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Research: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
- Amy R. Vandiver,
- Allen Herbst,
- Paul Stothard,
- and Jonathan Wanagat
Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
.... Disruption of Twinkle is known to induce a wide range of mtDNA deletion mutations that, following our hypothesis, would be prone to generating chimeric mtRNAs (Young and Copeland 2016). When our approach was used to quantify chimeric mtRNA in this patient population, we observed chimeric mtRNAs in all...
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Research: Alternative splicing generates HER2 isoform diversity underlying antibody–drug conjugate resistance in breast cancer
- Gabriela D.A. Guardia,
- Carlos H. dos Anjos,
- Aline Rangel-Pozzo,
- Filipe F. dos Santos,
- Alexander Birbrair,
- Paula F. Asprino,
- Anamaria A. Camargo,
- and Pedro A.F. Galante
Genome Res. September 2025 35: 1942-1958; Published in Advance July 15, 2025, doi:10.1101/gr.280304.124
...to produce multiple distinct mRNA transcripts, increasing protein diversity (Nilsen and Graveley 2010). In humans, >90% of multiexon genes undergo alternative splicing, generating roughly seven mRNA isoforms per gene on average, although only a fraction of these yield functionally distinct proteins (Pan et...
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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
...of the structure–function relationship in lncRNAs.The discovery of long noncoding RNAs (lncRNAs) has revolutionized scientific understanding of the and has led to an explosion of research into the complex mechanisms that regulate gene expression. Currently, lncRNAs are broadly defined as any RNA >200 nt in length...
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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
..., across cell lines, the remaining intronic signal originates either from 185 introns that have been spliced out but not yet degraded by nucleases, or from introns 186 with non-coding RNA functions protected from degradation. If transcription initiation 187 within these introns were generating small ncRNAs...
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Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
...), and similar results were reported for the mouse(Kiyosawa et al. 2003), Drosophila(Misra et al. 2002), Arabidopsis(Meyers et al. 2004; Wang et al. 2014), and rice s(Osato et al. 2003). In addition, many long intergenic non-coding RNAs (lincRNAs) have been identified as antisense transcripts, further...
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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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Research: Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals
- Antoine Molaro,
- Janet M. Young,
- and Harmit S. Malik
Genome Res. April 2018 28: 460-473; Published in Advance March 16, 2018, doi:10.1101/gr.229799.117
...in a limited subset of cells, or perhaps even because H2A.P mRNAs, which accumulate during spermatogenesis, may actually be delivered to the embryo and translated following fertilization. We note, however, our analysis cannot determine whether short H2A mRNAs, like those from H2A.P, might have noncoding...
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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
..., preserving the modification information at the single-read level (Garalde et al. 2018; Workman et al. 2019). As an RNA molecule passes through a nanopore, it generates a distinctive and typical shift in ion currents. Approximately five nucleotides, known as a k-mer, are present within the pore at any given...
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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 gr.281150.125; Published in Advance April 3, 2026, doi:10.1101/gr.281150.125
...complexity: the expression of distinct transcript isoforms. Alternative transcription 57 and splicing generate multiple mRNA variants from a single gene, enabling the production of 58 functionally diverse proteins that fine-tune cellular processes. During development, such isoform 59 switching is essential...
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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
- 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 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
..., showing us highly distinct distributions of RNA editing events (Liscovitch-Brauer et al. 2017; Porath et al. 2017; Duan et al. 2023a; Zhang et al. 2023). Although extensive RNA editing on noncoding repetitive elements was observed in most species (Porath et al. 2017; Cao and Duan 2025; Duan et al. 2025a...

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