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Method: High-throughput single-molecule telomere characterization
- Jennifer McCaffrey,
- Eleanor Young,
- Katy Lassahn,
- Justin Sibert,
- Steven Pastor,
- Harold Riethman,
- and Ming Xiao
Genome Res. November 2017 27: 1904-1915; Published in Advance October 12, 2017, doi:10.1101/gr.222422.117
.... An in vitro CRISPR/Cas9 RNA-directed nickase system directs the specific labeling of human (TTAGGG)n DNA tracts in s that have also been barcoded using a separate nickase enzyme that recognizes a 7bp motif -wide. High-throughput imaging and analysis of large DNA single molecules from s labeled in this fashion...
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Research: High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome
- Houssam Hajjoul,
- Julien Mathon,
- Hubert Ranchon,
- Isabelle Goiffon,
- Julien Mozziconacci,
- Benjamin Albert,
- Pascal Carrivain,
- Jean-Marc Victor,
- Olivier Gadal,
- Kerstin Bystricky,
- and Aurélien Bancaud
Genome Res. November 2013 23: 1829-1838; Published in Advance September 27, 2013, doi:10.1101/gr.157008.113
...simulation studies should therefore evaluate whether and how compact exploration is related to chromosome territoriality in the yeast . MSD fluctuations suggest that chromatin is highly flexible The level of flexibility of a chromatin fiber is a matter of debate. In vitro singlemolecule experiments have...
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Research: Sir3 mediates long-range chromosome interactions in budding yeast
- Myriam Ruault,
- Vittore F. Scolari,
- Luciana Lazar-Stefanita,
- Antoine Hocher,
- Isabelle Loïodice,
- Romain Koszul,
- and Angela Taddei
Genome Res. March 2021 31: 411-425; Published in Advance February 12, 2021, doi:10.1101/gr.267872.120
...compaction and accessibility (Oppikofer et al. 2013; Swygert et al. 2014, 2018; Behrouzi et al. 2016). However, these specific Sir3–Sir3 interactions could also build up molecular bridges between Sir3-bound regions in trans. Sir3 can bridge mononucleosomes or nucleosomal arrays in vitro (Georgel et al. 2001...
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Method: A novel assay to screen siRNA libraries identifies protein kinases required for chromosome transmission
- Mikhail Liskovykh,
- Nikolay V. Goncharov,
- Nikolai Petrov,
- Vasilisa Aksenova,
- Gianluca Pegoraro,
- Laurent L. Ozbun,
- William C. Reinhold,
- Sudhir Varma,
- Mary Dasso,
- Vadim Kumeiko,
- Hiroshi Masumoto,
- William C. Earnshaw,
- Vladimir Larionov,
- and Natalay Kouprina
Genome Res. October 2019 29: 1719-1732; Published in Advance September 12, 2019, doi:10.1101/gr.254276.119
...developed a novel high-throughput imaging (HTI) siRNA assay to identify unknown human CIN genes. This assay is based on a nonessential human artificial chromosome (HAC) expressing a short half-life green fluorescent protein (GFP). This HAC, like other HACs, follows the rules of mitosis and chromosome...
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Methods: High-throughput DNA methylation profiling using universal bead arrays
- Marina Bibikova,
- Zhenwu Lin,
- Lixin Zhou,
- Eugene Chudin,
- Eliza Wickham Garcia,
- Bonnie Wu,
- Dennis Doucet,
- Neal J. Thomas,
- Yunhua Wang,
- Ekkehard Vollmer,
- Torsten Goldmann,
- Carola Seifart,
- Wei Jiang,
- David L. Barker,
- Mark S. Chee,
- Joanna Floros,
- and Jian-Bing Fan
Genome Res. March 2006 16: 383-393; Published in Advance January 31, 2006, doi:10.1101/gr.4410706
...were methylated to &gt;50% of completion in the in vitro methylated reference DNA. In general, these results indicate that our assay is specific, and faithfully reports the methylation status of most of the targeted CpG sites in tested samples. Some degree of cross-hybridization may explain those...
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Methods: Cell-free cotranslation and selection using in vitro virus for high-throughput analysis of protein–protein interactions and complexes
- Etsuko Miyamoto-Sato,
- Masamichi Ishizaka,
- Kenichi Horisawa,
- Seiji Tateyama,
- Hideaki Takashima,
- Shinichiro Fuse,
- Kaori Sue,
- Naoya Hirai,
- Kazuyo Masuoka,
- and Hiroshi Yanagawa
Genome Res. May 2005 15: 710-717; doi:10.1101/gr.3510505
...Cell-free cotranslation and selection using in vitro virus for high-throughput analysis of protein–protein interactions and complexes Etsuko Miyamoto-Sato , Masamichi Ishizaka , Kenichi Horisawa , Seiji Tateyama , Hideaki Takashima...
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Research: Massive reshaping of genome–nuclear lamina interactions during oncogene-induced senescence
- Christelle Lenain,
- Carolyn A. de Graaf,
- Ludo Pagie,
- Nils L. Visser,
- Marcel de Haas,
- Sandra S. de Vries,
- Daniel Peric-Hupkes,
- Bas van Steensel,
- and Daniel S. Peeper
Genome Res. October 2017 27: 1634-1644; Published in Advance September 15, 2017, doi:10.1101/gr.225763.117
...), were shown to cause senescence when overexpressed or expressed as oncogenic forms. Work from several laboratories, including ours, demonstrated that this phenomenon, which was initially identified and characterized in vitro, acts as a robust tumor suppressive mechanism in vivo. For instance, we found...
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METHODS: Methylation-Specific Oligonucleotide Microarray: A New Potential for High-Throughput Methylation Analysis
- Raad S. Gitan,
- Huidong Shi,
- Chuan-Mu Chen,
- Pearlly S. Yan,
- and Tim Hui-Ming Huang
Genome Res. January 1, 2002 12: 158-164; Published in Advance December 14, 2001, doi:10.1101/gr.202801
...to be analyzed in MSO microarray. View larger version: In this window In a new window Figure 3. Standardization curve for MSO assays. ( A ) Mixtures of in vitro-methylated and untreated control DNA were prepared and amplified by PCR using bisulfite primers for the human ERα CpG island (see Methods). Target DNA...
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Methods: Development of a microscopic platform for real-time monitoring of biomolecular interactions
- Yasuhiro Sasuga,
- Tomomi Tani,
- Masahito Hayashi,
- Hisashi Yamakawa,
- Osamu Ohara,
- and Yoshie Harada
Genome Res. January 2006 16: 132-139; Published in Advance December 12, 2005, doi:10.1101/gr.4235806
...., Oyama, R., Miyamoto-Sato, E., Sawasaki, T., Endo, Y., et al. 2002 . Novel fluorescence labeling and high-throughput assay technologies for in vitro analysis of protein interaction. Genome Res. 12 : 487 -492. ↵ Funatsu, T., Harada, Y., Tokunaga, M., Saito, K., and Yanagida, T. 1995 . Imaging of single...
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Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
...and mice. The combination of these factors likely contributes to evolutionary differences in myosin expression. The immature nature of the in vitro CM models used in this study may not recapitulate all aspects of the evolutionary divergence between humans and mice (Lundy et al. 2013). Studies using mature...
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