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Research: microRNA target prediction programs predict many false positives
- Natalia Pinzón,
- Blaise Li,
- Laura Martinez,
- Anna Sergeeva,
- Jessy Presumey,
- Florence Apparailly,
- and Hervé Seitz
Genome Res. February 2017 27: 234-245; Published in Advance November 15, 2016, doi:10.1101/gr.205146.116
...of Medicine, 34060 Montpellier, France; 4Clinical Department for Osteoarticular Diseases, University Hospital Lapeyronie, 34295 Montpellier, France According to the current view, each microRNA regulates hundreds of genes. Computational tools aim at identifying microRNA targets, usually selecting...
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Research: MicroRNA evolution, expression, and function during short germband development in Tribolium castaneum
- Maria Ninova,
- Matthew Ronshaugen,
- and Sam Griffiths-Jones
Genome Res. January 2016 26: 85-96; Published in Advance October 30, 2015, doi:10.1101/gr.193367.115
...Corresponding authors: sam.griffiths-jones@manchester.ac.uk , matthew.ronshaugen@manchester.ac.uk Abstract MicroRNAs are well-established players in the development of multicellular animals. Most of our understanding of microRNA function in arthropod development comes from studies in Drosophila...
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RESOURCE: Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity
- Natalia J. Martinez,
- Maria C. Ow,
- John S. Reece-Hoyes,
- M. Inmaculada Barrasa,
- Victor R. Ambros,
- and Albertha J.M. Walhout
Genome Res. December 2008 18: 2005-2015; Published in Advance November 3, 2008, doi:10.1101/gr.083055.108
....1186/1471-2164-8-21 . ↵ Bartel, D.P. ( 2004 ) MicroRNAs: Genomics, biogenesis, mechanism, and function . Cell 116 : 281 – 297 . ↵ Baskerville, S. , Bartel, D.P. ( 2005 ) Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes . RNA 11 : 241 – 247 . ↵ Behlke, M. , Dames, S.A. , Mc...
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Research: A genomic portrait of the genetic architecture and regulatory impact of microRNA expression in response to infection
- Katherine J. Siddle,
- Matthieu Deschamps,
- Ludovic Tailleux,
- Yohann Nédélec,
- Julien Pothlichet,
- Geanncarlo Lugo-Villarino,
- Valentina Libri,
- Brigitte Gicquel,
- Olivier Neyrolles,
- Guillaume Laval,
- Etienne Patin,
- Luis B. Barreiro,
- and Lluís Quintana-Murci
Genome Res. May 2014 24: 850-859; Published in Advance January 30, 2014, doi:10.1101/gr.161471.113
...were purchased from Exiqon (miR-29 family 460039, control 199020-00) and miRIDIAN microRNA mimics from Thermo Fisher (miR-29a C-300504-07, control CN-001000-01). Transfection efficiency was assessed by flow cytometry using a fluorescently labeled control oligonucleotide (Exiqon, 19902004), and found...
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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
...cells. Known microRNAs identified in NK cells using the Illumina GA We established a bioinformatics analysis protocol for identifying and enumerating known (miRBase v13) miRNAs based on alignments tomaturemiRNA andminormiRNA* encoding coordinates in miRNA precursor hairpin sequences using SHRi...
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Research: CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors
- Kosuke Hashimoto,
- Ana Maria Suzuki,
- Alexandre Dos Santos,
- Christophe Desterke,
- Agnese Collino,
- Serena Ghisletti,
- Emilie Braun,
- Alessandro Bonetti,
- Alexandre Fort,
- Xian-Yang Qin,
- Enrico Radaelli,
- Bogumil Kaczkowski,
- Alistair R.R. Forrest,
- Soichi Kojima,
- Didier Samuel,
- Gioacchino Natoli,
- Marie Annick Buendia,
- Jamila Faivre,
- and Piero Carninci
Genome Res. December 2015 25: 1812-1824; Published in Advance October 28, 2015, doi:10.1101/gr.191031.115
...HCC have identified overexpressed genes (Ladeiro et al. 2008), activated pathways (Huang et al. 2011), and subtypes of HCC (Boyault et al. 2007). However, most of the studies focused on protein-coding genes or microRNAs, and the repertoire of long ncRNAs in HCC tumor tissues remains largely unexplored...
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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
...expression of microRNAs and their computationally predicted targets in the rat kidney provides a unique molecular basis for further exploring the biological role of microRNA. In addition, this study establishes a differential profile of microRNA expression between the renal cortex and the renal medulla...
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LETTER: Xenopus microRNA genes are predominantly located within introns and are differentially expressed in adult frog tissues via post-transcriptional regulation
- Guo-Qing Tang and
- E. Stuart Maxwell
Genome Res. January 2008 18: 104-112; Published in Advance November 21, 2007, doi:10.1101/gr.6539108
.... ↵ Baskerville, S. , Bartel, D. ( 2005 ) Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes . RNA 11 : 241 – 247 . ↵ Bartel, D. ( 2004 ) MicroRNAs: Genomics, biogenesis, mechanism, and function . Cell 116 : 281 – 297 . ↵ Bentwich, I. ( 2005 ) Prediction...
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Letter: Epigenetic profiling at mouse imprinted gene clusters reveals novel epigenetic and genetic features at differentially methylated regions
- Scott V. Dindot,
- Richard Person,
- Mark Strivens,
- Rejinaldo Garcia,
- and Arthur L. Beaudet
Genome Res. August 2009 19: 1374-1383; Published in Advance June 19, 2009, doi:10.1101/gr.089185.108
...). Currently there are about 100 known imprinted genes in the mouse, including protein coding genes, noncoding RNA transcripts, and micro-RNAs (www.har.mrc.ac.uk/research/ genomic_imprinting). Most of these genes are found in clusters, and in most cases the domains harbor a CpG rich imprinting control region...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...relevance, integrating the origin of DNA and protein elements (cis and trans) to evaluate false-positive and false-negative risks across experimental systems. Moreover, we explore how perturbation strategies—gain and loss of function—can complement steady-state profiling to establish causality in gene...
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