Searching journal content for articles similar to Wahlstedt et al. 19 (6): 978.

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  1. Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
    • Qiuhui Li,
    • Ayse G. Keskus,
    • Justin Wagner,
    • Michal B. Izydorczyk,
    • Winston Timp,
    • Fritz J. Sedlazeck,
    • Alison P. Klein,
    • Justin M. Zook,
    • Mikhail Kolmogorov,
    • and Michael C. Schatz
    Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
    ...exon 1 of the APC gene (Fig. 2D). RNA-seq analysis revealed a substantial decrease in APC expression in the tumor sample (tumor fragments per kilobase of transcript per million fragments mapped (FPKM): 0.296 vs. normal FPKM: 2.262). The SV was not detected by short-read sequencing, likely because...
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  2. Research: RNA editing in nascent RNA affects pre-mRNA splicing
    • Yun-Hua Esther Hsiao,
    • Jae Hoon Bahn,
    • Yun Yang,
    • Xianzhi Lin,
    • Stephen Tran,
    • Ei-Wen Yang,
    • Giovanni Quinones-Valdez,
    • and Xinshu Xiao
    Genome Res. June 2018 28: 812-823; Published in Advance May 3, 2018, doi:10.1101/gr.231209.117
    ...Drosophila and human cells induced global splicing changes (Agrawal and Stormo 2005; Solomon et al. 2013; St Laurent et al. 2013), although the molecular mechanisms are unknown.Despite the aforementioned progress, the kinetic timing of RNA editing during mRNA maturation in human cells remains...
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  3. Review: Leveraging the power of long reads for targeted sequencing
    • Shruti V. Iyer,
    • Sara Goodwin,
    • and William Richard McCombie
    Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
    ...is becoming a more viable method (Israeli et al. 2022).Transcript populations can also be explored with these methods as demonstrated by Adamopoulos et al. This group performed mRNA transcript-specific amplification for KRAS, NRAS, and HRAS, which are regulatory genes commonly mutated in various cancers...
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  4. Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
    • Natan Belchikov,
    • Justine Hsu,
    • Xiang Jennie Li,
    • Julien Jarroux,
    • Wen Hu,
    • Anoushka Joglekar,
    • and Hagen U. Tilgner
    Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
    ...-cell sequencing and long-read sequencing, have greatly expanded. Both have been used in transcriptomics to characterize the mRNA expression profiles of cells. Single-cell sequencing allows transcript molecules to be traced to individual cells, thus preserving cell-type-specific information about expression. Long...
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  5. Research: Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y
    • Shruthi Rengarajan,
    • Jason Derks,
    • Daniel W. Bellott,
    • Nikolai Slavov,
    • and David C. Page
    Genome Res. January 2025 35: 20-30; Published in Advance January 10, 2025, doi:10.1101/gr.279707.124
    ...in response to increasing DDX3Y dosage. We tested this prediction by labeling nascent mRNAs in 46,XY and 49,XYYYY LCLs with 5-EU and sequencing the resultant mRNA populations at discrete intervals to quantify the half-life (Fig. 6A). We calculated the ratio of nascent mRNA/total mRNA normalized to steady...
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  6. Research: A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing
    • Konstantin Licht,
    • Utkarsh Kapoor,
    • Fabian Amman,
    • Ernesto Picardi,
    • David Martin,
    • Prajakta Bajad,
    • and Michael F. Jantsch
    Genome Res. September 2019 29: 1453-1463; Published in Advance August 19, 2019, doi:10.1101/gr.242636.118
    ...-containing transcripts and mRNAs. The increase in editing upon splicing inhibition is particularly strong for exonic editing sites with adjacent intronic ECSs. Editing in UTRs does not follow a general trend, as a decrease was observed in bone marrow whereas UTR-editing in primary neurons was not shifted. Differences...
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  7. Research: Profiling neural editomes reveals a molecular mechanism to regulate RNA editing during development
    • Suba Rajendren,
    • Alfa Dhakal,
    • Pranathi Vadlamani,
    • Jack Townsend,
    • Sarah N. Deffit,
    • and Heather A. Hundley
    Genome Res. January 2021 31: 27-39; Published in Advance December 18, 2020, doi:10.1101/gr.267575.120
    ....0001; (*) P < 0.05; (ns) P > 0.05. (C) Editing levels of the Y75B8A.8 neural reporter were measured in wild-type and adr-1(-) worms in L1 (left) and adult (right) stages using Sanger sequencing. (D) qPCR was performed to measure the absolute mRNA levels of adr-2 relative to adr-1 in both life stages. (E...
  8. Research: A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations
    • Te-Lun Mai and
    • Trees-Juen Chuang
    Genome Res. November 2019 29: 1766-1776; Published in Advance September 12, 2019, doi:10.1101/gr.246033.118
    ...sequencing data from each LCL sample of 447 individuals, have provided a unique opportunity to determine RNA editing activities at A/G polymorphic sites within a human population. In other words, this data set provides an ideal resource for us to explore A-to-I RNA editing sites in some LCL individuals while...
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  9. Method: Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms
    • Kerstin C. Maier,
    • Saskia Gressel,
    • Patrick Cramer,
    • and Björn Schwalb
    Genome Res. September 2020 30: 1332-1344; Published in Advance September 4, 2020, doi:10.1101/gr.257857.119
    ...was purified from 1 mg of total RNA using the µMACS mRNA isolation kit (Milteny Biotec) following the manufacturer's protocol. The quality of poly(A) RNA selection was assessed using the TapeStation system (Agilent). Poly(A)-selected RNAs were subsequently subjected to direct RNA nanopore sequencing library...
  10. Research: Genome-wide analysis of differential RNA editing in epilepsy
    • Prashant Kumar Srivastava,
    • Marta Bagnati,
    • Andree Delahaye-Duriez,
    • Jeong-Hun Ko,
    • Maxime Rotival,
    • Sarah R. Langley,
    • Kirill Shkura,
    • Manuela Mazzuferi,
    • Bénédicte Danis,
    • Jonathan van Eyll,
    • Patrik Foerch,
    • Jacques Behmoaras,
    • Rafal M. Kaminski,
    • Enrico Petretto,
    • and Michael R. Johnson
    Genome Res. March 2017 27: 440-450; doi:10.1101/gr.210740.116
    ...). As an example, within the neural serotonin receptor HTR2C gene transcripts, five RE sites have been reported in close proximity to each other, which produce a diverse repertoire of 28 mRNAs and 20 protein isoforms (Du et al. 2006). RE may also occur within noncoding sequence such as within the 3′ untranslated...
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