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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
...RNA duplexes.Sequence differences and other features that mediate differences in guide half-livesTo address what might specify differences in guide half-lives, we assessed whether species with similar sequences had similar half-lives. MicroRNAs with the same seed region target largely overlapping sets of m...
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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
...maternal mRNAs (Dahanukar et al. 1999; Tadros et al. 2007). In Xenopus, AREs within the 3′ UTRs of maternal mRNAs trigger their deadenylation after egg activation and decay after the mid-blastula transition (MBT) (Audic et al. 1997; Voeltz and Steitz 1998). In zebrafish, zygotic transcription of microRNA...
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Research: Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism
- Yen-Ju Chen,
- Chia-Ying Chen,
- Te-Lun Mai,
- Chih-Fan Chuang,
- Yu-Chen Chen,
- Sachin Kumar Gupta,
- Laising Yen,
- Yi-Da Wang,
- and Trees-Juen Chuang
Genome Res. March 2020 30: 375-391; Published in Advance March 3, 2020, doi:10.1101/gr.255463.119
...RNA expression profiling in postmortem brains from individuals with ASD and controls and identified 60 circRNAs and three coregulated modules that were perturbed in ASD. By integrating circRNA, microRNA, and mRNA dysregulation data derived from the same cortex samples, we identified 8170 ASD-associated circRNA-microRNA...
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Research: nanoCAGE reveals 5′ UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs
- Valentina Gandin,
- Laia Masvidal,
- Laura Hulea,
- Simon-Pierre Gravel,
- Marie Cargnello,
- Shannon McLaughlan,
- Yutian Cai,
- Preetika Balanathan,
- Masahiro Morita,
- Arjuna Rajakumar,
- Luc Furic,
- Michael Pollak,
- John A. Porco, Jr.,
- Julie St-Pierre,
- Jerry Pelletier,
- Ola Larsson,
- and Ivan Topisirovic
Genome Res. May 2016 26: 636-648; Published in Advance March 16, 2016, doi:10.1101/gr.197566.115
...structural integrity, resulting in apoptosis. Conversely, simultaneous suppression of translation of both long and short 5′ UTR mRNAs by MTOR inhibitors results in metabolic dormancy and a predominantly cytostatic effect. Thus, 5′ UTR features define different modes of MTOR-sensitive translation...
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Research: Cnidarian microRNAs frequently regulate targets by cleavage
- Yehu Moran,
- David Fredman,
- Daniela Praher,
- Xin Z. Li,
- Liang Meng Wee,
- Fabian Rentzsch,
- Phillip D. Zamore,
- Ulrich Technau,
- and Hervé Seitz
Genome Res. April 2014 24: 651-663; Published in Advance March 18, 2014, doi:10.1101/gr.162503.113
...Cnidarian microRNAs frequently regulate targets by cleavage Yehu Moran 1 , 5 , 6 , David Fredman 1 , 5 , 7 , Daniela Praher 1 , Xin Z. Li 2 , Liang Meng Wee 2 , Fabian Rentzsch 3 , Phillip D. Zamore 2 , 8...
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Method: Next-generation sequencing identifies the natural killer cell microRNA transcriptome
- Todd A. Fehniger,
- Todd Wylie,
- Elizabeth Germino,
- Jeffrey W. Leong,
- Vincent J. Magrini,
- Sunita Koul,
- Catherine R. Keppel,
- Stephanie E. Schneider,
- Daniel C. Koboldt,
- Ryan P. Sullivan,
- Michael E. Heinz,
- Seth D. Crosby,
- Rakesh Nagarajan,
- Giridharan Ramsingh,
- Daniel C. Link,
- Timothy J. Ley,
- and Elaine R. Mardis
Genome Res. November 2010 20: 1590-1604; Published in Advance October 8, 2010, doi:10.1101/gr.107995.110
...molecule mRNAs (e.g., granzyme B, GzmB) through unclear molecular mechanisms. MicroRNAs (miRNAs) are small noncoding RNAs that post-transcriptionally regulate the translation of their mRNA targets, and are therefore candidates for mediating this control process. While the expression and importance of mi...
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Research: Polycomb preferentially targets stalled promoters of coding and noncoding transcripts
- Daniel Enderle,
- Christian Beisel,
- Michael B. Stadler,
- Moritz Gerstung,
- Prashanth Athri,
- and Renato Paro
Genome Res. February 2011 21: 216-226; Published in Advance December 22, 2010, doi:10.1101/gr.114348.110
...that the majority of PcG binding sites in S2 cells are present at core promoter regions. PcG proteins bind promoters of primary microRNA transcripts We questioned whether the nonannotated TSSs bound by PcG proteins merely consist of alternative promoters for already known genes or might contain novel ncRNA targets...
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Research: Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs
- Michael Schnall-Levin,
- Olivia S. Rissland,
- Wendy K. Johnston,
- Norbert Perrimon,
- David P. Bartel,
- and Bonnie Berger
Genome Res. September 2011 21: 1395-1403; Published in Advance June 17, 2011, doi:10.1101/gr.121210.111
...equally to this work. Abstract MicroRNAs (miRNAs) regulate numerous biological processes by base-pairing with target messenger RNAs (mRNAs), primarily through sites in 3′ untranslated regions (UTRs), to direct the repression of these targets. Although miRNAs have sometimes been observed...
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Resource: MicroRNA target prediction by expression analysis of host genes
- Vincenzo Alessandro Gennarino,
- Marco Sardiello,
- Raffaella Avellino,
- Nicola Meola,
- Vincenza Maselli,
- Santosh Anand,
- Luisa Cutillo,
- Andrea Ballabio,
- and Sandro Banfi
Genome Res. March 2009 19: 481-490; Published in Advance December 16, 2008, doi:10.1101/gr.084129.108
...RNA targets to be tested compared to the procedures based solely on target sequence recognition. Finally, our data further confirm that miRNAs have a significant impact on the mRNA levels of most of their targets. MicroRNAs (miRNAs) are a class of short noncoding RNAs controlling the expression levels...
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LETTER: MicroRNA–target pairs in the rat kidney identified by microRNA microarray, proteomic, and bioinformatic analysis
- Zhongmin Tian,
- Andrew S. Greene,
- Jennifer L. Pietrusz,
- Isaac R. Matus,
- and Mingyu Liang
Genome Res. March 2008 18: 404-411; Published in Advance January 29, 2008, doi:10.1101/gr.6587008
.... ↵ Stark, A. , Brennecke, J. , Bushati, N. , Russell, R.B. , Cohen, S.M. ( 2005 ) Animal microRNAs confer robustness to gene expression and have a significant impact on 3′UTR evolution . Cell 123 : 1133 – 1146 . ↵ Taylor, N.E. , Glocka, P. , Liang, M. , Cowley, A.W. ( 2006 ) NADPH oxidase in the renal...

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