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Research: Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy
- Dhanur P. Iyer,
- Lambert Moyon,
- Lars Wittler,
- Chieh-Yu Cheng,
- Francisca R. Ringeling,
- Stefan Canzar,
- Annalisa Marsico,
- and Aydan Bulut-Karslioğlu
Genome Res. April 2024 34: 572-589; Published in Advance May 6, 2024, doi:10.1101/gr.278662.123
...these processes are coordinated to successfully transition cells to the resting dormant state remains unclear. Here we show that microRNA activity, which is otherwise dispensable for preimplantation development, is essential for the adaptation of early mouse embryos to the dormant state of diapause. In particular...
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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
...highly conserved microRNA binding sites. It thus appears that biological functionality of microRNA binding sites depends on the dose-sensitivity of their host gene and that, conversely, it is unlikely that every predicted microRNA target is dose-sensitive enough to be functionally regulated by microRNAs...
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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...–D773. doi:10.1093/nar/gky955 ↵The Gene Ontology Consortium. 2000. Gene Ontology: tool for the unification of biology. Nat Genet 25: 25–29. doi:10.1038/75556 ↵Gennarino VA, Sardiello M, Avellino R, Meola N, Maselli V, Anand S, Cutillo L, Ballabio A, Banfi S. 2009. MicroRNA target prediction...
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Research: Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation
- Jack A. Collora and
- Ya-Chi Ho
Genome Res. June 9, 2023 gr.277698.123; Published in Advance June 9, 2023, doi:10.1101/gr.277698.123
...the 22 impact of HIV-1 promoter activity on host chromatin accessibility downstream of the integration site, we used 23 sgRNA targeting HIV-1 promoter versus nontargeting controls (NT) with CRISPR-activation (CRISPRa) and 24 CRISPR-inhibition (CRISPRi) cell line clones. We examined whether activation...
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Resource: Dynamics of microRNA expression during mouse prenatal development
- Sorena Rahmanian,
- Rabi Murad,
- Alessandra Breschi,
- Weihua Zeng,
- Mark Mackiewicz,
- Brian Williams,
- Carrie A. Davis,
- Brian Roberts,
- Sarah Meadows,
- Dianna Moore,
- Diane Trout,
- Chris Zaleski,
- Alex Dobin,
- Lei-Hoon Sei,
- Jorg Drenkow,
- Alex Scavelli,
- Thomas R. Gingeras,
- Barbara J. Wold,
- Richard M. Myers,
- Roderic Guigó,
- and Ali Mortazavi
Genome Res. November 2019 29: 1900-1909; Published in Advance October 23, 2019, doi:10.1101/gr.248997.119
....111 ↵Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281–297. doi:10.1016/S0092-8674(04)00045-5 ↵Bartel DP. 2009. MicroRNAs: target recognition and regulatory functions. Cell 136: 215–233. doi:10.1016/j.cell.2009.01.002 ↵Bernstein E, Kim SY, Carmell MA, Murchison EP...
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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 chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection
- Shudi Zhao,
- Yuedong Li,
- Guanping Chen,
- Xingyang Wang,
- Nan Chen,
- and Xiaofeng Wu
Genome Res. November 2023 33: 1958-1974; Published in Advance October 23, 2023, doi:10.1101/gr.277931.123
...at the ATAC-seq peaks after BmNPV infection. (B) BmNPV infection drastically attenuates cis-interaction. (C) Distances from all the predicted enhancers to the TSS of their target genes in mock- and BmNPV-infected cells. (D) Box plots of the distances showed in C. The median (center of box), lower and upper...
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Research: Tissue-specific reprogramming of host tRNA transcriptome by the microbiome
- Jia Huang,
- Wenjun Chen,
- Fan Zhou,
- Zhichang Pang,
- Luoluo Wang,
- Tao Pan,
- and Xiaoyun Wang
Genome Res. June 2021 31: 947-957; Published in Advance April 15, 2021, doi:10.1101/gr.272153.120
....02.053 ↵Heiss CN, Olofsson LE. 2018. Gut microbiota-dependent modulation of energy metabolism. J Innate Immun 10: 163–171. doi:10.1159/000481519 ↵Hoban AE, Stilling RM, Moloney GM, Moloney RD, Shanahan F, Dinan TG, Cryan JF, Clarke G. 2017. Microbial regulation of microRNA expression in the amygdala...
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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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Resource: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons
- Qicheng Ma,
- Satyam P. Srivastav,
- Stephanie Gamez,
- Gargi Dayama,
- Fabiana Feitosa-Suntheimer,
- Edward I. Patterson,
- Rebecca M. Johnson,
- Erik M. Matson,
- Alexander S. Gold,
- Douglas E. Brackney,
- John H. Connor,
- Tonya M. Colpitts,
- Grant L. Hughes,
- Jason L. Rasgon,
- Tony Nolan,
- Omar S. Akbari,
- and Nelson C. Lau
Genome Res. March 2021 31: 512-528; Published in Advance January 8, 2021, doi:10.1101/gr.265157.120
...hosts.Three main classes of animal small regulatory RNAs are microRNAs (miRNAs) and endogenous small interfering RNAs (endo-siRNAs), which range in size between 18 and 23 nt long and are typically bound by Argonaute proteins; and Piwi-interacting RNAs (piRNAs) that are bound by Piwi proteins and mainly...
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