Searching journal content for articles similar to Tierney et al. 34 (4): 530.

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  1. Resource: DEAD box RNA helicases are pervasive protein kinase interactors and activators
    • Alexander Hirth,
    • Edoardo Fatti,
    • Eugen Netz,
    • Sergio P. Acebron,
    • Dimitris Papageorgiou,
    • Andrea Švorinić,
    • Cristina-Maria Cruciat,
    • Emil Karaulanov,
    • Alexandr Gopanenko,
    • Tianheng Zhu,
    • Irmgard Sinning,
    • Jeroen Krijgsveld,
    • Oliver Kohlbacher,
    • and Christof Niehrs
    Genome Res. June 2024 34: 952-966; Published in Advance July 10, 2024, doi:10.1101/gr.278264.123
    ...(Linder and Jankowsky 2011). DDX helicases typically unwind RNA structures and dissociate RNA–protein complexes in reactions fuelled by ATP hydrolysis. Prominent cellular processes in which DDX proteins are involved include pre-mRNA splicing, ribosome biogenesis, protein biosynthesis, RNA decay, nuclear...
  2. Research: Ribosome profiling reveals an important role for translational control in circadian gene expression
    • Christopher Jang,
    • Nicholas F. Lahens,
    • John B. Hogenesch,
    • and Amita Sehgal
    Genome Res. December 2015 25: 1836-1847; Published in Advance September 3, 2015, doi:10.1101/gr.191296.115
    ...of small lengths of mRNAs (∼30 nt) by the ribosome during translation (Steitz 1969). Sequencing libraries canbe generated from these ribosome-protected fragments (RPFs) to determine which mRNAs are actively translated at any given time on a -wide scale with single codon resolution (Ingolia et al. 2009...
  3. Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
    • Jennifer A. Urban,
    • Daniel Ringwalt,
    • John M. Urban,
    • Wingel Xue,
    • Ryan Gleason,
    • Keji Zhao,
    • and Xin Chen
    Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
    ...SC-like enriched gene sets contained expected markers, supporting cluster identity and the robustness of our analysis (Fig. 2B; Supplemental Table S2). First, the long noncoding RNAs (lncRNAs), long non-coding RNA on the X 1 (lncRNA:roX1) and lncRNA:roX2, components of the male dosage compensation complex found...
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  4. Research: Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates
    • Étienne Fafard-Couture,
    • Pierre-Étienne Jacques,
    • and Michelle S. Scott
    Genome Res. April 2023 33: 525-540; Published in Advance April 18, 2023, doi:10.1101/gr.277483.122
    ...) are structured noncoding RNAs present in multiple copies within eukaryotic s. snoRNAs guide chemical modifications on their target RNA and regulate processes like ribosome assembly and splicing. Most human snoRNAs are embedded within host gene introns, the remainder being independently expressed from intergenic...
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  5. Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
    • Ezequiel Calvo-Roitberg,
    • Rachel F. Daniels,
    • and Athma A. Pai
    Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
    ...in ribosome loading and translation efficiency and can influence the expressed open reading frame (Leppek et al. 2018).At the other end, alternative PASs dictate the 3′ UTR, which is involved in the regulation of mRNA stability and localization and can also lead to protein truncation (Di Giammartino et al...
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  6. Research: Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells
    • Gabriel Kolle,
    • Jill L. Shepherd,
    • Brooke Gardiner,
    • Karin S. Kassahn,
    • Nicole Cloonan,
    • David L.A. Wood,
    • Ehsan Nourbakhsh,
    • Darrin F. Taylor,
    • Shivangi Wani,
    • Hun S. Chy,
    • Qi Zhou,
    • Kevin McKernan,
    • Scott Kuersten,
    • Andrew L. Laslett,
    • and Sean M. Grimmond
    Genome Res. December 2011 21: 2014-2025; Published in Advance October 31, 2011, doi:10.1101/gr.119321.110
    .../untranslated fractions of hESCs was used to identify RNAs encoding peptides destined for secretion and the extracellular space and to demonstrate preferential selection of transcription complexity for translation in vitro. The impact of this newly defined complexity on known gene-centric network models...
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  7. ARTICLE: Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world
    • Minglei Wang,
    • Liudmila S. Yafremava,
    • Derek Caetano-Anollés,
    • Jay E. Mittenthal,
    • and Gustavo Caetano-Anollés
    Genome Res. November 2007 17: 1572-1585; Published in Advance October 1, 2007, doi:10.1101/gr.6454307
    ...(HGT) was rampant in early evolution ( Doolittle 1999 ). In contrast, a tracing of the origins of the tripartite world from an ancient RNA world based on DNA sequence, RNA relics, and other considerations suggests that the ancestor was eukaryotic-like and complex ( Poole et al. 1998 ; Forterre...
  8. Research: mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus
    • Matthieu Legendre,
    • Stéphane Audic,
    • Olivier Poirot,
    • Pascal Hingamp,
    • Virginie Seltzer,
    • Deborah Byrne,
    • Audrey Lartigue,
    • Magali Lescot,
    • Alain Bernadac,
    • Julie Poulain,
    • Chantal Abergel,
    • and Jean-Michel Claverie
    Genome Res. May 2010 20: 664-674; Published in Advance April 1, 2010, doi:10.1101/gr.102582.109
    ...mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus Matthieu Legendre 1 , Stéphane Audic 1 , Olivier Poirot 1 , Pascal Hingamp 1 , Virginie Seltzer 1 , Deborah Byrne 1 , Audrey...
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  9. Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
    • Christine R. Keenan,
    • Hannah D. Coughlan,
    • Nadia Iannarella,
    • Andres Tapia del Fierro,
    • Andrew Keniry,
    • Timothy M. Johanson,
    • Wing Fuk Chan,
    • Alexandra L. Garnham,
    • Lachlan W. Whitehead,
    • Marnie E. Blewitt,
    • Gordon K. Smyth,
    • and Rhys S. Allan
    Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
    ...et al. 2019) and impeding the binding of diverse transcription factors (TFs) and RNA polymerase, unlike H3K27me3-marked domains (Becker et al. 2016, 2017).Loss of heterochromatin has been proposed as a potential universal molecular cause of aging, whereby over time, heterochromatin domains lose...
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  10. Research: Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish
    • Charles E. Vejnar,
    • Mario Abdel Messih,
    • Carter M. Takacs,
    • Valeria Yartseva,
    • Panos Oikonomou,
    • Romain Christiano,
    • Marlon Stoeckius,
    • Stephanie Lau,
    • Miler T. Lee,
    • Jean-Denis Beaudoin,
    • Damir Musaev,
    • Hiba Darwich-Codore,
    • Tobias C. Walther,
    • Saeed Tavazoie,
    • Daniel Cifuentes,
    • and Antonio J. Giraldez
    Genome Res. July 2019 29: 1100-1114; Published in Advance June 21, 2019, doi:10.1101/gr.245159.118
    ...a central regulatory hub that integrates multiple inputs to control mRNA translation, localization, stability, and polyadenylation status (Mayr 2017). In the cell, these inputs come from RNA-binding proteins (RBPs) and noncoding sequences such as microRNA binding sites and AU-rich elements (AREs), which...
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