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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...before (DAP-seq) and after PCR amplification (ampDAP-seq), where the amplification depletes the library of DNA methylation. MBD5 and MBD6 showed sequence enrichment, but only for DAP-seq, where DNA methylation was present, and with binding site profiles that closely match those identified by Ch...
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Resource: Human proteins that interact with RNA/DNA hybrids
- Isabel X. Wang,
- Christopher Grunseich,
- Jennifer Fox,
- Joshua Burdick,
- Zhengwei Zhu,
- Niema Ravazian,
- Markus Hafner,
- and Vivian G. Cheung
Genome Res. September 2018 28: 1405-1414; Published in Advance August 14, 2018, doi:10.1101/gr.237362.118
...hybrid-binding proteins were still specifically pulled down. Fold enrichment of proteins in pull down is calculated as the ratio of MS/MS counts of a detected protein from two samples. We set the threshold of fold enrichment ≥1.2 for a protein to be considered enriched.RNA/DNA hybrid immunoprecipitation...
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Research: The strand-biased mitochondrial DNA methylome and its regulation by DNMT3A
- Xiaoyang Dou,
- Jerome D. Boyd-Kirkup,
- Joseph McDermott,
- Xiaoli Zhang,
- Fang Li,
- Bowen Rong,
- Rui Zhang,
- Bisi Miao,
- Peilin Chen,
- Hao Cheng,
- Jianhuang Xue,
- David Bennett,
- Jiemin Wong,
- Fei Lan,
- and Jing-Dong J. Han
Genome Res. October 2019 29: 1622-1634; Published in Advance September 19, 2019, doi:10.1101/gr.234021.117
...in the EpiTect Whole Bisulfitome Kit (QIAGEN). MDA uses short random hexamer primers and a high-fidelity Phi 29 polymerase for amplification of large amounts of DNA in a nonspecific manner. All bisulfite-converted mtDNA was amplified according to the manufacturers’ protocol. Samples were cleaned using...
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Research: Environmentally induced plasticity of programmed DNA elimination boosts somatic variability in Paramecium tetraurelia
- Valerio Vitali,
- Rebecca Hagen,
- and Francesco Catania
Genome Res. October 2019 29: 1693-1704; Published in Advance September 23, 2019, doi:10.1101/gr.245332.118
..., and DCL5 silencing yields viable sexual offspring (Sandoval et al. 2014), demonstrating that inefficient IES excision can be tolerated to some degree.In addition to variable chromosome fragmentation (Caron 1992), two types of erroneous DNA elimination under spontaneous conditions were described even...
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Method: Transcript amplification from single bacterium for transcriptome analysis
- Yun Kang,
- Michael H. Norris,
- Jan Zarzycki-Siek,
- William C. Nierman,
- Stuart P. Donachie,
- and Tung T. Hoang
Genome Res. June 2011 21: 925-935; Published in Advance May 2, 2011, doi:10.1101/gr.116103.110
...independent amplifications of 2 pg of purified and diluted RNA. We correlated the fold-change of the amplified to nonamplified Figure 3. Fold-change scatter plots of expressed genes obtained from nonamplified versus amplified samples. 10–14 mg (A), 20–25mg (B), or 30–35mg (C ) of DNA amplified from five...
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Research: Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells
- Young Seok Ju,
- Jose M.C. Tubio,
- William Mifsud,
- Beiyuan Fu,
- Helen R. Davies,
- Manasa Ramakrishna,
- Yilong Li,
- Lucy Yates,
- Gunes Gundem,
- Patrick S. Tarpey,
- Sam Behjati,
- Elli Papaemmanuil,
- Sancha Martin,
- Anthony Fullam,
- Moritz Gerstung,
- ICGC Prostate Cancer Working Group,
- ICGC Bone Cancer Working Group,
- ICGC Breast Cancer Working Group,
- Jyoti Nangalia,
- Anthony R. Green,
- Carlos Caldas,
- Åke Borg,
- Andrew Tutt,
- Ming Ta Michael Lee,
- Laura J. van't Veer,
- Benita K.T. Tan,
- Samuel Aparicio,
- Paul N. Span,
- John W.M. Martens,
- Stian Knappskog,
- Anne Vincent-Salomon,
- Anne-Lise Børresen-Dale,
- Jórunn Erla Eyfjörd,
- Ola Myklebost,
- Adrienne M. Flanagan,
- Christopher Foster,
- David E. Neal,
- Colin Cooper,
- Rosalind Eeles,
- G. Steven Bova,
- Sunil R. Lakhani,
- Christine Desmedt,
- Gilles Thomas,
- Andrea L. Richardson,
- Colin A. Purdie,
- Alastair M. Thompson,
- Ultan McDermott,
- Fengtang Yang,
- Serena Nik-Zainal,
- Peter J. Campbell,
- and Michael R. Stratton
Genome Res. June 2015 25: 814-824; Published in Advance May 11, 2015, doi:10.1101/gr.190470.115
...rate 2.0%, 12 out of 587 samples), we observed 25 cancer-specific mitochondrial-nuclear DNA junctions (Table 1; Supplemental Figs. 1–6). Given that there are two junctions for a single integration event, we conclude that there are most likely 16 independent mtDNA insertions (Table 1). In addition...
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Method: Single-step capture and sequencing of natural DNA for detection of BRCA1 mutations
- John F. Thompson,
- Jeffrey G. Reifenberger,
- Eldar Giladi,
- Kristen Kerouac,
- Jaime Gill,
- Erik Hansen,
- Avak Kahvejian,
- Philipp Kapranov,
- Travis Knope,
- Doron Lipson,
- Kathleen E. Steinmann,
- and Patrice M. Milos
Genome Res. February 2012 22: 340-345; Published in Advance July 15, 2011, doi:10.1101/gr.122192.111
...-molecule sequencing. Gene isolation, amplification, or ligation is not necessary. Accurate and low-cost detection of DNA sequence variants is demonstrated for the BRCA1 gene. Disease-causing mutations as well as common variants from well-characterized samples are identified. Single-molecule sequencing generates very...
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Method: High resolution mapping of modified DNA nucleobases using excision repair enzymes
- D. Suzi Bryan,
- Monica Ransom,
- Biniam Adane,
- Kerri York,
- and Jay R. Hesselberth
Genome Res. September 2014 24: 1534-1542; Published in Advance July 11, 2014, doi:10.1101/gr.174052.114
..., or these could be false positive signals generated by, e.g., photolyase bias in the assay. Finally, other factors including the quality of DNA starting material for Excision-seq libraries could influence the false positive rate for individual samples. For example, predigestion Excision-seq libraries should...
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Method: True single-molecule DNA sequencing of a pleistocene horse bone
- Ludovic Orlando,
- Aurelien Ginolhac,
- Maanasa Raghavan,
- Julia Vilstrup,
- Morten Rasmussen,
- Kim Magnussen,
- Kathleen E. Steinmann,
- Philipp Kapranov,
- John F. Thompson,
- Grant Zazula,
- Duane Froese,
- Ida Moltke,
- Beth Shapiro,
- Michael Hofreiter,
- Khaled A.S. Al-Rasheid,
- M. Thomas P. Gilbert,
- and Eske Willerslev
Genome Res. October 2011 21: 1705-1719; Published in Advance July 29, 2011, doi:10.1101/gr.122747.111
...Arabia Abstract Second-generation sequencing platforms have revolutionized the field of ancient DNA, opening access to complete genomes of past individuals and extinct species. However, these platforms are dependent on library construction and amplification steps that may result in sequences...
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Research: CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize
- Jonathan I. Gent,
- Nathanael A. Ellis,
- Lin Guo,
- Alex E. Harkess,
- Yingyin Yao,
- Xiaoyu Zhang,
- and R. Kelly Dawe
Genome Res. April 2013 23: 628-637; Published in Advance December 26, 2012, doi:10.1101/gr.146985.112
...with default parameters, except for the following: ‘‘format fastq–trim-end right–adaptive-overlap yes– min-readlength 53–max-uncalled 20.’’ Bisulfite-treated DNA Libraries were prepared for bisulfite sequencing using a method similar to that of Lister et al. (2009). The sample was Illumina sequenced in two...

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