Searching journal content for articles similar to Bergmann et al. 25 (9): 1336.

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  1. 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
    ...the diversity of sedimentation profiles of native RNPs. We now refer to these stringently defined RNAs with discrete sedimentation profiles as gradient-enriched transcripts.To investigate if GETs are conserved, we performed the same set of experiments using mouse stem cells (mESCs) (Supplemental Fig. S3). After...
  2. Research: Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci
    • Richard D.W. Kelly,
    • Kristy R. Stengel,
    • Aditya Chandru,
    • Lyndsey C. Johnson,
    • Scott W. Hiebert,
    • and Shaun M. Cowley
    Genome Res. January 2024 34: 34-46; Published in Advance January 30, 2024, doi:10.1101/gr.278050.123
    ...inhibitor JQ1 (Fig. 4). PRO-seq allows high-resolution mapping of active RNA polymerases across the at both coding and noncoding regions and provides information on both the abundance and directionality of transcripts. Analysis of the transcriptome in LBH589-treated ESCs revealed that the majority of genes...
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  3. Research: Noncoding regions underpin avian bill shape diversification at macroevolutionary scales
    • Leeban Yusuf,
    • Matthew C. Heatley,
    • Joseph P.G. Palmer,
    • Henry J. Barton,
    • Christopher R. Cooney,
    • and Toni I. Gossmann
    Genome Res. April 2020 30: 553-565; Published in Advance April 8, 2020, doi:10.1101/gr.255752.119
    ...pattern, we identified that the ESC pathways are enriched in the coding and noncoding gene sets (Fig. 5C). This further supports the notion that fundamental cellular pathways, such as BMP and Wnt signaling pathways, play a crucial role in the development of bird beaks and that this signal is detectable...
  4. Research: Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction
    • Kimberly N. Griffin,
    • Benjamin William Walters,
    • Haixin Li,
    • Huafeng Wang,
    • Giulia Biancon,
    • Toma Tebaldi,
    • Carolyn B. Kaya,
    • Jean Kanyo,
    • TuKiet T. Lam,
    • Andy L. Cox,
    • Stephanie Halene,
    • Jean-Ju Chung,
    • and Bluma J. Lesch
    Genome Res. September 2022 32: 1655-1668; Published in Advance September 15, 2022, doi:10.1101/gr.276578.122
    ...be mediated by RNA-dependent interactions, analogous to the role of noncoding RNAs in recruitment and stabilization of chromatin regulators at heterochromatin (Johnson et al. 2017; Velazquez Camacho et al. 2017). Although AGO2–chromatin interactions appear to be resistant to RNase digestion in mESCs...
  5. Research: Acute depletion of METTL3 implicates N6-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome
    • Guifeng Wei,
    • Mafalda Almeida,
    • Greta Pintacuda,
    • Heather Coker,
    • Joseph S. Bowness,
    • Jernej Ule,
    • and Neil Brockdorff
    Genome Res. August 2021 31: 1395-1408; Published in Advance June 15, 2021, doi:10.1101/gr.271635.120
    ...depletion of METTL3 on nascent RNA splicing.ResultsMapping m6A in the nascent mESC transcriptomeChromatin-associated RNA (ChrRNA) is substantially enriched for nascent transcripts (Nesterova et al. 2019). Thus, to investigate the roles of m6A in nascent RNA processing in mouse embryonic stem cells, we...
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  6. Resource: Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring
    • Kyu-Hyeon Yeom,
    • Zhicheng Pan,
    • Chia-Ho Lin,
    • Han Young Lim,
    • Wen Xiao,
    • Yi Xing,
    • and Douglas L. Black
    Genome Res. June 2021 31: 1106-1119; Published in Advance April 8, 2021, doi:10.1101/gr.273904.120
    ...genes whose poly(A)+ transcripts remain sequestered with chromatin showed that their splicing was modulated across cell types. The chromatin-associated Meg3 noncoding RNA is well expressed in mESCs and neurons but not in mNPCs (Supplemental Fig. S2B). Meg3 is the host transcript for the miRNAs MiR-770...
  7. Resource: Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
    • Andrea Pauli,
    • Eivind Valen,
    • Michael F. Lin,
    • Manuel Garber,
    • Nadine L. Vastenhouw,
    • Joshua Z. Levin,
    • Lin Fan,
    • Albin Sandelin,
    • John L. Rinn,
    • Aviv Regev,
    • and Alexander F. Schier
    Genome Res. March 2012 22: 577-591; Published in Advance November 22, 2011, doi:10.1101/gr.133009.111
    ...Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis Andrea Pauli 1 , 7 , 8 , Eivind Valen 2 , 7 , Michael F. Lin 3 , 4 , Manuel Garber 4 , Nadine L. Vastenhouw 1 , Joshua Z. Levin 4...
  8. Method: Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing
    • Shilin Zhang,
    • Yichen Wang,
    • Lin Jia,
    • Xue Wen,
    • Zhonghua Du,
    • Cong Wang,
    • Yajing Hao,
    • Dehai Yu,
    • Lei Zhou,
    • Naifei Chen,
    • Jingcheng Chen,
    • Huiling Chen,
    • Hui Zhang,
    • Ilkay Celik,
    • Günhan Gülsoy,
    • Jianjun Luo,
    • Baoming Qin,
    • Xueling Cui,
    • Zhonghui Liu,
    • Songling Zhang,
    • Miguel A. Esteban,
    • Ferhat Ay,
    • Wei Xu,
    • Runsheng Chen,
    • Wei Li,
    • Andrew R. Hoffman,
    • Ji-Fan Hu,
    • and Jiuwei Cui
    Genome Res. September 2019 29: 1521-1532; Published in Advance July 17, 2019, doi:10.1101/gr.244996.118
    ...130021, P.R. China; 8La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, USA ↵9 These authors contributed equally to this work. Corresponding authors: cuijw@jlu.edu.cn, jifan@stanford.edu, arhoffman@stanford.eduAbstractLong noncoding RNAs (lncRNAs) can regulate the activity...
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  9. Research: Massive reshaping of genome–nuclear lamina interactions during oncogene-induced senescence
    • Christelle Lenain,
    • Carolyn A. de Graaf,
    • Ludo Pagie,
    • Nils L. Visser,
    • Marcel de Haas,
    • Sandra S. de Vries,
    • Daniel Peric-Hupkes,
    • Bas van Steensel,
    • and Daniel S. Peeper
    Genome Res. October 2017 27: 1634-1644; Published in Advance September 15, 2017, doi:10.1101/gr.225763.117
    ...Methods. Facultative and constitutive LAD definitions Microarray LMNB1 DamID data from Tig3 cells, ESCs (Meuleman et al. 2013), HTC75 (a human HT1080 line which stably expresses the Tet-off) (van Steensel and de Lange 1997), and KBM7 (Kind et al. 2015) were used in our definition of facultative...
  10. Research: De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements
    • Felix Schlesinger,
    • Andrew D. Smith,
    • Thomas R. Gingeras,
    • Gregory J. Hannon,
    • and Emily Hodges
    Genome Res. October 2013 23: 1601-1614; Published in Advance June 28, 2013, doi:10.1101/gr.157271.113
    ...(Supplemental Fig. S3E). Consistently, many of these bivalent pHMRs co-occur with nearby bivalent iHMRs (Fig. 3F), as defined in Figure 1. In B cells, the majority of bivalent iHMRs observed in H1 ESCs remains hypomethylated and are generally resolved into either an active (high H3K4 methylation and RNA Pol II...
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