Steensel and Henikoff 2000; Hass et al. 2015; Tosti et al. 2018). Another is CUT&RUN, in which...
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  6. Method: MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome
    • Dechao Tian,
    • Ruochi Zhang,
    • Yang Zhang,
    • Xiaopeng Zhu,
    • and Jian Ma
    Genome Res. February 2020 30: 227-238; Published in Advance January 6, 2020, doi:10.1101/gr.250316.119
    ...higher normalized number of super-enhancers than the non-HIMs across cell types (Fig. 3C; Supplemental Fig. S12). This significant pattern is consistent with varied window sizes from 20 kb to 1 Mb (Supplemental Fig. S12).Protein–protein interactions (PPIs) can further stabilize TF-DNA binding...
  7. Research: Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals
    • Daniel W. Bellott and
    • David C. Page
    Genome Res. February 2021 31: 198-210; Published in Advance January 21, 2021, doi:10.1101/gr.268516.120
    ...-specific gains and losses within snakes (Fig. 1A; Table 1; Supplemental Table S3; Supplemental Methods). We identified 45% more genes than previous reconstructions: a total of 1648 genes in 1300 protein-coding gene families on the ancestral autosomes that became the caenophidian Z and W sex chromosomes (Fig. 1B...
  8. Method: Time course regulatory analysis based on paired expression and chromatin accessibility data
    • Zhana Duren,
    • Xi Chen,
    • Jingxue Xin,
    • Yong Wang,
    • and Wing Hung Wong
    Genome Res. April 2020 30: 622-634; Published in Advance March 18, 2020, doi:10.1101/gr.257063.119
    ....Identification and quantification of REsWe define regulatory elements (REs) by the union of open peaks from ATAC-seq (called by MACS2) data on each time point. In the whole induction process, we get 174,059 REs in total. To quantify the accessibility of the peaks, we calculate the openness score for each sample in each region...
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  9. Method: Mapping functional transcription factor networks from gene expression data
    • Brian C. Haynes,
    • Ezekiel J. Maier,
    • Michael H. Kramer,
    • Patricia I. Wang,
    • Holly Brown,
    • and Michael R. Brent
    Genome Res. August 2013 23: 1319-1328; Published in Advance May 1, 2013, doi:10.1101/gr.150904.112
    ...budgets. Although great strides have been made in in vivo binding analysis using methods such as ChIP-seq ( Johnson et al. 2007; Landt et al. 2012), Bio-ChIP (vanWervenandTimmers 2006), or Calling Cards (Wang et al. 2012), these are challenging experiments that are not easily scaled to many TFs outside...
  10. Research: Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131
    • Teemu Kallonen,
    • Hayley J. Brodrick,
    • Simon R. Harris,
    • Jukka Corander,
    • Nicholas M. Brown,
    • Veronique Martin,
    • Sharon J. Peacock,
    • and Julian Parkhill
    Genome Res. August 2017 27: 1437-1449; Published in Advance July 18, 2017, doi:10.1101/gr.216606.116
    ...C was 68% for DNA and 69%/73% for protein. The ST131 espC island has genes coding for fimD, focC ( fimC), tsh, cfaD (regA), and espC, alongwith two poorly characterized proteins, one with similarity to fimbrial adhesins and one to DNA Figure 2. Proportions of STs during the 11-yr sampling framework...
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