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Resource: DEAD box RNA helicases are pervasive protein kinase interactors and activators
- Alexander Hirth,
- Edoardo Fatti,
- Eugen Netz,
- Sergio P. Acebron,
- Dimitris Papageorgiou,
- Andrea Švorinić,
- Cristina-Maria Cruciat,
- Emil Karaulanov,
- Alexandr Gopanenko,
- Tianheng Zhu,
- Irmgard Sinning,
- Jeroen Krijgsveld,
- Oliver Kohlbacher,
- and Christof Niehrs
Genome Res. June 2024 34: 952-966; Published in Advance July 10, 2024, doi:10.1101/gr.278264.123
...export, transcriptional regulation, and maintenance of stability (Jarmoskaite and Russell 2014; Cargill et al. 2021; Bohnsack et al. 2023).One well-characterized RNA helicase is DDX3X, which has a helicase-independent “moonlighting” function during Wnt signaling, in which it acts as a specific activator...
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Research: Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila
- Marcus H. Stoiber,
- Sara Olson,
- Gemma E. May,
- Michael O. Duff,
- Jan Manent,
- Robert Obar,
- K.G. Guruharsha,
- Peter J. Bickel,
- Spyros Artavanis-Tsakonas,
- James B. Brown,
- Brenton R. Graveley,
- and Susan E. Celniker
Genome Res. November 2015 25: 1692-1702; Published in Advance August 20, 2015, doi:10.1101/gr.182675.114
...and local levels. Cross-regulation of post-transcriptional networks Genome Research 1693 www..org they contained KH- or RRM-type RNA-binding domains or DEADbox RNA helicase domains or because they lacked known RNAbinding domains but have important roles in RNA biology (Supplemental Table 2). The proteins...
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Research: Post-transcriptional circadian regulation in macrophages organizes temporally distinct immunometabolic states
- Emily J. Collins,
- Mariana P. Cervantes-Silva,
- George A. Timmons,
- James R. O'Siorain,
- Annie M. Curtis,
- and Jennifer M. Hurley
Genome Res. February 2021 31: 171-185; Published in Advance January 12, 2021, doi:10.1101/gr.263814.120
...activity. We comprehensively profiled the transcriptome and proteome of murine bone marrow-derived macrophages and found that only 15% of the circadian proteome had corresponding oscillating mRNA, suggesting post-transcriptional regulation influences macrophage clock regulatory output to a greater extent...
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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
...by introducing Cas9/sgRNA ribonucleoprotein (RNP) complexes into mESCs via nucleofection (Kirton et al. 2013). The sgRNA was synthesized by Synthego (Supplemental Table 2). To form the RNP, 300 pmol of Cas9 protein (NEB M0386M) and 600 pmol of sgRNA were incubated in Cas9 Buffer (150 mM KCl, 1 mM MgCl2, 10% v...
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Research: Enhanced detection of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models
- Gregor Diensthuber,
- Leszek P. Pryszcz,
- Laia Llovera,
- Morghan C. Lucas,
- Anna Delgado-Tejedor,
- Sonia Cruciani,
- Jean-Yves Roignant,
- Oguzhan Begik,
- and Eva Maria Novoa
Genome Res. November 2024 34: 1865-1877; Published in Advance September 13, 2024, doi:10.1101/gr.278849.123
...data can arise because of various factors, such as homopolymeric regions, RNA secondary structures, or helicase missteps (Noakes et al. 2019; Shaw et al. 2023; Liu-Wei et al. 2024). However, a major factor affecting the basecalling “error” patterns is the RNA basecalling model of choice and, more...
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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
...) depletion to ensure that the samples to be sequenced are enriched in miRNAs and not in rRNAs.miRNAs are short noncoding RNAs ∼22 nucleotides (nt) in length that play a crucial role in post-transcriptional regulation by targeting messenger RNA (mRNA) for degradation or translational repression (Shang et al...
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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
...of Pharmaceutical Biotechnology and Department of Medicine, the University of Hong Kong, Hong Kong SAR, China ↵9 These authors contributed equally to this work. Corresponding authors: su@chemie.uni-siegen.de, zhouxm@scnu.edu.cn, qz.lian@siat.ac.cnAbstractRNA sequencing (RNA-seq) is a pivotal tool for transcriptomic...
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Method: Rapid and accurate demultiplexing of direct RNA nanopore sequencing data with SeqTagger
- Leszek P. Pryszcz,
- Gregor Diensthuber,
- Laia Llovera,
- Rebeca Medina,
- Anna Delgado-Tejedor,
- Luca Cozzuto,
- Julia Ponomarenko,
- and Eva Maria Novoa
Genome Res. April 2025 35: 956-966; Published in Advance January 29, 2025, doi:10.1101/gr.279290.124
...overview of the DRS and demultiplexing workflow. (A) Overview of the barcoded DRS workflow in which the standard RTA is replaced with a barcode-containing adapter. Following adapter ligation and reverse transcription, the RNA ligation adapter (RLA), containing the helicase enzyme, is ligated, making...
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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
...-fold in phosphate-buffered saline (PBS), were added to each well. The cells were then incubated for 10 min. Luminescence was measured using a GloMax Discover Microplate Reader (Promega, #GM3000).Direct RNA sequencingRNA was isolated using a NucleoSpin RNA mini kit (MACHEREY-NAGEL, #740955), treated with Recombinant...
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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
...Dynamic A-to-I RNA editing in response to gut microbiome 1 in honey bees 2 3 Yuange Duan1 #, Min Huang1 #, Lin Ye1 #, Ling Ma1, Yashuai Wu1, Yating Du1, Jiyao Liu1, 4 Fan Song1, Li Tian1, Wanzhi Cai1, Hu Li1, Xin Zhou1, Shiqi Luo1 * 5 6 1. State Key Laboratory of Agricultural and Forestry...
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