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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...Yuange Duan,1 Min Huang,1 Lin Ye,1 Ling Ma, Yashuai Wu, Yating Du, Jiyao Liu, Fan Song, Li Tian, Wanzhi Cai, Hu Li, Xin Zhou, and Shiqi Luo State Key Laboratory of Agricultural and Forestry Biosecurity, MOA Key Laboratory of Pest Monitoring and Green Management, Department of Entomology, College...
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Research: Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy
- Hadi Rahmaninejad,
- Yao Xiao,
- Maxime M.C. Tortora,
- and Geoffrey Fudenberg
Genome Res. August 2025 35: 1745-1757; Published in Advance July 8, 2025, doi:10.1101/gr.280108.124
...develop a dynamic barrier model, where CTCF sites switch between bound and unbound states. Using this model, we investigate how barrier dynamics would impact observables for a range of experimental genomic and imaging data sets, including ChIP-seq, Hi-C, and microscopy. We find the interplay of CTCF...
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Resource: Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level
- Wankun Deng,
- Citu Citu,
- Andi Liu,
- and Zhongming Zhao
Genome Res. October 2024 34: 1687-1699; Published in Advance October 18, 2024, doi:10.1101/gr.279363.124
...-cell transcriptome profiles from 12 data sets covering AD, PD, and MS, aiming to elucidate the dynamics of RTEs across different cell types and disease states. Our results highlight cell type–specific and disease-specific regulation of RTEs, offering a detailed single-cell-level landscape of RTE expression in normal...
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Method: A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data
- Cameron Park,
- Shouvik Mani,
- Nicolas Beltran-Velez,
- Katie Maurer,
- Teddy Huang,
- Shuqiang Li,
- Satyen Gohil,
- Kenneth J. Livak,
- David A. Knowles,
- Catherine J. Wu,
- and Elham Azizi
Genome Res. September 2024 34: 1384-1396; Published in Advance September 5, 2024, doi:10.1101/gr.279126.124
...successful in integrating time-series single-cell data sets (Lönnberg et al. 2017), and in identifying key cell states with distinct temporal dynamics shaping response to immunotherapy in human leukemia (Bachireddy et al. 2021). By utilizing GPs, which encode temporal dependencies between all pairs of time...
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Research: Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States
- Greta Bellinzona,
- Tiago Nardi,
- Michele Castelli,
- Gherard Batisti Biffignandi,
- Karim Adjou,
- Martha Betson,
- Yannick Blanchard,
- Ioana Bujila,
- Rachel Chalmers,
- Rebecca Davidson,
- Nicoletta D'Avino,
- Tuulia Enbom,
- Jacinto Gomes,
- Gregory Karadjian,
- Christian Klotz,
- Emma Östlund,
- Judith Plutzer,
- Ruska Rimhanen-Finne,
- Guy Robinson,
- Anna Rosa Sannella,
- Jacek Sroka,
- Christen Rune Stensvold,
- Karin Troell,
- Paolo Vatta,
- Barbora Zalewska,
- Claudio Bandi,
- Davide Sassera,
- and Simone M. Cacciò
Genome Res. June 2024 34: 877-887; Published in Advance July 8, 2024, doi:10.1101/gr.278830.123
...(IIa) clustered in population 3. Based on analyses of the population structure, population genetics, and recombination, we show that population 3 has recently emerged and expanded throughout Europe to then, possibly from the United Kingdom, reach the United States, where it also expanded. The reason...
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Research: Characterization of the distribution and dynamics of chromatin states in the C. elegans germline reveals substantial H3K4me3 remodeling during oogenesis
- Mariateresa Mazzetto,
- Lauren E. Gonzalez,
- Nancy Sanchez,
- and Valerie Reinke
Genome Res. January 2024 34: 57-69; Published in Advance December 26, 2023, doi:10.1101/gr.278247.123
...-specific chromatin state data permit investigation of the environment surrounding genes expressed throughout germline development, as well as the role of small RNA regulation in establishing the chromatin environment of target loci. Moreover, the identification of histone modifications that show particularly dynamic...
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Research: Dynamic DNA N⁶-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus
- Yongqiang Liu,
- Junhua Niu,
- Fei Ye,
- Therese Solberg,
- Borong Lu,
- Chundi Wang,
- Mariusz Nowacki,
- and Shan Gao
Genome Res. February 2024 34: 256-271; Published in Advance March 12, 2024, doi:10.1101/gr.278796.123
...the distribution of 6mA in trophonts and cysts by generating a novel P. persalinus assembly with single-nucleotide resolution of 6mA sites. We found that 6mA is a dynamic modification with the following characteristics in the s of two different physiological states: (1) 6mA is enriched in complementary Ap...
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Research: Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
- Akanksha Bafna,
- Gareth Banks,
- Michael H. Hastings,
- and Patrick M. Nolan
Genome Res. May 2023 33: 673-688; Published in Advance May 8, 2023, doi:10.1101/gr.277581.122
...al. 2003) and offered an excellent opportunity to understand the relationship between changing chromatin state and gene expression.Given the dynamic nature of histone acetylation in the SCN, we investigated the abundance of noncoding eRNAs that can regulate target gene expression, for instance...
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Resource: Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish
- Bryan B. Teefy,
- Ari Adler,
- Alan Xu,
- Katelyn Hsu,
- Param Priya Singh,
- and Bérénice A. Benayoun
Genome Res. January 2023 33: 141-153; Published in Advance December 28, 2022, doi:10.1101/gr.277301.122
...is crucial to allow the emergence of nonaging states, such as those found in the germline.Dynamic TE control in the aging African turquoise killifish ovaryIf piRNA metabolism dynamics in the turquoise killifish ovary are similar to those of zebrafish (with Piwil1 expression largely confined to immature germ...
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Resource: Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis
- Yingshu Li,
- Yongjie Liu,
- Hang Yang,
- Ting Zhang,
- Kiyoshi Naruse,
- and Qiang Tu
Genome Res. June 2020 30: 924-937; Published in Advance June 26, 2020, doi:10.1101/gr.258871.119
...Yingshu Li1,2,3,5, Yongjie Liu1,2,3,5, Hang Yang1,2,3, Ting Zhang1,2, Kiyoshi Naruse4 and Qiang Tu1,2,3 1State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China...
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