Searching journal content for articles similar to Hartley et al. 10 (11): 1788.

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  1. Methods: Concerted Assembly and Cloning of Multiple DNA Segments Using In Vitro Site-Specific Recombination: Functional Analysis of Multi-Segment Expression Clones
    • David L. Cheo,
    • Steven A. Titus,
    • Devon R.N. Byrd,
    • James L. Hartley,
    • Gary F. Temple,
    • and Michael A. Brasch
    Genome Res. October 15, 2004 14: 2111-2120; doi:10.1101/gr.2512204
    ...Concerted Assembly and Cloning of Multiple DNA Segments Using In Vitro Site-Specific Recombination: Functional Analysis of Multi-Segment Expression Clones David L. Cheo 1 , 2 , Steven A. Titus 1 , 2 , Devon R.N. Byrd 2 , 3 , James L. Hartley 2 , 4...
  2. Research: Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions
    • Yuning Zhang,
    • Tiffany D. Ho,
    • Nicolas E. Buchler,
    • and Raluca Gordân
    Genome Res. July 2021 31: 1216-1229; Published in Advance May 11, 2021, doi:10.1101/gr.275145.120
    ...not identical, DNA-binding specificities, as reflected by their position weight matrix (PWM) models (Sandelin et al. 2004). (C) Direct comparison between the in vitro binding levels of Cbf1 and Pho4 at their putative genomic binding sites, measured by genomic-context PBM (Gordân et al. 2013). Each data point...
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  3. Research: DDX54 regulates transcriptome dynamics during DNA damage response
    • Miha Milek,
    • Koshi Imami,
    • Neelanjan Mukherjee,
    • Francesca De Bortoli,
    • Ulrike Zinnall,
    • Orsalia Hazapis,
    • Christian Trahan,
    • Marlene Oeffinger,
    • Florian Heyd,
    • Uwe Ohler,
    • Matthias Selbach,
    • and Markus Landthaler
    Genome Res. August 2017 27: 1344-1359; Published in Advance June 8, 2017, doi:10.1101/gr.218438.116
    ...by a well-characterized network of DNA surveillance pathways. The contribution of post-transcriptional gene regulatory networks to the DNAdamage response (DDR) has not been extensively studied. Here, we systematically identified RNA-binding proteins differentially interacting with polyadenylated transcripts...
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  4. Method: A synergistic DNA logic predicts genome-wide chromatin accessibility
    • Tatsunori Hashimoto,
    • Richard I. Sherwood,
    • Daniel D. Kang,
    • Nisha Rajagopal,
    • Amira A. Barkal,
    • Haoyang Zeng,
    • Bart J.M. Emons,
    • Sharanya Srinivasan,
    • Tommi Jaakkola,
    • and David K. Gifford
    Genome Res. October 2016 26: 1430-1440; Published in Advance July 25, 2016, doi:10.1101/gr.199778.115
    ...cell types. We confirm that a SCM accurately predicts chromatin accessibility for thousands of synthetic DNA sequences using a novel CRISPR-based method of highly efficient site-specific DNA library integration. SCMs are directly interpretable and reveal that a logic based on local, nonspecific...
  5. Method: SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site
    • Liyang Zhang,
    • Gabriella D. Martini,
    • H. Tomas Rube,
    • Judith F. Kribelbauer,
    • Chaitanya Rastogi,
    • Vincent D. FitzPatrick,
    • Jon C. Houtman,
    • Harmen J. Bussemaker,
    • and Miles A. Pufall
    Genome Res. January 2018 28: 111-121; Published in Advance December 1, 2017, doi:10.1101/gr.222844.117
    ...These authors contributed equally to this work. Corresponding authors: miles-pufall@uiowa.edu, hjb2004@columbia.eduAbstractThe DNA-binding interfaces of the androgen (AR) and glucocorticoid (GR) receptors are virtually identical, yet these transcription factors share only about a third of their genomic binding...
  6. Method: Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays
    • Shaleen Shrestha,
    • Jared Allan Sewell,
    • Clarissa Stephanie Santoso,
    • Elena Forchielli,
    • Sebastian Carrasco Pro,
    • Melissa Martinez,
    • and Juan Ignacio Fuxman Bass
    Genome Res. September 2019 29: 1533-1544; doi:10.1101/gr.248823.119
    ...(∼50%), from differences between DNA motifs determined in vitro and those occupied in vivo, from motif quality, from limitations in prediction algorithms, or from DNase I cleavage biases.To determine whether eY1H assays can identify TFs that bind to some of these orphan DNA motifs, we tested seven 8-bp...
  7. Research: Numerical and spatial patterning of yeast meiotic DNA breaks by Tel1
    • Neeman Mohibullah and
    • Scott Keeney
    Genome Res. February 2017 27: 278-288; Published in Advance December 6, 2016, doi:10.1101/gr.213587.116
    ...DSBs or altered Spo11-oligo-complex lifespan caused by delayed meiotic progression. Thus, quantification of Spo11-oligo complexes, combined with prior analyses of recombination products (Zhang et al. 2011; Anderson et al. 2015) and some physical analyses of broken genomic DNA (Carballo et al. 2013...
  8. ARTICLE: A highly efficient procedure for site-specific mutagenesis of full-length plasmids using Vent DNA polymerase.
    • S Byrappa,
    • D K Gavin,
    • and K C Gupta
    Genome Res. November 1995 5: 404-407; doi:10.1101/gr.5.4.404
    .... 263: 4907 – 4913. 3. . Higuchi, R., , Krummel, B. , Saiki. R.K. Higuchi, R., Krummel, B. and Saiki. R.K. 1988. A general method of in vitro preparation and specific mutagenesis of DNA fragments: Study of protein and DNA interactions. Nucleic Acids Res. 16: 7351 – 7367. 4. . Rashtachian, A., , Thornton...
  9. Methods: Recombinatorial Cloning Using Heterologous Lox Sites
    • Robert W. Siegel,
    • Nileena Velappan,
    • Peter Pavlik,
    • Leslie Chasteen,
    • and Andrew Bradbury
    Genome Res. June 2004 14: 1119-1129; doi:10.1101/gr.1821804
    ...in vitro methods often requires moving the scFv gene from the phagemid display vector into a variety of more specialized vectors, creating fusion proteins better suited for a particular functional use of the isolated scFv antibody. Site-specific recombination offers many advantages over traditional cloning...
  10. RESOURCE: Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions
    • Chaochun Wei,
    • Philippe Lamesch,
    • Manimozhiyan Arumugam,
    • Jennifer Rosenberg,
    • Ping Hu,
    • Marc Vidal,
    • and Michael R. Brent
    Genome Res. April 2005 15: 577-582; doi:10.1101/gr.3329005
    ..., J.L., Temple, G.F., and Brasch, M.A. 2000 . DNA cloning using in vitro site-specific recombination. Genome Res. 10 : 1788 -1795. ↵ Howe, K.L., Chothia, T., and Durbin, R. 2002 . GAZE: A generic framework for the integration of gene-prediction data by dynamic programming. Genome Res. 12 : 1418 -1427...
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