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Method: A versatile type VI CRISPR-based approach for targeted m⁶A demethylation in mRNAs
- Panagiotis G. Adamopoulos,
- Konstantina Athanasopoulou,
- and Andreas Scorilas
Genome Res. January 2026 36: 169-182; Published in Advance December 11, 2025, doi:10.1101/gr.280476.125
...: padamopoulos@biol.uoa.grAbstractEpitranscriptomics, a rapidly evolving field mainly driven by massive parallel sequencing technologies, explores post-transcriptional RNA modifications. N6-methyladenosine (m6A) has emerged as the most prominent and dynamically regulated modification in human mRNAs, being...
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Method: Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize
- Shuai Wang,
- Merritt Khaipho-Burch,
- Lynn C. Johnson,
- Zachary R. Miller,
- Peter J. Bradbury,
- Doug Speed,
- William J. Allen,
- M. Cinta Romay,
- Jiquan Xue,
- Edward S. Buckler,
- Guillaume P. Ramstein,
- and Baoxing Song
Genome Res. January 2026 36: 214-225; Published in Advance October 31, 2025, doi:10.1101/gr.280514.125
...for biases introduced by LD, by including both SNP-based relationship and haplotype-based IBD matrices (Supplemental Fig. S6). A previous study predicted mRNA abundance for each haplotype in the NAM population, similar to our prediction of protein structures (Giri et al. 2021). Importantly, in this study...
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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
...such as RNA-binding and immunoprecipitation (RIP), CLIP results in significantly larger numbers of target sites, indicating possible cross-linking of low-specificity events or that only few mRNA copies of a given gene are actually bound in the same cell (Mukherjee et al. 2011; Plass et al. 2017). On the other...
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Research: Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences
- Arttu Jolma,
- Jilin Zhang,
- Estefania Mondragón,
- Ekaterina Morgunova,
- Teemu Kivioja,
- Kaitlin U. Laverty,
- Yimeng Yin,
- Fangjie Zhu,
- Gleb Bourenkov,
- Quaid Morris,
- Timothy R. Hughes,
- Louis James Maher III,
- and Jussi Taipale
Genome Res. July 2020 30: 962-973; Published in Advance July 23, 2020, doi:10.1101/gr.258848.119
...with the earlier observation that LARP6 binds to stem–loops with internal loops found in mRNAs encoding the collagen proteins COL1A1, COL1A2, and COL3A1 (Supplemental Fig. S6; Cai et al. 2010).View larger version: In this window In a new window Figure 2. Detection of linear or structured RNA-binding models. (A...
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Resource: Regulation of alternative splicing in Drosophila by 56 RNA binding proteins
- Angela N. Brooks,
- Michael O. Duff,
- Gemma May,
- Li Yang,
- Mohan Bolisetty,
- Jane Landolin,
- Ken Wan,
- Jeremy Sandler,
- Benjamin W. Booth,
- Susan E. Celniker,
- Brenton R. Graveley,
- and Steven E. Brenner
Genome Res. November 2015 25: 1771-1780; Published in Advance August 20, 2015, doi:10.1101/gr.192518.115
...@compbio.berkeley.edu Abstract Alternative splicing is regulated by RNA binding proteins (RBPs) that recognize pre-mRNA sequence elements and activate or repress adjacent exons. Here, we used RNA interference and RNA-seq to identify splicing events regulated by 56 Drosophila proteins, some previously unknown to regulate...
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Research: Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features
- Lisa Barros de Andrade e Sousa,
- Iris Jonkers,
- Laurène Syx,
- Ilona Dunkel,
- Julie Chaumeil,
- Christel Picard,
- Benjamin Foret,
- Chong-Jian Chen,
- John T. Lis,
- Edith Heard,
- Edda G. Schulz,
- and Annalisa Marsico
Genome Res. July 2019 29: 1087-1099; Published in Advance June 7, 2019, doi:10.1101/gr.245027.118
...to predict the silencing class of all unlabeled X-linked genes given the same set of input features. The predictions are validated by comparing them to measured half-times from undifferentiated mRNA-seq data, with pyrosequencing experiments (few selected genes) and with measured silencing dynamics of genes...
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Research: Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs
- Marta Melé,
- Kaia Mattioli,
- William Mallard,
- David M. Shechner,
- Chiara Gerhardinger,
- and John L. Rinn
Genome Res. January 2017 27: 27-37; Published in Advance December 7, 2016, doi:10.1101/gr.214205.116
...for some of the splicing differences between lincRNAs and mRNAs. Binding of U2AF65 and splice site conservation correlates with greater splicing efficiency in lincRNAs Based on the above observations, we hypothesized that weak internal 3′ splice-site signals may contribute to the lower splicing efficiency...
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Research: Translation initiation downstream from annotated start codons in human mRNAs coevolves with the Kozak context
- Maria S. Benitez-Cantos,
- Martina M. Yordanova,
- Patrick B.F. O'Connor,
- Alexander V. Zhdanov,
- Sergey I. Kovalchuk,
- Dmitri B. Papkovsky,
- Dmitry E. Andreev,
- and Pavel V. Baranov
Genome Res. July 2020 30: 974-984; Published in Advance July 15, 2020, doi:10.1101/gr.257352.119
...contributed equally to this work. Corresponding author: p.baranov@ucc.ieAbstractEukaryotic translation initiation involves preinitiation ribosomal complex 5′-to-3′ directional probing of mRNA for codons suitable for starting protein synthesis. The recognition of codons as starts depends on the codon identity...
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Research: Signatures of RNA binding proteins globally coupled to effective microRNA target sites
- Anders Jacobsen,
- Jiayu Wen,
- Debora S. Marks,
- and Anders Krogh
Genome Res. August 2010 20: 1010-1019; Published in Advance May 27, 2010, doi:10.1101/gr.103259.109
...changes after perturbations of these small RNAs are only partially explained by predicted miRNA/siRNA targeting. Targeting may be modulated by other mRNA sequence elements such as binding sites for the hundreds of RNA binding proteins (RNA-BPs) expressed in any cell, and this aspect has not been...
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Method: Quantitative proteomic analysis reveals concurrent RNA–protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae
- Daniel M. Klass,
- Marion Scheibe,
- Falk Butter,
- Gregory J. Hogan,
- Matthias Mann,
- and Patrick O. Brown
Genome Res. June 2013 23: 1028-1038; Published in Advance May 1, 2013, doi:10.1101/gr.153031.112
...for Biochemistry, 82152 Martinsried, Germany A growing body of evidence supports the existence of an extensive network of RNA-binding proteins (RBPs) whose combinatorial binding affects the post-transcriptional fate of every mRNA in the cell—yet we still do not have a complete understanding of which proteins bind...
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