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Research: Tyrosine 1–phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage
- Kamal Ajit,
- Adele Alagia,
- Kaspar Burger,
- and Monika Gullerova
Genome Res. February 2024 34: 201-216; Published in Advance March 11, 2024, doi:10.1101/gr.278644.123
.... S3D,E), whereas S5P transcription of lncRNA resulted in few detectable changes upon IR (Supplemental Fig. S3F).Overall, our data showed that IR-induced DNA damage leads to general down-regulation of PCGs and up-regulation of lncRNA, in particular, those that are in antisense orientation...
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Method: High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow
- Xue Dong,
- Mengzhu Hu,
- Xiaonan Cui,
- Wenjian Zhou,
- Jingtao Cai,
- Guangyao Mao,
- and Weiyang Shi
Genome Res. September 2025 35: 2052-2063; Published in Advance August 5, 2025, doi:10.1101/gr.279906.124
...washes to eliminate hybridization products between partially double-stranded sequences and cDNA in nonilluminated regions, reducing background noise. Fluorescent oligonucleotides were used to simulate this reaction, incorporating sequential illumination, adapter ligation, and high-concentration formamide...
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Method: RNA-DNA hybrid (R-loop) immunoprecipitation mapping: an analytical workflow to evaluate inherent biases
- László Halász,
- Zsolt Karányi,
- Beáta Boros-Oláh,
- Tímea Kuik-Rózsa,
- Éva Sipos,
- Éva Nagy,
- Ágnes Mosolygó-L,
- Anett Mázló,
- Éva Rajnavölgyi,
- Gábor Halmos,
- and Lóránt Székvölgyi
Genome Res. June 2017 27: 1063-1073; Published in Advance March 24, 2017, doi:10.1101/gr.219394.116
...(Supplemental Fig. S2C,D) applying fluorescent microscopic detection. Based on these experiences, RNase A digestion at high salt concentration (300 mM NaCl) was integrated into our DRIP protocol to test if removal of competing free RNA improves the specificity of the RNA-DNA hybrid signal. Also, RNase H1...
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METHODS: iFRET: An Improved Fluorescence System for DNA-Melting Analysis
- W. Mathias Howell,
- Magnus Jobs,
- and Anthony J. Brookes
Genome Res. September 1, 2002 12: 1401-1407; doi:10.1101/gr.297202
...resonance energy transfer (FRET) is a powerful tool for detecting spatial relationships between macromolecules, one use of which is the tracking of DNA hybridization status. The process involves measuring changes in fluorescence as FRET donor and acceptor moieties are brought closer together or moved...
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Research: Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators
- Lauren R. Polstein,
- Pablo Perez-Pinera,
- D. Dewran Kocak,
- Christopher M. Vockley,
- Peggy Bledsoe,
- Lingyun Song,
- Alexias Safi,
- Gregory E. Crawford,
- Timothy E. Reddy,
- and Charles A. Gersbach
Genome Res. August 2015 25: 1158-1169; Published in Advance May 29, 2015, doi:10.1101/gr.179044.114
...isolation kit (Qiagen). cDNA synthesis was performed using the SuperScript VILO cDNA Synthesis Kit (Invitrogen). Real-time PCR using PerfeCTa SYBR Green FastMix was performed with the CFX96 Real-Time PCR Detection System (Bio-Rad). Primer specificity was confirmed by agarose gel electrophoresis and melting...
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Research: DNA methylation at hepatitis B viral integrants is associated with methylation at flanking human genomic sequences
- Yoshiyuki Watanabe,
- Hiroyuki Yamamoto,
- Ritsuko Oikawa,
- Minoru Toyota,
- Masakazu Yamamoto,
- Norihiro Kokudo,
- Shinji Tanaka,
- Shigeki Arii,
- Hiroshi Yotsuyanagi,
- Kazuhiko Koike,
- and Fumio Itoh
Genome Res. March 2015 25: 328-337; Published in Advance February 4, 2015, doi:10.1101/gr.175240.114
.... Therefore, -wide methylation analysis of the integrated HBV sequence is necessary in relation to the methylation state of the adjacent human . We did not detect an association between HBx methylation levels and those of the LINE1 and AluYb8 repeats (Fig. 1B). Fluorescence in situ hybridization (FISH...
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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
...immunoprecipitation followed by sequencing (SPI-seq) to map genomic hotspots of DNA damage. We demonstrated this method with Rad52, a homologous recombination repair protein, which binds to ssDNA formed at DNA lesions. SPI-seq faithfully detected, in fission yeast, Rad52 enrichment at artificially induced double...
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Methods: Fluorescent Detection and Isolation of DNA Variants Using Stabilized RecA-Coated Oligonucleotides
- Michael C. Rice,
- Brandy M. Heckman,
- Yi Liu,
- and Eric B. Kmiec
Genome Res. January 2004 14: 116-125; Published in Advance December 12, 2003, doi:10.1101/gr.1386204
...; Zhong et al. 2001 ), have been developed. These assays use an isothermal linear amplification method to detect sequence variations. The Invader assay uses mismatch-specific DNA cleavage products, which release fluorophore quenching to emit a fluorescent signal, whereas RCA uses mismatch...
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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
.... 2019; Singh et al. 2019; Buikema et al. 2020). GSK3i promotes cell cycling, marked by DNA synthesis and mitosis; reduced cell ploidy; and sarcomere disassembly—all markers of CM immaturity (Mollova et al. 2013; Mills et al. 2019; Singh et al. 2019; Buikema et al. 2020).CHIR99021 (CHIR) is a potent GSK3...
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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
....Transcriptional regulation in eukaryotes is profoundly influenced by chromatin status, integrating diverse cellular signals to control gene expression (Berger 2007). Chromatin dynamics are modulated by multiple mechanisms, including histone modifications, DNA methylation, and chromatin remodeling complexes (Shilatifard 2006...

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