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Resource: Isoform- and pathway-specific regulation of post-transcriptional RNA processing in human cells
- Ishwarya Venkata Narayanan,
- Karan Bedi,
- Brian Magnuson,
- Ariel McShane,
- Mario Ashaka,
- Michelle Paulsen,
- Thomas E Wilson,
- and Mats Ljungman
Genome Res. March 26, 2026 gr.280892.125; Published in Advance March 26, 2026, doi:10.1101/gr.280892.125
...-specific turnover (Maier et al. 2020), while Dyrec-seq 73 utilizes double metabolic labeling with bromouridine and 4-thiouridine (4sU) to measure 74 both synthesis and degradation rates (Kawata et al. 2020). Finally, INSPEcT is a 75 computational method that estimates RNA turnover rates from steady-state RNA-seq 76...
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Research: Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection
- Shudi Zhao,
- Yuedong Li,
- Guanping Chen,
- Xingyang Wang,
- Nan Chen,
- and Xiaofeng Wu
Genome Res. November 2023 33: 1958-1974; Published in Advance October 23, 2023, doi:10.1101/gr.277931.123
...databases, were reanalyzed to generate the epigenomic landscape in a silkworm cell line (BmN). As revealed in the circle diagram, the distribution trends of accessible chromatin regions and activating histone modifications all over the were consistent with those of RNA polymerase II (RNA Pol II) (Fig. 1A...
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Research: KDM1A maintains genome-wide homeostasis of transcriptional enhancers
- Saurabh Agarwal,
- Katherine M. Bonefas,
- Patricia M. Garay,
- Emily Brookes,
- Yumie Murata-Nakamura,
- Robert S. Porter,
- Todd S. Macfarlan,
- Bing Ren,
- and Shigeki Iwase
Genome Res. February 2021 31: 186-197; Published in Advance January 7, 2021, doi:10.1101/gr.234559.118
...-mediated degradation (Wyers et al. 2005; Preker et al. 2008; De Santa et al. 2010). Global Run-On (GRO)-seq (Core et al. 2008) facilitates a sensitive and quantitative evaluation of transcriptionally engaged RNA polymerase molecules and thus serves as an indirect measure of nascent transcription at promoters...
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Method: Metabolic labeling of RNA using multiple ribonucleoside analogs enables the simultaneous evaluation of RNA synthesis and degradation rates
- Kentaro Kawata,
- Hiroyasu Wakida,
- Toshimichi Yamada,
- Kenzui Taniue,
- Han Han,
- Masahide Seki,
- Yutaka Suzuki,
- and Nobuyoshi Akimitsu
Genome Res. October 2020 30: 1481-1491; Published in Advance August 25, 2020, doi:10.1101/gr.264408.120
...20: 465–470. doi:10.1016/S0968-0004(00)89102-1 ↵De Pretis S, Kress T, Morelli MJ, Melloni GEM, Riva L, Amati B, Pelizzola M. 2015. INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments. Bioinformatics 31: 2829...
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Method: A systematic genome-wide account of binding sites for the model transcription factor Gcn4
- Christopher T. Coey and
- David J. Clark
Genome Res. February 2022 32: 367-377; Published in Advance December 16, 2021, doi:10.1101/gr.276080.121
..., the motif could be in a linker if the nucleosome is not in its average position (Chereji et al. 2019).Gcn4 occupancy at promoters correlates with increases in gene expressionPreviously, we calculated a gene induction ratio by dividing the average RNA polymerase II occupancy in induced cells...
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Research: Genome-wide transcript and protein analysis highlights the role of protein homeostasis in the aging mouse heart
- Isabela Gerdes Gyuricza,
- Joel M. Chick,
- Gregory R. Keele,
- Andrew G. Deighan,
- Steven C. Munger,
- Ron Korstanje,
- Steven P. Gygi,
- and Gary A. Churchill
Genome Res. May 2022 32: 838-852; Published in Advance March 11, 2022, doi:10.1101/gr.275672.121
...to leakage of cytoplasmic proteins into the nucleus (D'Angelo et al. 2009). Transcripts in the cytoplasm can be modified post-transcriptionally by micro-RNAs (miRNAs), which are primarily processed by the DROSHA complex, a RNase that cleaves primary miRNAs releasing hairpin-shaped ones (Han et al. 2004...
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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
.... Whereas much research has focused on the initiation of transcription, regulation of elongation plays an important role not only in transcription dynamics but also in cotranscriptional RNA processing and stability. Despite advances in high-throughput approaches for global quantification of RNA polymerase...
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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
...while meticulously preserving essential structural features crucial for bias identification. This sophisticated modeling allows precise tracking of local RNA-read conversion dynamics and the identification of complex, often overlooked bias sources. We rigorously validate the VAE-GMM model's performance...
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Research: Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence
- Manuela Baquero Pérez,
- Gertjan Laenen,
- Isabelle Loïodice,
- Mickaël Garnier,
- Ugo Szachnowski,
- Antonin Morillon,
- Myriam Ruault,
- and Angela Taddei
Genome Res. October 2025 35: 2226-2239; Published in Advance August 12, 2025, doi:10.1101/gr.279874.124
..., as monitored by single-cell RNA-seq. Our results point toward a role for quiescent-specific RNAPII distribution to ensure a rapid and robust transcriptional response upon return to growth.Eukaryotic organization is dynamic, varying across cell types and conditions, both functionally and spatially...
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Research: Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish
- Charles E. Vejnar,
- Mario Abdel Messih,
- Carter M. Takacs,
- Valeria Yartseva,
- Panos Oikonomou,
- Romain Christiano,
- Marlon Stoeckius,
- Stephanie Lau,
- Miler T. Lee,
- Jean-Denis Beaudoin,
- Damir Musaev,
- Hiba Darwich-Codore,
- Tobias C. Walther,
- Saeed Tavazoie,
- Daniel Cifuentes,
- and Antonio J. Giraldez
Genome Res. July 2019 29: 1100-1114; Published in Advance June 21, 2019, doi:10.1101/gr.245159.118
...and Steitz 1998; Wirsing et al. 2011; Kristjánsdóttir et al. 2015). Transcriptome-wide analyses of mRNA stability, using pulse labeling (Miller et al. 2011) or blocking transcription (Geisberg et al. 2014), have led to the identification of potential regulatory sequences by searching for common motifs within...

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