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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
...of microRNA expression analyses is reflected by the existence of thousands of sRNA-seq studies in which matched total RNA-seq data are often unavailable. The lack of paired sequencing experiments limits the analysis of microRNA–gene regulatory networks. Here, we explore whether protein-coding gene...
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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
.... 97 2020). 98 A recent study using the same Bru-seq and BruChase-seq datasets analyzed 99 here reported that allele-specific genetic variants can affect RNA stability by altering 100 conserved binding sequences of miRNAs and RNA-binding proteins (Huang et al. 101 2025). Many of the genes that have...
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Method: Deep neural networks for interpreting RNA-binding protein target preferences
- Mahsa Ghanbari and
- Uwe Ohler
Genome Res. February 2020 30: 214-226; Published in Advance January 28, 2020, doi:10.1101/gr.247494.118
.... Furthermore, RBPs may belong to complexes in which not all proteins directly bind to RNA in a sequence-specific manner. To investigate this, we ranked candidate binding sites of each RBP (positive CLIP samples of test data) based on the prediction score and extracted the 6-mers from the bottom 10% as well...
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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
...(RdDM). Best studied in Arabidopsis thaliana, during RdDM, H3K9me2 and DNA methylation recruit the plant-specific RNA polymerases (Pol) IV and V. Pol IV transcripts are processed into 24 nt siRNAs, which, loaded into members of the AGO4/6 clade, target Pol V transcripts to guide the sequence-specific...
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Method: Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories
- Borislav Hrisimirov Hristov,
- William Stafford Noble,
- and Alessandro Bertero
Genome Res. October 2024 34: 1610-1623; Published in Advance September 25, 2024, doi:10.1101/gr.278327.123
...not characterized by higher IDP scores (Supplemental Fig. S7A), indicating that other characteristics may explain their specific behavior in trans organization.View larger version: In this window In a new window Figure 6. Trans-C identifies RNA-binding protein (RBP)–associated trans cliques proximal to nuclear...
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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
...(Linder and Jankowsky 2011). DDX helicases typically unwind RNA structures and dissociate RNA–protein complexes in reactions fuelled by ATP hydrolysis. Prominent cellular processes in which DDX proteins are involved include pre-mRNA splicing, ribosome biogenesis, protein biosynthesis, RNA decay, nuclear...
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Research: Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins
- Rosario Avolio,
- Ilenia Agliarulo,
- Daniela Criscuolo,
- Daniela Sarnataro,
- Margherita Auriemma,
- Sabrina De Lella,
- Sara Pennacchio,
- Giovanni Calice,
- Martin Y. Ng,
- Carlotta Giorgi,
- Paolo Pinton,
- Barry S. Cooperman,
- Matteo Landriscina,
- Franca Esposito,
- and Danilo Swann Matassa
Genome Res. August 2023 33: 1242-1257; Published in Advance July 24, 2023, doi:10.1101/gr.277755.123
...TRAP1 and TUFM is conserved when protein levels are compared (Fig. 6D). Consistently, CLUH, which encodes an RNA-binding protein involved in the proper cytoplasmic distribution of mitochondria, is one of the most TRAP1-coexpressed genes (Fig. 6E). CLUH specifically binds mRNAs of nuclear...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...-associated tremor/ataxia syndrome (FXTAS), repeat expansions in the 3′ UTR, 5′ UTR, and introns aberrantly generate expanded repeat RNA products, which are bound by various RNA-binding proteins, often causing toxic RNA foci. The RNA-binding proteins can also be sequestered away from their proper functions, leading...
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Method: Allele-specific RNA N⁶-methyladenosine modifications reveal functional genetic variants in human tissues
- Shuo Cao,
- Haoran Zhu,
- Jinru Cui,
- Sun Liu,
- Yuhe Li,
- Junfang Shi,
- Junyuan Mo,
- Zihan Wang,
- Hailan Wang,
- Jiaxin Hu,
- Lizhi Chen,
- Yuan Li,
- Laixin Xia,
- and Shan Xiao
Genome Res. August 2023 33: 1369-1380; Published in Advance September 15, 2023, doi:10.1101/gr.277704.123
.... With the growth of sequencing data, the accuracy of functional variants discovery would increase, and the tissue specificity of the functional variants would offer more fine regulating details for m6A in human tissues.In summary, our work provides a new method to detect the dynamic network of RNA modifications...
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Method: Global mapping of RNA homodimers in living cells
- Marta M. Gabryelska,
- Andrew P. Badrock,
- Jian You Lau,
- Raymond T. O'Keefe,
- Yanick J. Crow,
- and Grzegorz Kudla
Genome Res. May 2022 32: 956-967; Published in Advance March 24, 2022, doi:10.1101/gr.275900.121
...-pairing. Intramolecular base-pairing determines the structure and function of RNA, including rRNA and tRNA; it regulates viral replication; and it influences the efficiency of mRNA translation into proteins. Intermolecular RNA–RNA base-pairing underlies codon–anticodon recognition, splicing, and regulation of gene...
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