Searching journal content for articles similar to Goff and Rinn 25 (10): 1456.

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Method: Cancer driver topologically associated domains identify oncogenic and tumor-suppressive lncRNAs
- Ziyan Rao,
- Min Zhang,
- Shaodong Huang,
- Chenyang Wu,
- Yuheng Zhou,
- Weijie Zhang,
- Xia Lin,
- and Dongyu Zhao
Genome Res. August 2025 35: 1842-1858; Published in Advance May 27, 2025, doi:10.1101/gr.280235.124
...al. 2012; Valton and Dekker 2016).Given the critical roles of lncRNAs’ strong correlations with the expression of proximate genes, potentially acting as cis-regulatory elements (Werner et al. 2017) and well-studied cancer driver PCGs, we hypothesized that linking lncRNAs to cancer driver PCGs would...
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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
...:10.1101/gr.140269.112 ↵Ratti M, Lampis A, Ghidini M, Salati M, Mirchev MB, Valeri N, Hahne JC. 2020. MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) as new tools for cancer therapy: first steps from bench to bedside. Target Oncol 15: 261–278. doi:10.1007/s11523-020-00717-x ↵R Core Team. 2004. R...
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Research: Dynamics and consequences of differential RNA isoform production during cardiomyocyte fate determination and early-stage maturation
- Joanna Delimata-Raczek,
- Natalia Koralewska,
- Bart Krist,
- Magdalena Rakoczy,
- Marek Figlerowicz,
- and Ireneusz Stolarek
Genome Res. April 3, 2026 ; Published in Advance April 3, 2026, doi:10.1101/gr.281150.125
..., and long noncoding RNA (lncRNA) transcripts (P<0.01). To experimentally validate the computationally identified isoform switches, we used RT-qPCR to measure the relative abundance of specific transcript variants for three representative genes (ATP2A2, TPM2, and GCNT2) at D4 and D30. For ATP2A2 and TPM2...
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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
...rate (Fig. 1C).View larger version: In this window In a new window Figure 1. DRB/TTchem-seq2 enables estimation of RNAPII elongation rates for a larger number of individual genes. (A) Metagene plots showing the mean read density of nonoverlapping protein-coding and lncRNA genes from DRB...
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Research: Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
- Karine Choquet,
- Louis-Philippe Chaumont,
- Simon Bache,
- Autum R. Baxter-Koenigs,
- and L. Stirling Churchman
Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124
...provide additional time for genetic variants to influence splicing and may result in a higher occurrence of allele-specific splicing orders. As dnRNA-seq read lengths continue to improve, similar analyses of cotranscriptional splicing will help unravel the link between splicing timing and the effect...
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Research: Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA
- Uditi Bhatt,
- Anne Cucchiarini,
- Yu Luo,
- Cameron W. Evans,
- Jean-Louis Mergny,
- K. Swaminathan Iyer,
- and Nicole M. Smith
Genome Res. February 2024 34: 217-230; Published in Advance February 14, 2024, doi:10.1101/gr.278236.123
...showed the prevalent but transient formation of rG4s in the transcriptome by first cross-linking the structures in cells before extracting the RNA (Kwok et al. 2016). Regardless, information on rG4s in lncRNAs is rarely included, instead focusing on poly(A)-enriched or cytoplasmic RNAs (Guo and Bartel...
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Research: Widespread specific intron retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts
- Isabela T. Pereira,
- Izabela Mamede,
- Paulo P. Amaral,
- Gloria R. Franco,
- and John L. Rinn
Genome Res. October 2025 35: 2189-2198; Published in Advance August 26, 2025, doi:10.1101/gr.280431.125
...transcriptome-wide using sucrose gradient sedimentation coupled with RNA sequencing (RNA-seq). We also wanted to test whether known nuclear lncRNAs will appear as discrete RNPs. Specifically, we sedimented native human induced pluripotent cell (hiPSC) extracts and collected 10 distinct fractions of each sucrose...
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Research: High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes
- Walter Muskovic,
- Eve Slavich,
- Ben Maslen,
- Dominik C. Kaczorowski,
- Joseph Cursons,
- Edmund Crampin,
- and Maria Kavallaris
Genome Res. August 2022 32: 1463-1473; Published in Advance June 27, 2022, doi:10.1101/gr.276818.122
...that lncRNAs, as a class, may maintain broad regulatory roles. Expression of lncRNAs is strongly linked with adjacent protein-coding gene expression, suggesting potential cis-regulatory functions. A more detailed understanding of these regulatory roles may be obtained through careful examination...
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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
...: arturo.mari-ordonez@gmi.oeaw.ac.atAbstractA handful of model plants have provided insight into silencing of transposable elements (TEs) through RNA-directed DNA methylation (RdDM). Guided by 24 nt long small-interfering RNAs (siRNAs), this epigenetic regulation installs DNA methylation and histone...
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Perspective: Ribosome decision graphs for the representation of eukaryotic RNA translation complexity
- Jack A.S. Tierney,
- Michał Świrski,
- Håkon Tjeldnes,
- Jonathan M. Mudge,
- Joanna Kufel,
- Nicola Whiffin,
- Eivind Valen,
- and Pavel V. Baranov
Genome Res. April 2024 34: 530-538; Published in Advance May 7, 2024, doi:10.1101/gr.278810.123
..., especially long noncoding RNAs (lncRNAs) (Ingolia et al. 2011; Michel et al. 2012; Ruiz-Orera et al. 2014; Andreev et al. 2015; Ji et al. 2015; Calviello et al. 2016; Johnstone et al. 2016; Chong et al. 2020; Chothani et al. 2022; Wright et al. 2022). These studies also showed the translation of N...
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