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Baar T, Dümcke S, Gressel S, Schwalb B, Dilthey A, Cramer P, Tresch A. RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history. G3 GENES|GENOMES|GENETICS 2022; 12:6543614. [PMID: 35253846 PMCID: PMC9073682 DOI: 10.1093/g3journal/jkac054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/25/2022] [Indexed: 11/16/2022]
Abstract
Alu elements are one of the most successful groups of RNA retrotransposons and make up 11% of the human genome with over 1 million individual loci. They are linked to genetic defects, increases in sequence diversity, and influence transcriptional activity. Still, their RNA metabolism is poorly understood yet. It is even unclear whether Alu elements are mostly transcribed by RNA Polymerase II or III. We have conducted a transcription shutoff experiment by α-amanitin and metabolic RNA labeling by 4-thiouridine combined with RNA fragmentation (TT-seq) and RNA-seq to shed further light on the origin and life cycle of Alu transcripts. We find that Alu RNAs are more stable than previously thought and seem to originate in part from RNA Polymerase II activity, as previous reports suggest. Their expression however seems to be independent of the transcriptional activity of adjacent genes. Furthermore, we have developed a novel statistical test for detecting the expression of quantitative trait loci in Alu elements that relies on the de Bruijn graph representation of all Alu sequences. It controls for both statistical significance and biological relevance using a tuned k-mer representation, discovering influential sequence features missed by regular motif search. In addition, we discover several point mutations using a generalized linear model, and motifs of interest, which also match transcription factor-binding motifs.
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Affiliation(s)
- Till Baar
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne 50937, Germany
| | | | - Saskia Gressel
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Björn Schwalb
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Alexander Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Achim Tresch
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne 50937, Germany
- CECAD, University of Cologne, Cologne 50931, Germany
- Center for Data and Simulation Science, University of Cologne, Cologne 50923, Germany
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Chan SH, Tang Y, Miao L, Darwich-Codore H, Vejnar CE, Beaudoin JD, Musaev D, Fernandez JP, Benitez MDJ, Bazzini AA, Moreno-Mateos MA, Giraldez AJ. Brd4 and P300 Confer Transcriptional Competency during Zygotic Genome Activation. Dev Cell 2020; 49:867-881.e8. [PMID: 31211993 DOI: 10.1016/j.devcel.2019.05.037] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 01/10/2019] [Accepted: 05/21/2019] [Indexed: 12/28/2022]
Abstract
The awakening of the genome after fertilization is a cornerstone of animal development. However, the mechanisms that activate the silent genome after fertilization are poorly understood. Here, we show that transcriptional competency is regulated by Brd4- and P300-dependent histone acetylation in zebrafish. Live imaging of transcription revealed that genome activation, beginning at the miR-430 locus, is gradual and stochastic. We show that genome activation does not require slowdown of the cell cycle and is regulated through the translation of maternally inherited mRNAs. Among these, the enhancer regulators P300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked, whereas inhibition of histone acetylation blocks genome activation. We conclude that P300 and Brd4 are sufficient to trigger genome-wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical for initiating zygotic development and developmental reprogramming.
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Affiliation(s)
- Shun Hang Chan
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Yin Tang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Liyun Miao
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Hiba Darwich-Codore
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Jean-Denis Beaudoin
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Damir Musaev
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Juan P Fernandez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Maria D J Benitez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Ariel A Bazzini
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | | | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Stem Cell Center, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA.
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Cano FR, Kuo SC, Lampen JO. Lomofungin, an inhibitor of deoxyribonucleic acid-dependent ribonucleic acid polymerases. Antimicrob Agents Chemother 1973; 3:723-8. [PMID: 4790624 PMCID: PMC444488 DOI: 10.1128/aac.3.6.723] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Lomofungin, an antibiotic active against fungi, yeasts, and bacteria, was found to be a potent inhibitor of purified Escherichia coli deoxyribonucleic acid (DNA)-dependent ribonucleic acid (RNA) polymerase. It prevents RNA synthesis by a direct interaction with the polymerase and not with the template or substrate; chain elongation is halted promptly. Three DNA-dependent RNA polymerases isolated from Saccharomyces strain 1016 were also sensitive to the antibiotic. Lomofungin does not appear to react generally with proteins, as bovine serum albumin did not prevent the inhibitory effect and numerous other enzymes were not affected by lomofungin.
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