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Research: Transcriptome analyses of rhesus monkey preimplantation embryos reveal a reduced capacity for DNA double-strand break repair in primate oocytes and early embryos
- Xinyi Wang,
- Denghui Liu,
- Dajian He,
- Shengbao Suo,
- Xian Xia,
- Xiechao He,
- Jing-Dong J. Han,
- and Ping Zheng
Genome Res. April 2017 27: 567-579; Published in Advance February 21, 2017, doi:10.1101/gr.198044.115
...for HR-mediated DNA double-strand break repair between primate and rodent To examine if similar regulatory circuitry exists in human and mouse, we performed NP network analysis and identified the three-node loops traversing the maternal-zygotic interfaces in human (Fig. 4B; Supplemental Fig. S10...
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Research: Characterization of the role of spatial proximity of DNA double-strand breaks in the formation of CRISPR-Cas9-induced large structural variations
- Mikkel Dahl-Jessen,
- Thorkild Terkelsen,
- Rasmus O. Bak,
- and Uffe Birk Jensen
Genome Res. February 2025 35: 231-241; Published in Advance January 13, 2025, doi:10.1101/gr.278575.123
...diversity, evolution, and carcinogenesis and are, as such, important for human health. However, it remains unclear how spatial proximity of double-strand breaks (DSBs) affects the formation of SVs. To investigate if spatial proximity between two DSBs affects DNA repair, we used data from 3C experiments (Hi...
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Research: A DNA methylation haplotype block landscape in human tissues and preimplantation embryos reveals regulatory elements defined by comethylation patterns
- Yan Feng,
- Zhiqiang Zhang,
- Yuyang Hong,
- Yi Ding,
- Leiqin Liu,
- Siqi Gao,
- Hai Fang,
- and Jiantao Shi
Genome Res. December 2023 33: 2041-2052; Published in Advance November 8, 2023, doi:10.1101/gr.278146.123
...preimplantation embryos using well-curated WGBS data sets. We aim to characterize the tissue-specific regulatory potential of MHBs through large-scale data integration. We examined MHB enrichment in open chromatin regions, association with gene expression, and tissue-specific genes in comparison to known DNA...
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Research: Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion
- Brittany L. Daughtry,
- Jimi L. Rosenkrantz,
- Nathan H. Lazar,
- Suzanne S. Fei,
- Nash Redmayne,
- Kristof A. Torkenczy,
- Andrew Adey,
- Melissa Yan,
- Lina Gao,
- Byung Park,
- Kimberly A. Nevonen,
- Lucia Carbone,
- and Shawn L. Chavez
Genome Res. March 2019 29: 367-382; Published in Advance January 25, 2019, doi:10.1101/gr.239830.118
...fragmentation is conserved between primatesTo determine the aneuploidy and micronucleation frequency in rhesus cleavage-stage embryos, we developed an experimental approach using scDNA-seq and TLM to noninvasively assess preimplantation development (Fig. 1A). Mature metaphase II (MII) oocytes underwent...
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Research: Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids
- Cheng Zhao,
- Savana Biondic,
- Katherine Vandal,
- Åsa K. Björklund,
- Michael Hagemann-Jensen,
- Theresa Maria Sommer,
- Jesica Canizo,
- Stephen Clark,
- Pascal Raymond,
- Daniel R. Zenklusen,
- Nicolas Rivron,
- Wolf Reik,
- and Sophie Petropoulos
Genome Res. September 2022 32: 1627-1641; Published in Advance August 10, 2022, doi:10.1101/gr.276665.122
...emphasized that the TE sublineages display a differential response to glucocorticoid exposure and dysregulation of metabolic signaling and inflammatory response (Supplemental Table S3).Impact of glucocorticoid exposure on human preimplantation embryo methylomeDNA methylation plays a critical role...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J Smith,
- and Falk Butter
Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...E, Cervantes MD, Hamilton EP. 2011. Tetrahymena thermophila, a unicellular 556 eukaryote with separate germline and somatic s. Res Microbiol 162: 578–557 586. 558 18 Pannunzio NR, Watanabe G, Lieber MR. 2018. Nonhomologous DNA end-joining for 559 repair of DNA double-strand breaks. J Biol Chem 293...
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Research: Somatic retrotransposition in the developing rhesus macaque brain
- Victor Billon,
- Francisco J. Sanchez-Luque,
- Jay Rasmussen,
- Gabriela O. Bodea,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Seth W. Cheetham,
- Stephanie N. Schauer,
- Prabha Ajjikuttira,
- Thomas J. Meyer,
- Cora E. Layman,
- Kimberly A. Nevonen,
- Natasha Jansz,
- Jose L. Garcia-Perez,
- Sandra R. Richardson,
- Adam D. Ewing,
- Lucia Carbone,
- and Geoffrey J. Faulkner
Genome Res. July 2022 32: 1298-1314; Published in Advance June 21, 2022, doi:10.1101/gr.276451.121
...and 5′ truncated to remove almost all of the upstream PRDM4 exons; or (4) DNA methylation does not as strongly underpin macaque L1RS2 transcriptional repression as it does human L1HS repression.L1RSPRDM4 is the first endogenously mobile nonhuman primate L1, to our knowledge, to be tested in a cultured...
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Research: Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication
- Vinay Tripuraneni,
- Gonen Memisoglu,
- Heather K. MacAlpine,
- Trung Q. Tran,
- Wei Zhu,
- Alexander J. Hartemink,
- James E. Haber,
- and David M. MacAlpine
Genome Res. May 2021 31: 775-788; Published in Advance April 2, 2021, doi:10.1101/gr.271155.120
...-establishment of the prelesion chromatin landscape suggests that a DNA replication-independent mechanism exists to preserve epi organization following DSB repair.Failure to repair DNA double-strand breaks (DSBs) results in cell cycle arrest and ultimately programmed cell death, whereas improper repair can lead to profound...
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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
...in double-stranded DNA and ∼200 years in single-stranded DNA (Frederico et al. 1990). In contrast, the rate of deamination is vastly accelerated for cytosine bases in CPDs, with a half-life of tens to hundreds of hours (Taylor 2022). Because even error-free replicative bypass of a deaminated CPD (d...
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Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
...on both strands. In addition, the GENCODE database, a well-regarded repository of gene annotations, was utilized to search for cis-NAT regions. We identified 12,793 genomic regions annotated as being expressed from both the positive and negative DNA strands (regardless of whether they are expressed...
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