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Research: Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models
- Yiqiao Zheng,
- Gary D. Stormo,
- and Shiming Chen
Genome Res. February 2025 35: 242-256; Published in Advance December 23, 2024, doi:10.1101/gr.279340.124
...Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models Yiqiao Zheng1,2,5, Gary D. Stormo3 and Shiming Chen2,4 1Molecular Genetics and Genomics Graduate Program, Division of Biology & Biomedical Sciences, Washington...
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Research: Semiconservative transmission of DNA N⁶-adenine methylation in a unicellular eukaryote
- Yalan Sheng,
- Yuanyuan Wang,
- Wentao Yang,
- Xue Qing Wang,
- Jiuwei Lu,
- Bo Pan,
- Bei Nan,
- Yongqiang Liu,
- Fei Ye,
- Chun Li,
- Jikui Song,
- Yali Dou,
- Shan Gao,
- and Yifan Liu
Genome Res. May 2024 34: 740-756; Published in Advance May 14, 2024, doi:10.1101/gr.277843.123
....Liu@med.usc.eduAbstractAlthough DNA N6-adenine methylation (6mA) is best known in prokaryotes, its presence in eukaryotes has recently generated great interest. Biochemical and genetic evidence supports that AMT1, an MT-A70 family methyltransferase (MTase), is crucial for 6mA deposition in unicellular eukaryotes. Nonetheless, the 6m...
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Research: Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction
- Kimberly N. Griffin,
- Benjamin William Walters,
- Haixin Li,
- Huafeng Wang,
- Giulia Biancon,
- Toma Tebaldi,
- Carolyn B. Kaya,
- Jean Kanyo,
- TuKiet T. Lam,
- Andy L. Cox,
- Stephanie Halene,
- Jean-Ju Chung,
- and Bluma J. Lesch
Genome Res. September 2022 32: 1655-1668; Published in Advance September 15, 2022, doi:10.1101/gr.276578.122
...proteins. Correspondingly, Ago2 cKO males show abnormal sperm head morphology and reduced sperm count, along with reduced postnatal viability of offspring. Together, our data reveal an unexpected nuclear role for AGO2 in enhancing expression of developmentally important genes during mammalian male...
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Research: High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes
- Walter Muskovic,
- Eve Slavich,
- Ben Maslen,
- Dominik C. Kaczorowski,
- Joseph Cursons,
- Edmund Crampin,
- and Maria Kavallaris
Genome Res. August 2022 32: 1463-1473; Published in Advance June 27, 2022, doi:10.1101/gr.276818.122
.... Indeed, existing limited investigations of lncRNA dynamics in transitioning mammalian cells indicate that lncRNA production precedes activation of protein-coding genes (De Santa et al. 2010; Aitken et al. 2015; Arner et al. 2015), providing evidence for lncRNAs as ubiquitous cis-regulators of gene...
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Research: Chromatin conformation and transcriptional activity are permissive regulators of DNA replication initiation in Drosophila
- Robin L. Armstrong,
- Taylor J.R. Penke,
- Brian D. Strahl,
- A. Gregory Matera,
- Daniel J. McKay,
- David M. MacAlpine,
- and Robert J. Duronio
Genome Res. November 2018 28: 1688-1700; Published in Advance October 2, 2018, doi:10.1101/gr.239913.118
...that H4K16 modification is dispensable for replication and gene expression.Animal cells duplicate large, complex s by initiating replication at distinct locations within the at different times during S phase. An evolutionarily conserved feature of this regulatory paradigm is a temporal order of DNA...
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Research: Common genomic elements promote transcriptional and DNA replication roadblocks
- Kevin Roy,
- Jason Gabunilas,
- Abigail Gillespie,
- Duy Ngo,
- and Guillaume F. Chanfreau
Genome Res. October 2016 26: 1363-1375; Published in Advance August 18, 2016, doi:10.1101/gr.204776.116
...Common genomic elements promote transcriptional and DNA replication roadblocks Kevin Roy 1 , 2 , Jason Gabunilas 1 , Abigail Gillespie 1 , Duy Ngo 1 and Guillaume F. Chanfreau 1 , 2 1Department of Chemistry and Biochemistry...
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Method: SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells
- Kyung Yeon Han,
- Kyu-Tae Kim,
- Je-Gun Joung,
- Dae-Soon Son,
- Yeon Jeong Kim,
- Areum Jo,
- Hyo-Jeong Jeon,
- Hui-Sung Moon,
- Chang Eun Yoo,
- Woosung Chung,
- Hye Hyeon Eum,
- Sangmin Kim,
- Hong Kwan Kim,
- Jeong Eon Lee,
- Myung-Ju Ahn,
- Hae-Ock Lee,
- Donghyun Park,
- and Woong-Yang Park
Genome Res. January 2018 28: 75-87; Published in Advance December 5, 2017, doi:10.1101/gr.223263.117
...technically challenging to analyze both the and transcriptome in the same cell. Here, we report a novel method for simultaneous isolation of genomic DNA and total RNA (SIDR) from single cells, achieving high recovery rates with minimal cross-contamination, as is crucial for accurate description...
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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
..., et al. 2010. Mammalian mitochondrial DNA replication intermediates are essentially duplex but contain extensive tracts of RNA/DNA hybrid. J Mol Biol 397: 1144–1155. ↵Rigby RE, Webb LM, Mackenzie KJ, Li Y, Leitch A, Reijns MAM, Lundie RJ, Revuelta A, Davidson DJ, Diebold S, et al. 2014. RNA:DNA...
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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
...of the Saccharomyces cerevisiae DNA damage-responsive kinase Tel1 (ortholog of mammalian ATM). A tel1Δ mutant has globally increased amounts of Spo11-oligonucleotide complexes and altered Spo11-oligonucleotide lengths, consistent with conserved roles for Tel1 in control of DSB number and processing. A kinase-dead tel1...
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Research: Global genome nucleotide excision repair is organized into domains that promote efficient DNA repair in chromatin
- Shirong Yu,
- Katie Evans,
- Patrick van Eijk,
- Mark Bennett,
- Richard M. Webster,
- Matthew Leadbitter,
- Yumin Teng,
- Raymond Waters,
- Stephen P. Jackson,
- and Simon H. Reed
Genome Res. October 2016 26: 1376-1387; Published in Advance July 28, 2016, doi:10.1101/gr.209106.116
...Global genome nucleotide excision repair is organized into domains that promote efficient DNA repair in chromatin Shirong Yu 1 , 3 , 4 , Katie Evans 1 , 3 , Patrick van Eijk 1 , Mark Bennett 1 , Richard M. Webster 1 , Matthew...
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