1
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Ugolini M, Kerlin MA, Kuznetsova K, Oda H, Kimura H, Vastenhouw NL. Transcription bodies regulate gene expression by sequestering CDK9. Nat Cell Biol 2024; 26:604-612. [PMID: 38589534 PMCID: PMC11021188 DOI: 10.1038/s41556-024-01389-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 02/28/2024] [Indexed: 04/10/2024]
Abstract
The localization of transcriptional activity in specialized transcription bodies is a hallmark of gene expression in eukaryotic cells. It remains unclear, however, if and how transcription bodies affect gene expression. Here we disrupted the formation of two prominent endogenous transcription bodies that mark the onset of zygotic transcription in zebrafish embryos and analysed the effect on gene expression using enriched SLAM-seq and live-cell imaging. We find that the disruption of transcription bodies results in the misregulation of hundreds of genes. Here we focus on genes that are upregulated. These genes have accessible chromatin and are poised to be transcribed in the presence of the two transcription bodies, but they do not go into elongation. Live-cell imaging shows that disruption of the two large transcription bodies enables these poised genes to be transcribed in ectopic transcription bodies, suggesting that the large transcription bodies sequester a pause release factor. Supporting this hypothesis, we find that CDK9-the kinase that releases paused polymerase II-is highly enriched in the two large transcription bodies. Overexpression of CDK9 in wild-type embryos results in the formation of ectopic transcription bodies and thus phenocopies the removal of the two large transcription bodies. Taken together, our results show that transcription bodies regulate transcription by sequestering machinery, thereby preventing genes elsewhere in the nucleus from being transcribed.
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Affiliation(s)
- Martino Ugolini
- Center for Integrative Genomics (CIG), University of Lausanne (UNIL), Lausanne, Switzerland
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Maciej A Kerlin
- Center for Integrative Genomics (CIG), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Ksenia Kuznetsova
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Haruka Oda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- Institute of Human Genetics, CNRS, Montpellier, France
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Nadine L Vastenhouw
- Center for Integrative Genomics (CIG), University of Lausanne (UNIL), Lausanne, Switzerland.
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.
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2
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Wille CK, Neumann EN, Deshpande AJ, Sridharan R. DOT1L interaction partner AF10 controls patterning of H3K79 methylation and RNA polymerase II to maintain cell identity. Stem Cell Reports 2023; 18:2451-2463. [PMID: 37995701 PMCID: PMC10724070 DOI: 10.1016/j.stemcr.2023.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023] Open
Abstract
Histone 3 lysine 79 methylation (H3K79me) is enriched on gene bodies proportional to gene expression levels and serves as a strong barrier for the reprogramming of somatic cells to induced pluripotent stem cells (iPSCs). DOT1L is the sole histone methyltransferase that deposits all three orders-mono (me1), di (me2), and tri (me3) methylation-at H3K79. Here, we leverage genetic and chemical approaches to parse the specific functions of orders of H3K79me in maintaining cell identity. DOT1L interacts with AF10 (Mllt10), which recognizes unmodified H3K27 and boosts H3K79me2/3 methylation. AF10 deletion evicts H3K79me2/3 and reorganizes H3K79me1 to the transcription start site to facilitate iPSC formation in the absence of steady-state transcriptional changes. Instead, AF10 loss redistributes RNA polymerase II to a uniquely pluripotent pattern at highly expressed, rapidly transcribed housekeeping genes. Taken together, we reveal a specific mechanism for H3K79me2/3 located at the gene body in reinforcing cell identity.
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Affiliation(s)
- Coral K Wille
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Edwin N Neumann
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Aniruddha J Deshpande
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA.
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3
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Wille CK, Zhang X, Haws SA, Denu JM, Sridharan R. DOT1L is a barrier to histone acetylation during reprogramming to pluripotency. SCIENCE ADVANCES 2023; 9:eadf3980. [PMID: 37976354 PMCID: PMC10656071 DOI: 10.1126/sciadv.adf3980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 10/18/2023] [Indexed: 11/19/2023]
Abstract
Embryonic stem cells (ESCs) have transcriptionally permissive chromatin enriched for gene activation-associated histone modifications. A striking exception is DOT1L-mediated H3K79 dimethylation (H3K79me2) that is considered a positive regulator of transcription. We find that ESCs are depleted for H3K79me2 at shared locations of enrichment with somatic cells, which are highly and ubiquitously expressed housekeeping genes, and have lower RNA polymerase II (RNAPII) at the transcription start site (TSS) despite greater nascent transcription. Inhibiting DOT1L increases the efficiency of reprogramming of somatic to induced pluripotent stem cells, enables an ESC-like RNAPII pattern at the TSS, and functionally compensates for enforced RNAPII pausing. DOT1L inhibition increases H3K27 methylation and RNAPII elongation-enhancing histone acetylation without changing the expression of the causal histone-modifying enzymes. Only the maintenance of elevated histone acetylation is essential for enhanced reprogramming and occurs at loci that are depleted for H3K79me2. Thus, DOT1L inhibition promotes the hyperacetylation and hypertranscription pluripotent properties.
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Affiliation(s)
- Coral K. Wille
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Xiaoya Zhang
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Spencer A. Haws
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John M. Denu
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
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4
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Zimmer JT, Vock IW, Schofield JA, Kiefer L, Moon MH, Simon MD. Improving the study of RNA dynamics through advances in RNA-seq with metabolic labeling and nucleotide-recoding chemistry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.542133. [PMID: 37292657 PMCID: PMC10245837 DOI: 10.1101/2023.05.24.542133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
RNA metabolic labeling using 4-thiouridine (s4U) captures the dynamics of RNA synthesis and decay. The power of this approach is dependent on appropriate quantification of labeled and unlabeled sequencing reads, which can be compromised by the apparent loss of s4U-labeled reads in a process we refer to as dropout. Here we show that s4U-containing transcripts can be selectively lost when RNA samples are handled under sub-optimal conditions, but that this loss can be minimized using an optimized protocol. We demonstrate a second cause of dropout in nucleotide recoding and RNA sequencing (NR-seq) experiments that is computational and downstream of library preparation. NR-seq experiments involve chemically converting s4U from a uridine analog to a cytidine analog and using the apparent T-to-C mutations to identify the populations of newly synthesized RNA. We show that high levels of T-to-C mutations can prevent read alignment with some computational pipelines, but that this bias can be overcome using improved alignment pipelines. Importantly, kinetic parameter estimates are affected by dropout independent of the NR chemistry employed, and all chemistries are practically indistinguishable in bulk, short-read RNA-seq experiments. Dropout is an avoidable problem that can be identified by including unlabeled controls, and mitigated through improved sample handing and read alignment that together improve the robustness and reproducibility of NR-seq experiments.
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Affiliation(s)
- Joshua T. Zimmer
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Isaac W. Vock
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Jeremy A. Schofield
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
- Current address: Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98105, USA
| | - Lea Kiefer
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
- Current address: Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Michelle H. Moon
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Matthew D. Simon
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
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5
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Sugio Y, Yamagami R, Shigi N, Hori H. A selective and sensitive detection system for 4-thiouridine modification in RNA. RNA (NEW YORK, N.Y.) 2023; 29:241-251. [PMID: 36411056 PMCID: PMC9891261 DOI: 10.1261/rna.079445.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
4-Thiouridine (s4U) is a modified nucleoside, found at positions 8 and 9 in tRNA from eubacteria and archaea. Studies of the biosynthetic pathway and physiological role of s4U in tRNA are ongoing in the tRNA modification field. s4U has also recently been utilized as a biotechnological tool for analysis of RNAs. Therefore, a selective and sensitive system for the detection of s4U is essential for progress in the fields of RNA technologies and tRNA modification. Here, we report the use of biotin-coupled 2-aminoethyl-methanethiosulfonate (MTSEA biotin-XX) for labeling of s4U and demonstrate that the system is sensitive and quantitative. This technique can be used without denaturation; however, addition of a denaturation step improves the limit of detection. Thermus thermophilus tRNAs, which abundantly contain 5-methyl-2-thiouridine, were tested to investigate the selectivity of the MTSEA biotin-XX s4U detection system. The system did not react with 5-methyl-2-thiouridine in tRNAs from a T. thermophilus tRNA 4-thiouridine synthetase (thiI) gene deletion strain. Thus, the most useful advantage of the MTSEA biotin-XX s4U detection system is that MTSEA biotin-XX reacts only with s4U and not with other sulfur-containing modified nucleosides such as s2U derivatives in tRNAs. Furthermore, the MTSEA biotin-XX s4U detection system can analyze multiple samples in a short time span. The MTSEA biotin-XX s4U detection system can also be used for the analysis of s4U formation in tRNA. Finally, we demonstrate that the MTSEA biotin-XX system can be used to visualize newly transcribed tRNAs in S. cerevisiae cells.
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Affiliation(s)
- Yuzuru Sugio
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Naoki Shigi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
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6
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Wille CK, Sridharan R. Connecting the DOTs on Cell Identity. Front Cell Dev Biol 2022; 10:906713. [PMID: 35733849 PMCID: PMC9207516 DOI: 10.3389/fcell.2022.906713] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/18/2022] [Indexed: 01/04/2023] Open
Abstract
DOT1-Like (DOT1L) is the sole methyltransferase of histone H3K79, a modification enriched mainly on the bodies of actively transcribing genes. DOT1L has been extensively studied in leukemia were some of the most frequent onco-fusion proteins contain portions of DOT1L associated factors that mislocalize H3K79 methylation and drive oncogenesis. However, the role of DOT1L in non-transformed, developmental contexts is less clear. Here we assess the known functional roles of DOT1L both in vitro cell culture and in vivo models of mammalian development. DOT1L is evicted during the 2-cell stage when cells are totipotent and massive epigenetic and transcriptional alterations occur. Embryonic stem cell lines that are derived from the blastocyst tolerate the loss of DOT1L, while the reduction of DOT1L protein levels or its catalytic activity greatly enhances somatic cell reprogramming to induced pluripotent stem cells. DOT1L knockout mice are embryonically lethal when organogenesis commences. We catalog the rapidly increasing studies of total and lineage specific knockout model systems that show that DOT1L is broadly required for differentiation. Reduced DOT1L activity is concomitant with increased developmental potential. Contrary to what would be expected of a modification that is associated with active transcription, loss of DOT1L activity results in more upregulated than downregulated genes. DOT1L also participates in various epigenetic networks that are both cell type and developmental stage specific. Taken together, the functions of DOT1L during development are pleiotropic and involve gene regulation at the locus specific and global levels.
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Affiliation(s)
- Coral K. Wille
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, United States
- *Correspondence: Coral K. Wille, , Rupa Sridharan,
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, United States
- *Correspondence: Coral K. Wille, , Rupa Sridharan,
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7
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Hersch M, Biasini A, Marques AC, Bergmann S. Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic labeling experiment. BMC Bioinformatics 2022; 23:147. [PMID: 35459101 PMCID: PMC9034570 DOI: 10.1186/s12859-022-04672-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 04/04/2022] [Indexed: 11/05/2022] Open
Abstract
Background Over the past decade, experimental procedures such as metabolic labeling for determining RNA turnover rates at the transcriptome-wide scale have been widely adopted and are now turning to single cell measurements. Several computational methods to estimate RNA synthesis, processing and degradation rates from such experiments have been suggested, but they all require several RNA sequencing samples. Here we present a method that can estimate those three rates from a single sample. Methods Our method relies on the analytical solution to the Zeisel model of RNA dynamics. It was validated on metabolic labeling experiments performed on mouse embryonic stem cells. Resulting degradation rates were compared both to previously published rates on the same system and to a state-of-the-art method applied to the same data. Results Our method is computationally efficient and outputs rates that correlate well with previously published data sets. Using it on a single sample, we were able to reproduce the observation that dynamic biological processes tend to involve genes with higher metabolic rates, while stable processes involve genes with lower rates. This supports the hypothesis that cells control not only the mRNA steady-state abundance, but also its responsiveness, i.e., how fast steady state is reached. Moreover, degradation rates obtained with our method compare favourably with the other tested method. Conclusions In addition to saving experimental work and computational time, estimating rates for a single sample has several advantages. It does not require an error-prone normalization across samples and enables the use of replicates to estimate uncertainty and assess sample quality. Finally the method and theoretical results described here are general enough to be useful in other contexts such as nucleotide conversion methods and single cell metabolic labeling experiments. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04672-4.
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Affiliation(s)
- Micha Hersch
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, 1015, Lausanne, CH, Switzerland.
| | - Adriano Biasini
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ana C Marques
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Sven Bergmann
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, 1015, Lausanne, CH, Switzerland
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8
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Moreno S, Brunner M, Delazer I, Rieder D, Lusser A, Micura R. Synthesis of 4-thiouridines with prodrug functionalization for RNA metabolic labeling. RSC Chem Biol 2022; 3:447-455. [PMID: 35441143 PMCID: PMC8985182 DOI: 10.1039/d2cb00001f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/18/2022] [Indexed: 12/22/2022] Open
Abstract
Metabolic labeling has emerged as a powerful tool to endow RNA with reactive handles allowing for subsequent chemical derivatization and processing. Recently, thiolated nucleosides, such as 4-thiouridine (4sU), have attracted great interest in metabolic labeling-based RNA sequencing approaches (TUC-seq, SLAM-seq, TimeLapse-seq) to study cellular RNA expression and decay dynamics. For these and other applications (e.g. PAR-CLIP), thus far only the naked nucleoside 4sU has been applied. Here we examined the concept of derivatizing 4sU into a 5′-monophosphate prodrug that would allow for cell permeation and potentially improve labeling efficiency by bypassing the rate-limiting first step of 5′ phosphorylation of the nucleoside into the ultimately bioactive 4sU triphosphate (4sUTP). To this end, we developed robust synthetic routes towards diverse 4sU monophosphate prodrugs. Using metabolic labeling assays, we found that most of the newly introduced 4sU prodrugs were well tolerated by the cells. One derivative, the bis(4-acetyloxybenzyl) 5′-monophosphate of 4sU, was also efficiently incorporated into nascent RNA. Synthetic access to 4-thiouridine (4sU) derivatives with monophosphate prodrug patterns creates additional possibilities for metabolic labeling of RNA for different applications.![]()
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Affiliation(s)
- Sarah Moreno
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Melanie Brunner
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Isabel Delazer
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Dietmar Rieder
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innrain 82, 6020 Innsbruck, Austria
| | - Alexandra Lusser
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
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9
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Wille CK, Sridharan R. DOT1L inhibition enhances pluripotency beyond acquisition of epithelial identity and without immediate suppression of the somatic transcriptome. Stem Cell Reports 2021; 17:384-396. [PMID: 34995500 PMCID: PMC8828533 DOI: 10.1016/j.stemcr.2021.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/21/2022] Open
Abstract
Inhibiting the histone 3 lysine 79 (H3K79) methyltransferase, disruptor of telomeric silencing 1-like (DOT1L), increases the efficiency of reprogramming somatic cells to induced pluripotent stem cells (iPSCs). Here, we find that, despite the enrichment of H3K79 methylation on thousands of actively transcribed genes in somatic cells, DOT1L inhibition (DOT1Li) does not immediately cause the shutdown of the somatic transcriptional profile to enable transition to pluripotency. Contrary to the prevalent view, DOT1Li promotes iPSC generation beyond the mesenchymal to epithelial transition and even from already epithelial cell types. DOT1Li is most potent at the midpoint of reprogramming in part by repressing Nfix that persists at late stages of reprogramming. Importantly, regulation of single genes cannot substitute for DOT1Li, demonstrating that H3K79 methylation has pleiotropic effects in maintaining cell identity. DOT1L is a barrier of reprogramming, especially at the mid-point DOT1L inhibition increases pluripotency beyond MET DOT1L inhibition does not immediately suppress somatic expression Single factors cannot replace the pleiotropic effects of DOT1L inhibition
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Affiliation(s)
- Coral K Wille
- Wisconsin Institute for Discovery, University of Wisconsin, 330 North Orchard Street, Room 2118, Madison, WI 53715, USA
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin, 330 North Orchard Street, Room 2118, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA.
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10
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Shang J, He L, Wang J, Tong A, Xiang Y. In Situ Visualizing Nascent RNA by Exploring DNA-Templated Oxidative Amination of 4-Thiouridine. Bioconjug Chem 2021; 33:164-171. [PMID: 34910465 DOI: 10.1021/acs.bioconjchem.1c00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tracking and mapping the nascent RNA molecules in cells is essential for deciphering embryonic development and neuronal differentiation. Here, we utilized 4-thiouridine (s4U) as a metabolic tag to label nascent RNA and developed a fluorescence imaging method based on the DNA-templated oxidative amination (DTOA) reaction of s4U. The DTOA reaction occurred between amine-modified DNA and s4U-containing RNA with high sequence specificity and chemical selectivity. Target nascent mRNAs in HeLa cells, including those encoding green fluorescent proteins (GFPs) and endogenous BAG-1, were thus lit up selectively by DTOA-based fluorescence in situ hybridization (DTOA FISH). We believe the DTOA conjugation chemistry shown in this study could be generally applied to investigate the spatial distribution of nascent transcription dynamics in cellular processes.
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Affiliation(s)
- Jiachen Shang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Luo He
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Jingyi Wang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
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11
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Zhao Y, Dukler N, Barshad G, Toneyan S, Danko CG, Siepel A. Deconvolution of Expression for Nascent RNA sequencing data (DENR) highlights pre-RNA isoform diversity in human cells. Bioinformatics 2021; 37:4727-4736. [PMID: 34382072 PMCID: PMC8665767 DOI: 10.1093/bioinformatics/btab582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/24/2021] [Accepted: 08/09/2021] [Indexed: 12/03/2022] Open
Abstract
Motivation Quantification of isoform abundance has been extensively studied at the mature RNA level using RNA-seq but not at the level of precursor RNAs using nascent RNA sequencing. Results We address this problem with a new computational method called Deconvolution of Expression for Nascent RNA-sequencing data (DENR), which models nascent RNA-sequencing read-counts as a mixture of user-provided isoforms. The baseline algorithm is enhanced by machine-learning predictions of active transcription start sites and an adjustment for the typical ‘shape profile’ of read-counts along a transcription unit. We show that DENR outperforms simple read-count-based methods for estimating gene and isoform abundances, and that transcription of multiple pre-RNA isoforms per gene is widespread, with frequent differences between cell types. In addition, we provide evidence that a majority of human isoform diversity derives from primary transcription rather than from post-transcriptional processes. Availability and implementation DENR and nascentRNASim are freely available at https://github.com/CshlSiepelLab/DENR (version v1.0.0) and https://github.com/CshlSiepelLab/nascentRNASim (version v0.3.0). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yixin Zhao
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Noah Dukler
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Gilad Barshad
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Shushan Toneyan
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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12
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Zaidan NZ, Sridharan R. HP1γ regulates H3K36 methylation and pluripotency in embryonic stem cells. Nucleic Acids Res 2020; 48:12660-12674. [PMID: 33237287 PMCID: PMC7736818 DOI: 10.1093/nar/gkaa1091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/12/2020] [Accepted: 10/27/2020] [Indexed: 01/01/2023] Open
Abstract
The heterochromatin protein 1 (HP1) family members are canonical effectors and propagators of gene repression mediated by histone H3 lysine 9 (H3K9) methylation. HP1γ exhibits an increased interaction with active transcription elongation-associated factors in embryonic stem cells (ESCs) compared to somatic cells. However, whether this association has a functional consequence remains elusive. Here we find that genic HP1γ colocalizes and enhances enrichment of transcription elongation-associated H3K36me3 rather than H3K9me3. Unexpectedly, sustained H3K36me3 deposition is dependent on HP1γ. HP1γ-deleted ESCs display reduced H3K36me3 enrichment, concomitant with decreased expression at shared genes which function to maintain cellular homeostasis. Both the H3K9me3-binding chromodomain and histone binding ability of HP1γ are dispensable for maintaining H3K36me3 levels. Instead, the chromoshadow together with the hinge domain of HP1γ that confer protein and nucleic acid-binding ability are sufficient because they retain the ability to interact with NSD1, an H3K36 methyltransferase. HP1γ-deleted ESCs have a slower self-renewal rate and an impaired ability to differentiate towards cardiac mesoderm. Our findings reveal a requirement for HP1γ in faithful establishment of transcription elongation in ESCs, which regulates pluripotency.
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Affiliation(s)
- Nur Zafirah Zaidan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.,Genetics Training Program, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53715, USA
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13
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Gregersen LH, Mitter R, Svejstrup JQ. Using TT chem-seq for profiling nascent transcription and measuring transcript elongation. Nat Protoc 2020; 15:604-627. [PMID: 31915390 DOI: 10.1038/s41596-019-0262-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/29/2019] [Indexed: 01/08/2023]
Abstract
The dynamics of transcription can be studied genome wide by high-throughput sequencing of nascent and newly synthesized RNA. 4-thiouridine (4SU) labeling in vivo enables the specific capture of such new transcripts, with 4SU residues being tagged by biotin linkers and captured using streptavidin beads before library production and high-throughput sequencing. To achieve high-resolution profiles of transcribed regions, an RNA fragmentation step before biotin tagging was introduced, in an approach known as transient transcriptome sequencing (TT-seq). We recently introduced a chemical approach for RNA fragmentation that we refer to as TTchem-seq. We describe how TTchem-seq can be used in combination with transient inhibition of early elongation using the reversible CDK9 inhibitor, 5,6-dichlorobenzimidazole 1-β-D-ribofuranoside (DRB), to measure RNA polymerase II (RNAPII) elongation rates in vivo, a technique we call DRB/TTchem-seq. Here, we provide detailed protocols for carrying out TTchem-seq and DRB/TTchem-seq, including computational analysis. Experiments and data analysis can be performed over a period of 10-13 d and require molecular biology and bioinformatics skills.
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Affiliation(s)
- Lea H Gregersen
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK.
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14
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Boxer LD, Renthal W, Greben AW, Whitwam T, Silberfeld A, Stroud H, Li E, Yang MG, Kinde B, Griffith EC, Bonev B, Greenberg ME. MeCP2 Represses the Rate of Transcriptional Initiation of Highly Methylated Long Genes. Mol Cell 2019; 77:294-309.e9. [PMID: 31784358 DOI: 10.1016/j.molcel.2019.10.032] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 09/09/2019] [Accepted: 10/23/2019] [Indexed: 12/14/2022]
Abstract
Mutations in the methyl-DNA-binding repressor protein MeCP2 cause the devastating neurodevelopmental disorder Rett syndrome. It has been challenging to understand how MeCP2 regulates transcription because MeCP2 binds broadly across the genome and MeCP2 mutations are associated with widespread small-magnitude changes in neuronal gene expression. We demonstrate here that MeCP2 represses nascent RNA transcription of highly methylated long genes in the brain through its interaction with the NCoR co-repressor complex. By measuring the rates of transcriptional initiation and elongation directly in the brain, we find that MeCP2 has no measurable effect on transcriptional elongation, but instead represses the rate at which Pol II initiates transcription of highly methylated long genes. These findings suggest a new model of MeCP2 function in which MeCP2 binds broadly across highly methylated regions of DNA, but acts at transcription start sites to attenuate transcriptional initiation.
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Affiliation(s)
- Lisa D Boxer
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - William Renthal
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Alexander W Greben
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Tess Whitwam
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Andrew Silberfeld
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Hume Stroud
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Emmy Li
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Marty G Yang
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Benyam Kinde
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Eric C Griffith
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Boyan Bonev
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Michael E Greenberg
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA.
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15
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Wang J, Shang J, Qin Z, Tong A, Xiang Y. Selective and sensitive fluorescence "turn-on" detection of 4-thiouridine in nucleic acids via oxidative amination. Chem Commun (Camb) 2019; 55:13096-13099. [PMID: 31612162 DOI: 10.1039/c9cc06312a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A fluorescence "turn-on" method for digestion-free analysis of 4-thiouridine (s4U) in nucleic acids was developed in this work based on the oxidative amination of s4U by fluoresceinamine (FAM-NH2) and periodate (IO4-). It was 125-fold more sensitive for s4U detection than the traditional UV330 absorption method, and showed excellent selectivity to s4U over 2-thiouridine (s2U) analogues and biological thiols.
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Affiliation(s)
- Jingyi Wang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China.
| | - Jiachen Shang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China.
| | - Zichen Qin
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China.
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China.
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China.
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16
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Muthmann N, Hartstock K, Rentmeister A. Chemo-enzymatic treatment of RNA to facilitate analyses. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1561. [PMID: 31392842 DOI: 10.1002/wrna.1561] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/17/2019] [Accepted: 07/04/2019] [Indexed: 12/11/2022]
Abstract
Labeling RNA is a recurring problem to make RNA compatible with state-of-the-art methodology and comes in many flavors. Considering only cellular applications, the spectrum still ranges from site-specific labeling of individual transcripts, for example, for live-cell imaging of mRNA trafficking, to metabolic labeling in combination with next generation sequencing to capture dynamic aspects of RNA metabolism on a transcriptome-wide scale. Combining the specificity of RNA-modifying enzymes with non-natural substrates has emerged as a valuable strategy to modify RNA site- or sequence-specifically with functional groups suitable for subsequent bioorthogonal reactions and thus label RNA with reporter moieties such as affinity or fluorescent tags. In this review article, we will cover chemo-enzymatic approaches (a) for in vitro labeling of RNA for application in cells, (b) for treatment of total RNA, and (c) for metabolic labeling of RNA. This article is categorized under: RNA Processing < RNA Editing and Modification RNA Methods < RNA Analyses in vitro and In Silico RNA Methods < RNA Analyses in Cells.
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Affiliation(s)
- Nils Muthmann
- Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Katja Hartstock
- Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
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17
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Duffy EE, Schofield JA, Simon MD. Gaining insight into transcriptome-wide RNA population dynamics through the chemistry of 4-thiouridine. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1513. [PMID: 30370679 DOI: 10.1002/wrna.1513] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 12/11/2022]
Abstract
Cellular RNA levels are the result of a juggling act between RNA transcription, processing, and degradation. By tuning one or more of these parameters, cells can rapidly alter the available pool of transcripts in response to stimuli. While RNA sequencing (RNA-seq) is a vital method to quantify RNA levels genome-wide, it is unable to capture the dynamics of different RNA populations at steady-state or distinguish between different mechanisms that induce changes to the steady-state (i.e., altered rate of transcription vs. degradation). The dynamics of different RNA populations can be studied by targeted incorporation of noncanonical nucleosides. 4-Thiouridine (s4 U) is a commonly used and versatile RNA metabolic label that allows the study of many properties of RNA metabolism from synthesis to degradation. Numerous experimental strategies have been developed that leverage the power of s4 U to label newly transcribed RNA in whole cells, followed by enrichment with activated disulfides or chemistry to induce C mutations at sites of s4 U during sequencing. This review presents existing methods to study RNA population dynamics genome-wide using s4 U metabolic labeling, as well as a discussion of considerations and challenges when designing s4 U metabolic labeling experiments. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Erin E Duffy
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut
| | - Jeremy A Schofield
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut
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