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Research: A 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 ; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
...5290002, Israel; 3Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel A-to-I RNA editing, catalyzed by the adenosine deaminase acting on RNA (ADAR) enzymes, is a posttranscriptional process that modifies RNA sequences and diversifies the transcriptome...
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Research: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
- Alicja Pacholewska,
- Matthias Lienhard,
- Mirko Brüggemann,
- Heike Hänel,
- Lorina Bilalli,
- Anja Königs,
- Felix Heß,
- Kerstin Becker,
- Karl Köhrer,
- Jesko Kaiser,
- Holger Gohlke,
- Norbert Gattermann,
- Michael Hallek,
- Carmen D. Herling,
- Julian König,
- Christina Grimm,
- Ralf Herwig,
- Kathi Zarnack,
- and Michal R. Schweiger
Genome Res. November 2024 34: 1832-1848; Published in Advance September 13, 2024, doi:10.1101/gr.279327.124
...Genomics and Transcriptomics Laboratory, Biological and Medical Research Center, Heinrich Heine University and West German Genome Center, 40225 Düsseldorf, Germany; 7Cologne Center for Genomics (CCG), Faculty of Medicine, University of Cologne, 50931 Cologne, Germany; 8Institute for Pharmaceutical...
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Research: Single-cell transcriptome and metagenome profiling reveals the genetic basis of rumen functions and convergent developmental patterns in ruminants
- Juan Deng,
- Ya-Jing Liu,
- Wen-Tian Wei,
- Qi-Xuan Huang,
- Li-Ping Zhao,
- Ling-Yun Luo,
- Qi Zhu,
- Lin Zhang,
- Yuan Chen,
- Yan-Ling Ren,
- Shan-Gang Jia,
- Yu-Luan Lin,
- Ji Yang,
- Feng-Hua Lv,
- Hong-Ping Zhang,
- Feng-E Li,
- Li Li,
- and Meng-Hua Li
Genome Res. October 2023 33: 1690-1707; Published in Advance October 26, 2023, doi:10.1101/gr.278239.123
...and metabolism in the rumen microbiome (Fig. 7B). The other cluster consisted of stromal cells, SMCs, enteroendocrine cells, and neuron cells and subtypes of BCs, SCs, and Fib and was negatively correlated with 12 bacterial genera (Agrobacterium, Brachybacterium, Cutibacterium, Enterococcus, Escherichia...
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Research: Systematic transcriptome analysis associated with physiological and chronological aging in Caenorhabditis elegans
- Seokjin Ham,
- Sieun S. Kim,
- Sangsoon Park,
- Eun Ji E. Kim,
- Sujeong Kwon,
- Hae-Eun H. Park,
- Yoonji Jung,
- and Seung-Jae V. Lee
Genome Res. November/December 2022 32: 2003-2014; Published in Advance November 9, 2022, doi:10.1101/gr.276515.121
...maintained under standard laboratory culture conditions on nematode growth media (NGM) seeded on Escherichia coli OP50. The list of strains and RNAi clones used in this study are described as follows.Strains: wild-type N2, CF1041 daf-2(e1370) III, SS104 glp-4(bn2ts) IRNAi plasmids: control, daf-16, F30A10...
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Research: Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131
- Teemu Kallonen,
- Hayley J. Brodrick,
- Simon R. Harris,
- Jukka Corander,
- Nicholas M. Brown,
- Veronique Martin,
- Sharon J. Peacock,
- and Julian Parkhill
Genome Res. August 2017 27: 1437-1449; Published in Advance July 18, 2017, doi:10.1101/gr.216606.116
...2 0QQ, United Kingdom; 6Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom; 7British Society of Antimicrobial Chemotherapy, Birmingham B1 3NJ, United Kingdom; 8London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom Escherichia coli...
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Resource: The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity
- Zhemin Zhou,
- Nabil-Fareed Alikhan,
- Khaled Mohamed,
- Yulei Fan,
- the Agama Study Group,
- and Mark Achtman
Genome Res. January 2020 30: 138-152; Published in Advance December 6, 2019, doi:10.1101/gr.251678.119
...by Damgaard et al. (2018) as 0.PE5.Case Study 3: Thinking big. An overview of the core genomic diversity of Escherichia/ShigellaEscherichia coli has long been one of the primary workhorses of molecular biology. Most studies of Escherichia have concentrated on a few well-characterized strains of E. coli...
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Method: Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ
- Yongkang Long,
- Bin Zhang,
- Shuye Tian,
- Jia Jia Chan,
- Juexiao Zhou,
- Zhongxiao Li,
- Yisheng Li,
- Zheng An,
- Xingyu Liao,
- Yu Wang,
- Shiwei Sun,
- Ying Xu,
- Yvonne Tay,
- Wei Chen,
- and Xin Gao
Genome Res. April 2023 33: 644-657; Published in Advance April 28, 2023, doi:10.1101/gr.277177.122
...) from RNA-seq data, which can accurately identify PAS and quantify PAU in a transcriptome-wide manner. Using 3′ end-seq data as the benchmark, we showed that APAIQ outperforms current methods on PAS identification and PAU quantification, including DaPars2, Aptardi, mountainClimber, SANPolyA, and QAPA...
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Resource: Recounting the FANTOM CAGE-Associated Transcriptome
- Eddie Luidy Imada,
- Diego Fernando Sanchez,
- Leonardo Collado-Torres,
- Christopher Wilks,
- Tejasvi Matam,
- Wikum Dinalankara,
- Aleksey Stupnikov,
- Francisco Lobo-Pereira,
- Chi-Wai Yip,
- Kayoko Yasuzawa,
- Naoto Kondo,
- Masayoshi Itoh,
- Harukazu Suzuki,
- Takeya Kasukawa,
- Chung-Chau Hon,
- Michiel J.L. de Hoon,
- Jay W. Shin,
- Piero Carninci,
- Andrew E. Jaffe,
- Jeffrey T. Leek,
- Alexander Favorov,
- Gloria R. Franco,
- Ben Langmead,
- and Luigi Marchionni
Genome Res. July 2020 30: 1073-1081; Published in Advance February 20, 2020, doi:10.1101/gr.254656.119
...human diseases. We present here FC-R2, a comprehensive expression atlas across a broadly defined human transcriptome, inclusive of over 109,000 coding and noncoding genes, as described in the FANTOM CAGE-Associated Transcriptome (FANTOM-CAT) study. This atlas greatly extends the gene annotation used...
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Research: Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina
- Meng Wang,
- Yumei Li,
- Jun Wang,
- Soo Hwan Oh,
- Yexuan Cao,
- and Rui Chen
Genome Res. April 2025 35: 740-754; Published in Advance March 6, 2025, doi:10.1101/gr.279167.124
...@bcm.eduAbstractThe vast majority of protein-coding genes in the human produce multiple mRNA isoforms through alternative splicing, significantly enhancing the complexity of the transcriptome and proteome. To establish an efficient method for characterizing transcript isoforms within tissue samples, we conducted...
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Research: Tissue-specific reprogramming of host tRNA transcriptome by the microbiome
- Jia Huang,
- Wenjun Chen,
- Fan Zhou,
- Zhichang Pang,
- Luoluo Wang,
- Tao Pan,
- and Xiaoyun Wang
Genome Res. June 2021 31: 947-957; Published in Advance April 15, 2021, doi:10.1101/gr.272153.120
...is responsible for reversible changes in host DNA modifications and gene expression (Qin et al. 2018; Kim et al. 2019; Louwies et al. 2020). We have recently demonstrated that the presence of the microbiome can markedly influence m6A modifications in the mouse messenger RNA (mRNA) transcriptome in a tissue...
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