Searching journal content for articles similar to Legendre et al. 20 (5): 664.

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Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
- Qiang Su,
- Yi Long,
- Deming Gou,
- Junmin Quan,
- Xiaoming Zhou,
- and Qizhou Lian
Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
...(Picelli et al. 2014; SEQC/MAQC-III Consortium 2014; Conesa et al. 2016; Kiselev et al. 2019). However, its accuracy depends on standardized workflows that convert RNA into sequencing reads, such as the TruSeq Stranded mRNA protocol. This RNA-templated conversion step is a major source of variability...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...sizes and the constraints of bulk sequencing.In this study, we aim to systematically characterize the landscape of TE-chimeric transcripts and their clinical relevance in pancreatic cancer using large-scale patient-derived organoid and bulk sample cohorts. Our objective is to clarify the potential...
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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
...motif and coding sequences. METTL2A knockdown alters expression of S100A4 mRNA isoforms, which contains METTL2A-mediated m3C sites. Notably, many transcripts with METTL2A-mediated m3C sites are upregulated upon METTL2A knockdown. We reveal the transcriptome-wide presence of m3C sites in poly(A) RNA...
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Method: Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
- Alexander J. Ritter,
- Jolene M. Draper,
- Christopher Vollmers,
- and Jeremy R. Sanford
Genome Res. November 2024 34: 2000-2011; Published in Advance June 5, 2024, doi:10.1101/gr.279170.124
...of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA ↵3 These authors contributed equally to this work. Corresponding author: jsanfor2@ucsc.eduAbstractAlternative splicing (AS) alters the cis-regulatory landscape of mRNA isoforms, leading to transcripts with distinct...
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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...enhancing effect in both HCC cell lines (Fig. 7C). Subsequently, HBx-SINE and the truncated mutant sequences were cloned and inserted into the MYC-pGL3-Basic and PVT1-pGL3-Basic plasmids. The results revealed that HBx-SINE could enhance the transcriptional regulation of the MYC promoter, whereas the role...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...represent candidate active enhancers and 206 promoters that are primed for activation but may require additional regulatory inputs for 207 transcriptional induction (Figure 3C), (3) genes where mRNA expression is increased but 208 lacking changes in chromatin accessibility (1,008 genes; set 3) (Figure 3D...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...↵Castells-Roca L, García-Martínez J, Moreno J, Herrero E, Bellí G, Pérez-Ortín JE. 2011. Heat shock response in yeast involves changes in both transcription rates and mRNA stabilities. PLoS One 6: e17272. doi:10.1371/journal.pone.0017272 ↵Chen Y-C, Chen C-Y, Chiang T-W, Chan M-H, Hsiao M, Ke H-M, Tsai IJ...
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Research: Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
- Marcel Tarbier,
- Sebastian D. Mackowiak,
- Vaishnovi Sekar,
- Franziska Bonath,
- Etka Yapar,
- Bastian Fromm,
- Omid R. Faridani,
- Inna Biryukova,
- and Marc R. Friedländer
Genome Res. February 2026 36: 291-302; Published in Advance January 12, 2026, doi:10.1101/gr.279914.124
...of microRNA dynamics at the single-cell level.microRNAs (miRNAs) are ∼22 nucleotide (nt) small noncoding RNAs that guide Argonaute effector proteins to target mRNAs in a sequence-specific manner, leading to their translational inhibition and increased degradation through deadenylation and decapping (Bartel...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...sequencing error, and robust computational pipelines. Although much focus has been placed on defining mRNA exon composition and structure with LRS data, less careful characterization has been done of the ability to assess the terminal ends of isoforms, specifically, transcription start and end sites...
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Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
- Samuel H. Kim,
- Georgi K. Marinov,
- and William J. Greenleaf
Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
...KAS-ATAC reveals the -wide single-stranded accessible chromatin landscape of the human Samuel H. Kim1,6, Georgi K. Marinov2,6 and William J. Greenleaf2,3,4,5 1Cancer Biology Programs, School of Medicine, Stanford University, Stanford, California 94305, USA; 2Department of Genetics, School...

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