Searching journal content for articles similar to Dombey et al. 35 (3): 522.

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  1. Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
    • DongAhn Yoo,
    • Katherine M. Munson,
    • and Evan E. Eichler
    Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
    ...insertions and lineage-specific duplicated genes. Our findings suggest independent evolution of subterminal caps converging on a common genetic and epigenetic structure that promoted ectopic exchange as well as the emergence of novel genes at transition regions between euchromatin and heterochromatin...
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  2. Research: Dynamic A-to-I RNA editing in response to gut microbiome in honey bees
    • 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 gr.280291.124; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
    ...behavior in mammals (Koh et al. 2016). 398 22 Thus, A-to-I RNA editing in animals is more flexible than we previously understood. 399 Eusocial insects are typical examples showing the powerful epigenetic plasticity that can 400 generate phenotypically distinct individuals from the same . RNA editing...
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  3. Research: Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
    • Xiu Fan,
    • Qili Qian,
    • Wenran Li,
    • Tianzi Liu,
    • Changqing Zeng,
    • Peilin Jia,
    • Huandong Lin,
    • Xin Gao,
    • Li Jin,
    • Mingfeng Xia,
    • Sijia Wang,
    • and Fan Liu
    Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
    ...decreased variability (negative drift). Integration with single-cell RNA-seq data demonstrates that positive drift-CpGs are associated with increased transcriptional variability and upregulation in specific cell types, whereas negative drift-CpGs exhibit the opposite effect. We develop epigenetic drift...
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  4. Resource: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons
    • Qicheng Ma,
    • Satyam P. Srivastav,
    • Stephanie Gamez,
    • Gargi Dayama,
    • Fabiana Feitosa-Suntheimer,
    • Edward I. Patterson,
    • Rebecca M. Johnson,
    • Erik M. Matson,
    • Alexander S. Gold,
    • Douglas E. Brackney,
    • John H. Connor,
    • Tonya M. Colpitts,
    • Grant L. Hughes,
    • Jason L. Rasgon,
    • Tony Nolan,
    • Omar S. Akbari,
    • and Nelson C. Lau
    Genome Res. March 2021 31: 512-528; Published in Advance January 8, 2021, doi:10.1101/gr.265157.120
    ...infection has little impact on mosquito health. This immunity is caused in part by mosquito RNA interference (RNAi) pathways that generate antiviral small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). RNAi also maintains integrity by potently repressing mosquito transposon activity...
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  5. Research: Nanopore direct RNA sequencing reveals METTL2A-mediated m3C sites in poly(A) RNA
    • Shuhei Mitsutomi,
    • Anzu Sugawara,
    • Masahide Seki,
    • Yutaka Suzuki,
    • Sotaro Miyao,
    • Haozhe Du,
    • Kenji Takahashi,
    • Yusuke Mizukami,
    • Kenzui Taniue,
    • and Nobuyoshi Akimitsu
    Genome Res. November 2025 35: 2406-2417; Published in Advance October 30, 2025, doi:10.1101/gr.280269.124
    ...sequence motifs were identified outside the k-mer sequence (Supplemental Fig. S2G). Although the shift in current intensity was small (Supplemental Fig. S2H), similar to observations of other RNA modifications (Garalde et al. 2018; Anreiter et al. 2021), it was reproducible across replicates (Supplemental...
  6. Research: Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains
    • Marta Coronado-Zamora and
    • Josefa González
    Genome Res. September 2023 33: 1541-1553; Published in Advance October 4, 2023, doi:10.1101/gr.277565.122
    ...transcripts can have different insertions in different s. Gray boxes represent exons; red boxes, a TE fragment incorporated in the mRNA; and white boxes, a TE fragment that is not incorporated in the final mRNA. The black lines connecting the exons represent the splicing events.ResultsNine percent of D...
  7. Method: Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression
    • Howard J. Womersley,
    • Daniel Muliaditan,
    • Ramanuj DasGupta,
    • and Lih Feng Cheow
    Genome Res. January 2025 35: 162-177; Published in Advance December 2, 2024, doi:10.1101/gr.279105.124
    ...Fig. S4A). Furthermore, we confirmed the downregulation of TP63 and KRT5, as well as the upregulation of TEAD4 and KRT8/18 during HNSCC metastasis, upon analyzing two previously published scRNA-seq data sets from primary and metastatic HNSCC (Supplemental Fig. S4B–J; Puram et al. 2017; Sharma et al...
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  8. Method: Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications
    • Dayea Park and
    • Can Cenik
    Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
    ...as only one allele is expressed. Allele-specific DNA methylation and chromatin composition are two well-established epigenetic systems that control imprinted gene expression (Fournier et al. 2002; Singh et al. 2010; Prendergast et al. 2012).ASE can reflect differential rates of transcription, mRNA...
  9. Method: Tree-based differential testing using inferential uncertainty for RNA-seq
    • Noor Pratap Singh,
    • Euphy Y. Wu,
    • Jason Fan,
    • Michael I. Love,
    • and Rob Patro
    Genome Res. October 2025 35: 2326-2338; Published in Advance August 21, 2025, doi:10.1101/gr.279981.124
    ...share sequences. Commonly used RNA-seq quantification methods such as RSEM (Li and Dewey 2011), Salmon (Patro et al. 2017), and kallisto (Bray et al. 2016) probabilistically assign each observed fragment to the transcripts using maximum likelihood or Bayesian inference methods. A probabilistic model...
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  10. Method: Analysis of coding gene expression from small RNA sequencing
    • Aygun Azadova,
    • Anthonia Ekperuoh,
    • Greg N. Brooke,
    • and Antonio Marco
    Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
    ...expression can be quantified directly from transcript fragments present in sRNA-seq experiments. We analyze studies containing matched total RNA and small RNA from four human tissues and recover transcript fragments from the sRNA-seq data sets. We find that the expression levels of protein-coding gene...
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