Searching journal content for articles similar to Vrba et al. 21 (12): 2026.

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  1. Research: ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development
    • Charlie Y. Shi,
    • Lara E. Elcavage,
    • Raghu R. Chivukula,
    • Joanna Stefano,
    • Benjamin Kleaveland,
    • and David P. Bartel
    Genome Res. September 2023 33: 1482-1496; Published in Advance August 2, 2023, doi:10.1101/gr.278073.123
    ...author: dbartel@wi.mit.eduAbstractMicroRNAs (miRNAs) pair to sites in mRNAs to direct the degradation of these RNA transcripts. Conversely, certain RNA transcripts can direct the degradation of particular miRNAs. This target-directed miRNA degradation (TDMD) requires the ZSWIM8 E3 ubiquitin ligase. Here...
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  2. Research: Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers
    • Yumeng Wang,
    • Xiaoyan Xu,
    • Shuangxing Yu,
    • Kang Jin Jeong,
    • Zhicheng Zhou,
    • Leng Han,
    • Yiu Huen Tsang,
    • Jun Li,
    • Hu Chen,
    • Lingegowda S. Mangala,
    • Yuan Yuan,
    • A. Karina Eterovic,
    • Yiling Lu,
    • Anil K. Sood,
    • Kenneth L. Scott,
    • Gordon B. Mills,
    • and Han Liang
    Genome Res. July 2017 27: 1112-1125; Published in Advance April 14, 2017, doi:10.1101/gr.219741.116
    ...as a new player in cancer biology. Recent studies have reported key roles for individual miRNA editing events, but a comprehensive picture of miRNA editing in human cancers remains largely unexplored. Here, we systematically characterized the miRNA editing profiles of 8595 samples across 20 cancer types...
  3. Resource: Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage
    • Daniel E. Goszczynski,
    • Michelle M. Halstead,
    • Alma D. Islas-Trejo,
    • Huaijun Zhou,
    • and Pablo J. Ross
    Genome Res. April 2021 31: 732-744; Published in Advance March 15, 2021, doi:10.1101/gr.267336.120
    ...File S2) and 259 TSCs associated with potential mRNAs (Supplemental File S3). Lastly, we predicted pre-miRNA structures among the remaining models and identified 11,266 TSCs for candidate miRNA genes (Supplemental File S4), which is slightly over the estimated number of human miRNA candidates (Alles et...
  4. Research: An integrated systems genetics screen reveals the transcriptional structure of inherited predisposition to metastatic disease
    • Farhoud Faraji,
    • Ying Hu,
    • Gang Wu,
    • Natalie E. Goldberger,
    • Renard C. Walker,
    • Jinghui Zhang,
    • and Kent W. Hunter
    Genome Res. February 2014 24: 227-240; Published in Advance December 9, 2013, doi:10.1101/gr.166223.113
    ...-associated transcriptional networks. It has been demonstrated that microRNAs (miRNAs) play a key role in the initiation and progression ofmultiple tumor types (Tavazoie et al. 2008; Pencheva and Tavazoie 2013). Our group recently showed that heritable differences in miRNA expression underlie metastatic susceptibility...
  5. LETTER: In-depth characterization of the microRNA transcriptome in a leukemia progression model
    • Florian Kuchenbauer,
    • Ryan D. Morin,
    • Bob Argiropoulos,
    • Oleh I. Petriv,
    • Malachi Griffith,
    • Michael Heuser,
    • Eric Yung,
    • Jessica Piper,
    • Allen Delaney,
    • Anna-Liisa Prabhu,
    • Yongjun Zhao,
    • Helen McDonald,
    • Thomas Zeng,
    • Martin Hirst,
    • Carl L. Hansen,
    • Marco A. Marra,
    • and R. Keith Humphries
    Genome Res. November 2008 18: 1787-1797; Published in Advance October 10, 2008, doi:10.1101/gr.077578.108
    ..., Vancouver V6T 1Z1, British Columbia, Canada ↵ 4 These authors contributed equally to this work. ↵ 5 These authors contributed equally to this work. Abstract MicroRNAs (miRNAs) have been shown to play important roles in physiological as well as multiple malignant...
  6. Method: ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs
    • Piotr J. Balwierz,
    • Mikhail Pachkov,
    • Phil Arnold,
    • Andreas J. Gruber,
    • Mihaela Zavolan,
    • and Erik van Nimwegen
    Genome Res. May 2014 24: 869-884; Published in Advance February 10, 2014, doi:10.1101/gr.169508.113
    ...encoded by constellations of binding sites recognized by regulators such as transcriptions factors (TFs) and microRNAs (miRNAs), our understanding of this regulatory code and its context-dependent read-out remains very limited. Given that there are thousands of potential regulators in mammals...
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  7. Resource: A limited set of transcriptional programs define major cell types
    • Alessandra Breschi,
    • Manuel Muñoz-Aguirre,
    • Valentin Wucher,
    • Carrie A. Davis,
    • Diego Garrido-Martín,
    • Sarah Djebali,
    • Jesse Gillis,
    • Dmitri D. Pervouchine,
    • Anna Vlasova,
    • Alexander Dobin,
    • Chris Zaleski,
    • Jorg Drenkow,
    • Cassidy Danyko,
    • Alexandra Scavelli,
    • Ferran Reverter,
    • Michael P. Snyder,
    • Thomas R. Gingeras,
    • and Roderic Guigó
    Genome Res. July 2020 30: 1047-1059; Published in Advance July 29, 2020, doi:10.1101/gr.263186.120
    .... The three vials were combined, and we isolated total RNA from them using the Ambion mirVana miRNA Isolation kit (AM1561). The rRNA was removed using the RiboZero Gold Protocol (RZG1224). The libraries are made using a homebrew “dUTP” protocol (Parkhomchuk et al. 2009), which generates stranded libraries...
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  8. Method: Accurate and efficient detection of gene fusions from RNA sequencing data
    • Sebastian Uhrig,
    • Julia Ellermann,
    • Tatjana Walther,
    • Pauline Burkhardt,
    • Martina Fröhlich,
    • Barbara Hutter,
    • Umut H. Toprak,
    • Olaf Neumann,
    • Albrecht Stenzinger,
    • Claudia Scholl,
    • Stefan Fröhling,
    • and Benedikt Brors
    Genome Res. March 2021 31: 448-460; Published in Advance January 13, 2021, doi:10.1101/gr.257246.119
    ...MCF10A cells, an EGF-dependent, immortalized human mammary epithelial cell line frequently used to determine the transforming potential of oncogenes (Stolze et al. 2015; Ng et al. 2018). Both fusions significantly enhanced EGF-independent colony formation relative to empty vector control (Fig. 4C...
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  9. Method: Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
    • Bo Zhang,
    • Yan Zhou,
    • Nan Lin,
    • Rebecca F. Lowdon,
    • Chibo Hong,
    • Raman P. Nagarajan,
    • Jeffrey B. Cheng,
    • Daofeng Li,
    • Michael Stevens,
    • Hyung Joo Lee,
    • Xiaoyun Xing,
    • Jia Zhou,
    • Vasavi Sundaram,
    • GiNell Elliott,
    • Junchen Gu,
    • Taoping Shi,
    • Philippe Gascard,
    • Mahvash Sigaroudinia,
    • Thea D. Tlsty,
    • Theresa Kadlecek,
    • Arthur Weiss,
    • Henriette O’Geen,
    • Peggy J. Farnham,
    • Cécile L. Maire,
    • Keith L. Ligon,
    • Pamela A.F. Madden,
    • Angela Tam,
    • Richard Moore,
    • Martin Hirst,
    • Marco A. Marra,
    • Baoxue Zhang,
    • Joseph F. Costello,
    • and Ting Wang
    Genome Res. September 2013 23: 1522-1540; Published in Advance June 26, 2013, doi:10.1101/gr.156539.113
    ...-suppressor miRNA MIRLET7, MIRLET7A3, and MIRLET7B. The MIRLET7 family was discovered inCaenorhabditis elegans and is functionally conserved from worm to human. The human MIRLET7 family includes 13 isoforms located on nine different chromosomes. Silencing of MIRLET7 plays an important role in breast cancer...
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  10. LETTER: Altered adenosine-to-inosine RNA editing in human cancer
    • Nurit Paz,
    • Erez Y. Levanon,
    • Ninette Amariglio,
    • Amy B. Heimberger,
    • Zvi Ram,
    • Shlomi Constantini,
    • Zohar S. Barbash,
    • Konstantin Adamsky,
    • Michal Safran,
    • Avi Hirschberg,
    • Meir Krupsky,
    • Issachar Ben-Dov,
    • Simona Cazacu,
    • Tom Mikkelsen,
    • Chaya Brodie,
    • Eli Eisenberg,
    • and Gideon Rechavi
    Genome Res. November 2007 17: 1586-1595; Published in Advance October 1, 2007, doi:10.1101/gr.6493107
    ..., heterochromatic silencing, protection from retrotransposition, and destabilization of viral duplexes ( Kim et al. 2004 ; Levanon et al. 2004 ; Fernandez et al. 2005 ; Scadden and O’Connell 2005 ; Nie et al. 2006 ). In addition, RNA editing was shown to be involved in the regulation of nuclear retention and in miRNAs...
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