Searching journal content for articles similar to Polak and Arndt 18 (8): 1216.

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Method: Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications
- Xudong Liu,
- Ying Ni,
- Lianwei Ye,
- Zhihao Guo,
- Lu Tan,
- Jun Li,
- Mengsu Yang,
- Sheng Chen,
- and Runsheng Li
Genome Res. November 2024 34: 2025-2038; Published in Advance October 2, 2024, doi:10.1101/gr.279012.124
...are found only in one strand but not the other, showing a strand-specific bias. Leveraging this discovery, we developed Hammerhead, a pioneering pipeline designed for de novo methylation discovery that circumvents the necessity of raw signal inference and a methylation-free control. The majority (14 out...
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Method: Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing
- Yanjun Zhang,
- Yin Tang,
- Zhongxing Sun,
- Junqi Jia,
- Yuan Fang,
- Xinyi Wan,
- and Dong Fang
Genome Res. March 2023 33: 412-426; Published in Advance March 23, 2023, doi:10.1101/gr.277213.122
..., the ratios of identified reads at exons and introns were similar between these two kinds of libraries (Fig. 3E).To analyze the strand specificity of sequencing reads, we profiled sequencing reads at the sense and antisense strands spanning 2 kb of the transcription start site (TSS) of all genes (Fig. 3F...
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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
...proportion of Schwann cells, which are functionally required for supporting/myelinating peripheral neurons. In a previous study, Sandy-Hindmarch et al. (2025) performed strand-specific bulk RNA-seq on Morton's neuroma and control samples from males and females independently. These samples were collected from...
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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
...sensitive approach with the concomitant ability to determine TSSs by using sequence-specific DNA probes together with single-strand-specific nucleases to preserve hybridized RNA fragments while degrading unprotected single-stranded RNAs (Zhao et al. 2020). This method enables precise quantification of RNA...
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Method: DENT-seq for genome-wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution
- Juniper J. Elacqua,
- Navpreet Ranu,
- Sarah E. DiIorio,
- and Paul C. Blainey
Genome Res. January 2021 31: 75-87; Published in Advance December 21, 2020, doi:10.1101/gr.265223.120
...and sequencing, sequence coverage and mutational information allow for sensitive single-nucleotide-resolved and strand-specific identification of nick sites.To characterize the mutational signatures that arise from P and K, we annealed custom oligonucleotides to obtain four DNA molecules, each with a nick...
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Method: Mapping genomic hotspots of DNA damage by a single-strand-DNA-compatible and strand-specific ChIP-seq method
- Zhi-Xiong Zhou,
- Mei-Jun Zhang,
- Xu Peng,
- Yuko Takayama,
- Xing-Ya Xu,
- Ling-Zhi Huang,
- and Li-Lin Du
Genome Res. April 2013 23: 705-715; Published in Advance December 17, 2012, doi:10.1101/gr.146357.112
...Mapping genomic hotspots of DNA damage by a single-strand-DNA-compatible and strand-specific ChIP-seq method Zhi-Xiong Zhou 1 , 2 , 4 , Mei-Jun Zhang 2 , 4 , Xu Peng 2 , Yuko Takayama 3 , Xing-Ya Xu 2 , Ling-Zhi Huang 2...
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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...CPD-seq data reveal that sequence context significantly modulates CPD deamination rates in UV-irradiated yeast cells, with CPDs in TCG contexts showing particularly rapid deamination rates. Our analysis indicates that rapid CPD deamination can explain why UV-induced mutations are specifically enriched at TCG...
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Research: Linking the dynamics of chromatin occupancy and transcription with predictive models
- Trung Q. Tran,
- Heather K. MacAlpine,
- Vinay Tripuraneni,
- Sneha Mitra,
- David M. MacAlpine,
- and Alexander J. Hartemink
Genome Res. June 2021 31: 1035-1046; Published in Advance April 23, 2021, doi:10.1101/gr.267237.120
...to cadmium and samples were collected over a two-hour time course. Chromatin occupancy and positioning dynamics were profiled using paired-end MNase-seq to map DNA-binding factors at base-pair resolution (Fig. 1A; Supplemental Method S1). Concurrently, transcripts were interrogated using strand-specific...
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Resource: A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells
- William K.M. Lai,
- Luca Mariani,
- Gerson Rothschild,
- Edwin R. Smith,
- Bryan J. Venters,
- Thomas R. Blanda,
- Prashant K. Kuntala,
- Kylie Bocklund,
- Joshua Mairose,
- Sarah N. Dweikat,
- Katelyn Mistretta,
- Matthew J. Rossi,
- Daniela James,
- James T. Anderson,
- Sabrina K. Phanor,
- Wanwei Zhang,
- Zibo Zhao,
- Avani P. Shah,
- Katherine Novitzky,
- Eileen McAnarney,
- Michael-C. Keogh,
- Ali Shilatifard,
- Uttiya Basu,
- Martha L. Bulyk,
- and B. Franklin Pugh
Genome Res. September 2021 31: 1663-1679; Published in Advance August 23, 2021, doi:10.1101/gr.275472.121
...2012; Rossi et al. 2018). Briefly, proteins were formaldehyde cross-linked to DNA and each other within cells. Chromatin was then isolated, fragmented, and immunoprecipitated. While on the beads, the fragmented DNA was trimmed with a strand-specific 5′–3′ exonuclease up to the point of cross-linking (i...
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Research: BRF1 mutations alter RNA polymerase III–dependent transcription and cause neurodevelopmental anomalies
- Guntram Borck,
- Friederike Hög,
- Maria Lisa Dentici,
- Perciliz L. Tan,
- Nadine Sowada,
- Ana Medeira,
- Lucie Gueneau,
- Holger Thiele,
- Maria Kousi,
- Francesca Lepri,
- Larissa Wenzeck,
- Ian Blumenthal,
- Antonio Radicioni,
- Tito Livio Schwarzenberg,
- Barbara Mandriani,
- Rita Fischetto,
- Deborah J. Morris-Rosendahl,
- Janine Altmüller,
- Alexandre Reymond,
- Peter Nürnberg,
- Giuseppe Merla,
- Bruno Dallapiccola,
- Nicholas Katsanis,
- Patrick Cramer,
- and Christian Kubisch
Genome Res. February 2015 25: 155-166; Published in Advance January 5, 2015, doi:10.1101/gr.176925.114
...BRF1 mutations alter RNA polymerase III–dependent transcription and cause neurodevelopmental anomalies Guntram Borck 1 , 20 , Friederike Hög 2 , 20 , Maria Lisa Dentici 3 , 20 , Perciliz L. Tan 4 , 20 , Nadine Sowada 1...

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