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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
...the parameters consistently changed (P-value < 0.05) under both siRNAs targeting METTL2A were identified as sites with parameter variation. Sequence logos for k-mer sequences with changes in the current signal parameter were generated using WebLogo (version 3.7.9) (Crooks et al. 2004). MEME motif analysis...
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Research: SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress
- Fu-Yuan Zhu,
- Xin Chen,
- Yu-Chen Song,
- Lydia Pui Ying Lam,
- Yuki Tobimatsu,
- Bei Gao,
- Mo-Xian Chen,
- and Fu-Liang Cao
Genome Res. March 2023 33: 371-385; Published in Advance March 24, 2023, doi:10.1101/gr.277473.122
...by WebLogo and multiple sequence alignment revealed that the other 5 orthologs harbor the same 5′ and 3′ splicing sites, although the corresponding spliced isoforms were not found in the databases (Fig. 7B,C). In contrast, the genes encoding proteins distantly related to PtHSP70 experience different...
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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
...is their nuclear dimorphism, hosting two functionally distinct nuclei within a single cell: the diploid micronucleus (MIC) and the highly polyploid macronucleus (MAC) (Karrer 2012). Additionally, ciliates are ideal organisms for studying cyst formation, owing to their general ease of culturing and genetic...
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Method: Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment
- Bo Yan,
- Duan Wang,
- Romualdas Vaisvila,
- Zhiyi Sun,
- and Laurence Ettwiller
Genome Res. November/December 2022 32: 2079-2091; Published in Advance November 4, 2022, doi:10.1101/gr.277080.122
...-SNP-seq applied to bacteria. (A) Summary of assembly using deconvoluted reads. Genome coverage was measured against E. coli or E. coli + C. acetobutylicum reference using QUAST. (B) Hierarchy clustering of significantly enriched 8-mers and the corresponding motif logo (generated by WebLogo [Crooks et al. 2004...
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Research: Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development
- Patricia Gerdes,
- Dorothy Chan,
- Mischa Lundberg,
- Francisco J. Sanchez-Luque,
- Gabriela O. Bodea,
- Adam D. Ewing,
- Geoffrey J. Faulkner,
- and Sandra R. Richardson
Genome Res. September 2023 33: 1465-1481; Published in Advance October 5, 2023, doi:10.1101/gr.278003.123
...(Pfizer-University of Granada-Andalusian Regional Government), PTS Granada, 18016, Spain; 5MRC Human Genetics Unit, Institute of Genetics and Cancer (IGC), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom; 6Queensland Brain Institute, University of Queensland, Brisbane...
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Research: Developmental timing of programmed DNA elimination in Paramecium tetraurelia recapitulates germline transposon evolutionary dynamics
- Coralie Zangarelli,
- Olivier Arnaiz,
- Mickaël Bourge,
- Kevin Gorrichon,
- Yan Jaszczyszyn,
- Nathalie Mathy,
- Loïc Escoriza,
- Mireille Bétermier,
- and Vinciane Régnier
Genome Res. November/December 2022 32: 2028-2042; Published in Advance November 23, 2022, doi:10.1101/gr.277027.122
...development. Whereas TE elimination is generally imprecise, excision of approximately 45,000 TE-derived internal eliminated sequences (IESs) is precise, allowing for functional gene assembly. Programmed DNA elimination is concomitant with amplification. It is guided by noncoding RNAs and repressive chromatin...
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Research: Embryonic LTR retrotransposons supply promoter modules to somatic tissues
- Kosuke Hashimoto,
- Eeva-Mari Jouhilahti,
- Virpi Töhönen,
- Piero Carninci,
- Juha Kere,
- and Shintaro Katayama
Genome Res. November 2021 31: 1983-1993; Published in Advance October 21, 2021, doi:10.1101/gr.275354.121
...” option (Katoh and Standley 2013), and sequence logos were generated by using WebLogo version 3.6.0 (Crooks et al. 2004).Phylogenetic analysisThe RepeatMasker tracks of seven primates ( assemblies: panTro6, panPan2, rheMac8, calJac3, saiBol1, tarSyr2, micMur2) and mouse (mm10) were downloaded from...
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Research: Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites
- Kurt Patterson,
- Farbod Shavarebi,
- Christophe Magnan,
- Ivan Chang,
- Xiaojie Qi,
- Pierre Baldi,
- Virginia Bilanchone,
- and Suzanne B. Sandmeyer
Genome Res. August 2019 29: 1298-1309; Published in Advance June 27, 2019, doi:10.1101/gr.240861.118
...frequency and analyzed with WebLogo (Crooks et al. 2004). In all sequences, C and A were overrepresented at positions 4 and 6, respectively, and G was depleted throughout (Fig. 4A). Cold targets were additionally enriched for T/A at nucleotide positions 0–3.View larger version: In this window In a new...
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Research: Thermal stress accelerates Arabidopsis thaliana mutation rate
- Eric J. Belfield,
- Carly Brown,
- Zhong Jie Ding,
- Lottie Chapman,
- Mengqian Luo,
- Eleanor Hinde,
- Sam W. van Es,
- Sophie Johnson,
- Youzheng Ning,
- Shao Jian Zheng,
- Aziz Mithani,
- and Nicholas P. Harberd
Genome Res. January 2021 31: 40-50; Published in Advance December 17, 2020, doi:10.1101/gr.259853.119
...were reverse-complemented to create C-to-T mutations and merged with the sequences flanking C mutation sites. These flanking sequences were captured from the TAIR10 reference forward strand. Flanking sequence motifs were created in Excel and displayed as stacked columns. Using the WebLogo 2...
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Research: The Enterprise, a massive transposon carrying Spok meiotic drive genes
- Aaron A. Vogan,
- S. Lorena Ament-Velásquez,
- Eric Bastiaans,
- Ola Wallerman,
- Sven J. Saupe,
- Alexander Suh,
- and Hanna Johannesson
Genome Res. May 2021 31: 789-798; Published in Advance April 19, 2021, doi:10.1101/gr.267609.120
...of the tyrosine recombinase domain (i and ii), the Zn-finger region (iii), and the chromodomain region (iv) using WebLogo. Residues corresponding to the catalytic pentad of the tyrosine recombinase are highlighted in yellow. (B) Alignment of the Kirc sequence with an active site region of known tyrosine...
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