Searching journal content for articles similar to Paloviita et al. 31 (8): 1474.

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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...different cell types during spermatogenesis. The upper heat map represents genes with shortened 3′ UTRs, and the lower shows genes with lengthened 3′ UTRs. (G) Significant biological process terms of genes with dynamic 3′ isoform changes. (H) Expression levels, PAS usage, and miRNA binding sites around...
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Research: Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids
- Cheng Zhao,
- Savana Biondic,
- Katherine Vandal,
- Åsa K. Björklund,
- Michael Hagemann-Jensen,
- Theresa Maria Sommer,
- Jesica Canizo,
- Stephen Clark,
- Pascal Raymond,
- Daniel R. Zenklusen,
- Nicolas Rivron,
- Wolf Reik,
- and Sophie Petropoulos
Genome Res. September 2022 32: 1627-1641; Published in Advance August 10, 2022, doi:10.1101/gr.276665.122
...). They are composed of multiple biotypes including miRNA, transfer RNA (tRNA), long intergenic noncoding RNA (lincRNA), small nuclear RNA (snRNA), and small nucleolar RNA (snoRNA). To date, the complete small RNA profile in the human embryo remains unknown. We therefore wanted to examine the small RNA biotypes...
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Method: Global mapping of RNA homodimers in living cells
- Marta M. Gabryelska,
- Andrew P. Badrock,
- Jian You Lau,
- Raymond T. O'Keefe,
- Yanick J. Crow,
- and Grzegorz Kudla
Genome Res. May 2022 32: 956-967; Published in Advance March 24, 2022, doi:10.1101/gr.275900.121
...expression by miRNA and siRNAs. Intramolecular and intermolecular interactions are interdependent, and according to the competing endogenous RNA (ceRNA) hypothesis (Salmena et al. 2011; Gardiner et al. 2015), intermolecular RNA interactions have the potential to rewire regulatory networks and expand...
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Research: Sperm is epigenetically programmed to regulate gene transcription in embryos
- Marta Teperek,
- Angela Simeone,
- Vincent Gaggioli,
- Kei Miyamoto,
- George E. Allen,
- Serap Erkek,
- Taejoon Kwon,
- Edward M. Marcotte,
- Philip Zegerman,
- Charles R. Bradshaw,
- Antoine H.F.M. Peters,
- John B. Gurdon,
- and Jerome Jullien
Genome Res. August 2016 26: 1034-1046; Published in Advance March 31, 2016, doi:10.1101/gr.201541.115
...at supporting mRNA transcription (Ziyyat and Lefevre 2001; Vassena et al. 2007; Ihara et al. 2014), we tested this hypothesis using haploid, sperm- and spermatid-derived embryos. Embryos were rigorously staged (see Supplemental Experimental Procedures) and collected at gastrulation, before the onset...
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Research: Global analyses of the dynamics of mammalian microRNA metabolism
- Elena R. Kingston and
- David P. Bartel
Genome Res. November 2019 29: 1777-1790; Published in Advance September 13, 2019, doi:10.1101/gr.251421.119
...@wi.mit.eduAbstractRates of production and degradation together specify microRNA (miRNA) abundance and dynamics. Here, we used approach-to-steady-state metabolic labeling to assess these rates for 176 miRNAs in contact-inhibited mouse embryonic fibroblasts (MEFs), 182 miRNAs in dividing MEFs, and 127 miRNAs in mouse embryonic stem...
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Research: A comprehensive survey of 3′ animal miRNA modification events and a possible role for 3′ adenylation in modulating miRNA targeting effectiveness
- A. Maxwell Burroughs,
- Yoshinari Ando,
- Michiel J.L. de Hoon,
- Yasuhiro Tomaru,
- Takahiro Nishibu,
- Ryo Ukekawa,
- Taku Funakoshi,
- Tsutomu Kurokawa,
- Harukazu Suzuki,
- Yoshihide Hayashizaki,
- and Carsten O. Daub
Genome Res. October 2010 20: 1398-1410; Published in Advance August 18, 2010, doi:10.1101/gr.106054.110
...A comprehensive survey of 3′ animal miRNA modification events and a possible role for 3′ adenylation in modulating miRNA targeting effectiveness A. Maxwell Burroughs 1 , 4 , 5 , Yoshinari Ando 1 , 4 , 5 , Michiel J.L. de Hoon 1 , Yasuhiro Tomaru 1...
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Resource: The full-length transcriptome of C. elegans using direct RNA sequencing
- Nathan P. Roach,
- Norah Sadowski,
- Amelia F. Alessi,
- Winston Timp,
- James Taylor,
- and John K. Kim
Genome Res. February 2020 30: 299-312; Published in Advance February 5, 2020, doi:10.1101/gr.251314.119
...of the 5′-most 10–15 bases prevented us from examining splice leader-based trans splicing, a common RNA modification in C. elegans (see discussion in Supplemental Material). The average length of unique splice isoforms identified in our sequencing libraries was 1596 nt (Fig. 1E,F and discussed below...
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Research: Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements
- Joanne L. Harding,
- Stuart Horswell,
- Claire Heliot,
- Javier Armisen,
- Lyle B. Zimmerman,
- Nicholas M. Luscombe,
- Eric A. Miska,
- and Caroline S. Hill
Genome Res. January 2014 24: 96-106; Published in Advance September 24, 2013, doi:10.1101/gr.144469.112
...of gastrula embryos. This analysis allowed us to identify novel microRNAs and we show that microRNA expression is highly dynamic and spatially localized in early embryos. In addition, we have developed a microRNA prediction pipeline and demonstrate that it has the power to predict new miRNAs...
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Research: Dynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition
- Vladimir Despic,
- Mario Dejung,
- Mengting Gu,
- Jayanth Krishnan,
- Jing Zhang,
- Lydia Herzel,
- Korinna Straube,
- Mark B. Gerstein,
- Falk Butter,
- and Karla M. Neugebauer
Genome Res. July 2017 27: 1184-1194; Published in Advance April 5, 2017, doi:10.1101/gr.215954.116
...that the Hnrnpa1 AGGGA motif is necessary for proper Hnrnpa1 binding to RNA targets in vivo. 3′ UTRs are common targets of RBPs and miRNAs that regulate mRNA stability and translation (Matoulkova et al. 2012). In transcriptionally silent embryos, maternal mRNA translation is tightly controlled by regulation...
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Research: Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition
- Håvard Aanes,
- Cecilia L. Winata,
- Chi Ho Lin,
- Jieqi P. Chen,
- Kandhadayar G. Srinivasan,
- Serene G.P. Lee,
- Adrian Y.M. Lim,
- Hajira Shreen Hajan,
- Philippe Collas,
- Guillaume Bourque,
- Zhiyuan Gong,
- Vladimir Korzh,
- Peter Aleström,
- and Sinnakaruppan Mathavan
Genome Res. August 2011 21: 1328-1338; Published in Advance May 9, 2011, doi:10.1101/gr.116012.110
...is known about their abundance and the mechanisms regulating their maturation and translation. A role of microRNAs (miRNAs) as mediator of maternal RNA clearance has been documented for miR-430 (Giraldez et al. 2006; Bushati et al. 2008; Takeda et al. 2009); however, to what extent miRNAs regulate 9These...
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