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Research: ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development
- Charlie Y. Shi,
- Lara E. Elcavage,
- Raghu R. Chivukula,
- Joanna Stefano,
- Benjamin Kleaveland,
- and David P. Bartel
Genome Res. September 2023 33: 1482-1496; Published in Advance August 2, 2023, doi:10.1101/gr.278073.123
...author: dbartel@wi.mit.eduAbstractMicroRNAs (miRNAs) pair to sites in mRNAs to direct the degradation of these RNA transcripts. Conversely, certain RNA transcripts can direct the degradation of particular miRNAs. This target-directed miRNA degradation (TDMD) requires the ZSWIM8 E3 ubiquitin ligase. Here...
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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...17). In total, 10/12 cervid-specific sites possessed significantly lower expression than the rats’ sites (P-value < 0.05; Student's t-test), which further indicated potential down-regulation of cervid-specific mRNA expression. Together, these results indicated that the gBGC-induced alteration of UCEs...
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Research: MicroRNAs reinforce repression of PRC2 transcriptional targets independently and through a feed-forward regulatory network
- Haridha Shivram,
- Steven V. Le,
- and Vishwanath R. Iyer
Genome Res. February 2019 29: 184-192; Published in Advance January 16, 2019, doi:10.1101/gr.238311.118
...-forward-regulated genes as a group were likely to be targeted by EZH2-activated miRNAs, we tested whether the number of predicted interactions between them were higher than expected by random chance. There were 342 unique interactions predicted between 14 EZH2-activated miRNAs (conserved miRNAs with mRNA target...
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Research: Cotargeting among microRNAs in the brain
- Jennifer M. Cherone,
- Vjola Jorgji,
- and Christopher B. Burge
Genome Res. November 2019 29: 1791-1804; Published in Advance October 24, 2019, doi:10.1101/gr.249201.119
...perturbations (van Rooij et al. 2007; Zheng et al. 2011) and leaving an incomplete picture of the functional roles of most miRNAs.Each conserved miRNA typically has hundreds of target genes or more that are conserved across mammals, together encompassing at least 60% of mammalian mRNAs, as well as additional...
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Research: A compendium of conserved cleavage and polyadenylation events in mammalian genes
- Ruijia Wang,
- Dinghai Zheng,
- Ghassan Yehia,
- and Bin Tian
Genome Res. October 2018 28: 1427-1441; Published in Advance August 24, 2018, doi:10.1101/gr.237826.118
...isoforms with different 3′ UTRs and/or coding sequences. Here, we present a compendium of conserved cleavage and polyadenylation sites (PASs) in mammalian genes, based on approximately 1.2 billion 3′ end sequencing reads from more than 360 human, mouse, and rat samples. We show that ∼80% of mammalian mRNA...
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Research: Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
- Akanksha Bafna,
- Gareth Banks,
- Michael H. Hastings,
- and Patrick M. Nolan
Genome Res. May 2023 33: 673-688; Published in Advance May 8, 2023, doi:10.1101/gr.277581.122
...the relationship between observed rhythmic H3K27ac occupancy and target gene expression. Along with rhythms in the coding mRNA fraction, we also noticed cycling expression in the noncoding bidirectional eRNA. Thereby, our study offers a framework to understand the dynamic pretranscriptional regulation operative...
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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
...knockouts of Ago2 are embryonic lethal (Alisch et al. 2007). AGO2 canonically acts in the cytoplasm to inhibit target mRNA translation (Huang and Li 2014), but several roles for AGO2 in the nucleus have also been described. In Drosophila larvae and human fibroblasts, AGO2 mediates gene silencing...
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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
...are conserved in corals and hydras, suggesting that microRNA gene turnover in Cnidaria greatly exceeds that of other metazoan groups. We further show that Nematostella miRNAs frequently direct the cleavage of their mRNA targets via nearly perfect complementarity. This mode of action resembles that of small...
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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
..., these results establish a framework for describing the dynamics and regulation of miRNAs throughout their life cycle.MicroRNAs (miRNAs) are small RNAs that mediate posttranscriptional gene regulation by targeting mRNAs for degradation and translational repression. In animals, miRNAs typically recognize their mRNA...
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Research: Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs
- Marta Melé,
- Kaia Mattioli,
- William Mallard,
- David M. Shechner,
- Chiara Gerhardinger,
- and John L. Rinn
Genome Res. January 2017 27: 27-37; Published in Advance December 7, 2016, doi:10.1101/gr.214205.116
...share similar biogenesis pathways, these transcript classes differ in many regards. LincRNAs are less evolutionarily conserved, less abundant, and more tissue-specific, suggesting that their pre- and post-transcriptional regulation is different from that of mRNAs. Here, we perform an in...
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