1
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Flemr M, Schwaiger M, Hess D, Iesmantavicius V, Ahel J, Tuck AC, Mohn F, Bühler M. Mouse nuclear RNAi-defective 2 promotes splicing of weak 5' splice sites. RNA 2023; 29:1140-1165. [PMID: 37137667 PMCID: PMC10351895 DOI: 10.1261/rna.079465.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/19/2023] [Indexed: 05/05/2023]
Abstract
Removal of introns during pre-mRNA splicing, which is central to gene expression, initiates by base pairing of U1 snRNA with a 5' splice site (5'SS). In mammals, many introns contain weak 5'SSs that are not efficiently recognized by the canonical U1 snRNP, suggesting alternative mechanisms exist. Here, we develop a cross-linking immunoprecipitation coupled to a high-throughput sequencing method, BCLIP-seq, to identify NRDE2 (nuclear RNAi-defective 2), and CCDC174 (coiled-coil domain-containing 174) as novel RNA-binding proteins in mouse ES cells that associate with U1 snRNA and 5'SSs. Both proteins bind directly to U1 snRNA independently of canonical U1 snRNP-specific proteins, and they are required for the selection and effective processing of weak 5'SSs. Our results reveal that mammalian cells use noncanonical splicing factors bound directly to U1 snRNA to effectively select suboptimal 5'SS sequences in hundreds of genes, promoting proper splice site choice, and accurate pre-mRNA splicing.
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Affiliation(s)
- Matyas Flemr
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Michaela Schwaiger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | | | - Josip Ahel
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Alex Charles Tuck
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Fabio Mohn
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- University of Basel, 4003 Basel, Switzerland
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2
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Gil N, Perry RBT, Mukamel Z, Tuck A, Bühler M, Ulitsky I. Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus. Cell Rep 2023; 42:112569. [PMID: 37256750 PMCID: PMC10320833 DOI: 10.1016/j.celrep.2023.112569] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/07/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are implicated in a plethora of cellular processes, but an in-depth understanding of their functional features or their mechanisms of action is currently lacking. Here we study Meteor, a lncRNA transcribed near the gene encoding EOMES, a pleiotropic transcription factor implicated in various processes throughout development and in adult tissues. Using a wide array of perturbation techniques, we show that transcription elongation through the Meteor locus is required for Eomes activation in mouse embryonic stem cells, with Meteor repression linked to a change in the subpopulation primed to differentiate to the mesoderm lineage. We further demonstrate that a distinct functional feature of the locus-namely, the underlying DNA element-is required for suppressing Eomes expression following neuronal differentiation. Our results demonstrate the complex regulation that can be conferred by a single locus and emphasize the importance of careful selection of perturbation techniques when studying lncRNA loci.
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Affiliation(s)
- Noa Gil
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Ben-Tov Perry
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Zohar Mukamel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alex Tuck
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel.
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3
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Kuzdere T, Flury V, Schalch T, Iesmantavicius V, Hess D, Bühler M. Differential phosphorylation of Clr4 SUV39H by Cdk1 accompanies a histone H3 methylation switch that is essential for gametogenesis. EMBO Rep 2022; 24:e55928. [PMID: 36408846 PMCID: PMC9827552 DOI: 10.15252/embr.202255928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/18/2022] [Accepted: 10/27/2022] [Indexed: 11/22/2022] Open
Abstract
Methylation of histone H3 at lysine 9 (H3K9) is a hallmark of heterochromatin that plays crucial roles in gene silencing, genome stability, and chromosome segregation. In Schizosaccharomyces pombe, Clr4 mediates both di- and tri-methylation of H3K9. Although H3K9 methylation has been intensely studied in mitotic cells, its role during sexual differentiation remains unclear. Here, we map H3K9 methylation genome-wide during meiosis and show that constitutive heterochromatin temporarily loses H3K9me2 and becomes H3K9me3 when cells commit to meiosis. Cells lacking the ability to tri-methylate H3K9 exhibit meiotic chromosome segregation defects. Finally, the H3K9 methylation switch is accompanied by differential phosphorylation of Clr4 by the cyclin-dependent kinase Cdk1. Our results suggest that a conserved master regulator of the cell cycle controls the specificity of an H3K9 methyltransferase to prevent ectopic H3K9 methylation and to ensure faithful gametogenesis.
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Affiliation(s)
- Tahsin Kuzdere
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland,University of BaselBaselSwitzerland
| | - Valentin Flury
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland,University of BaselBaselSwitzerland
| | - Thomas Schalch
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
| | | | - Daniel Hess
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland,University of BaselBaselSwitzerland
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4
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Duda KJ, Ching RW, Jerabek L, Shukeir N, Erikson G, Engist B, Onishi-Seebacher M, Perrera V, Richter F, Mittler G, Fritz K, Helm M, Knuckles P, Bühler M, Jenuwein T. m6A RNA methylation of major satellite repeat transcripts facilitates chromatin association and RNA:DNA hybrid formation in mouse heterochromatin. Nucleic Acids Res 2021; 49:5568-5587. [PMID: 33999208 PMCID: PMC8191757 DOI: 10.1093/nar/gkab364] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 04/17/2021] [Accepted: 04/26/2021] [Indexed: 12/26/2022] Open
Abstract
Heterochromatin has essential functions in maintaining chromosome structure, in protecting genome integrity and in stabilizing gene expression programs. Heterochromatin is often nucleated by underlying DNA repeat sequences, such as major satellite repeats (MSR) and long interspersed nuclear elements (LINE). In order to establish heterochromatin, MSR and LINE elements need to be transcriptionally competent and generate non-coding repeat RNA that remain chromatin associated. We explored whether these heterochromatic RNA, similar to DNA and histones, may be methylated, particularly for 5-methylcytosine (5mC) or methyl-6-adenosine (m6A). Our analysis in mouse ES cells identifies only background level of 5mC but significant enrichment for m6A on heterochromatic RNA. Moreover, MSR transcripts are a novel target for m6A RNA modification, and their m6A RNA enrichment is decreased in ES cells that are mutant for Mettl3 or Mettl14, which encode components of a central RNA methyltransferase complex. Importantly, MSR transcripts that are partially deficient in m6A RNA methylation display impaired chromatin association and have a reduced potential to form RNA:DNA hybrids. We propose that m6A modification of MSR RNA will enhance the functions of MSR repeat transcripts to stabilize mouse heterochromatin.
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Affiliation(s)
- Katarzyna J Duda
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Reagan W Ching
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Lisa Jerabek
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Nicholas Shukeir
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Galina Erikson
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Bettina Engist
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | | | - Valentina Perrera
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Florian Richter
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany.,Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg - University, Mainz 55128, Germany
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Katharina Fritz
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg - University, Mainz 55128, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg - University, Mainz 55128, Germany
| | - Philip Knuckles
- Friedrich Miescher Institute for Biomedical Research, Basel, 4058, Switzerland and University of Basel, Basel 4051, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Basel, 4058, Switzerland and University of Basel, Basel 4051, Switzerland
| | - Thomas Jenuwein
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
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5
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Shimada Y, Carl SH, Skribbe M, Flury V, Kuzdere T, Kempf G, Bühler M. An enhancer screen identifies new suppressors of small-RNA-mediated epigenetic gene silencing. PLoS Genet 2021; 17:e1009645. [PMID: 34157021 PMCID: PMC8253403 DOI: 10.1371/journal.pgen.1009645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 07/02/2021] [Accepted: 06/04/2021] [Indexed: 11/19/2022] Open
Abstract
Small non-protein coding RNAs are involved in pathways that control the genome at the level of chromatin. In Schizosaccharomyces pombe, small interfering RNAs (siRNAs) are required for the faithful propagation of heterochromatin that is found at peri-centromeric repeats. In contrast to repetitive DNA, protein-coding genes are refractory to siRNA-mediated heterochromatin formation, unless siRNAs are expressed in mutant cells. Here we report the identification of 20 novel mutant alleles that enable de novo formation of heterochromatin at a euchromatic protein-coding gene by using trans-acting siRNAs as triggers. For example, a single amino acid substitution in the pre-mRNA cleavage factor Yth1 enables siRNAs to trigger silent chromatin formation with unparalleled efficiency. Our results are consistent with a kinetic nascent transcript processing model for the inhibition of small-RNA-directed de novo formation of heterochromatin and lay a foundation for further mechanistic dissection of cellular activities that counteract epigenetic gene silencing.
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Affiliation(s)
- Yukiko Shimada
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Sarah H. Carl
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Merle Skribbe
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Valentin Flury
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Tahsin Kuzdere
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
- * E-mail:
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6
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Abstract
Some long non-coding RNA (lncRNA) genes encode a functional RNA product, whereas others act as DNA elements or via the act of transcription . We describe here a ribozyme-based approach to deplete an endogenous lncRNA in mouse embryonic stem cells, with minimal disruption of its gene. This enables the role of the lncRNA product to be tested.
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Affiliation(s)
- Alex C Tuck
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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7
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Bühler M, Tuck AC. Scaling up dissection of functional RNA elements. Nat Struct Mol Biol 2020; 27:771-773. [PMID: 32747786 DOI: 10.1038/s41594-020-0482-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
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8
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Carl SH, Duempelmann L, Shimada Y, Bühler M. A fully automated deep learning pipeline for high-throughput colony segmentation and classification. Biol Open 2020; 9:bio052936. [PMID: 32487517 PMCID: PMC7328007 DOI: 10.1242/bio.052936] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/14/2020] [Indexed: 11/29/2022] Open
Abstract
Adenine auxotrophy is a commonly used non-selective genetic marker in yeast research. It allows investigators to easily visualize and quantify various genetic and epigenetic events by simply reading out colony color. However, manual counting of large numbers of colonies is extremely time-consuming, difficult to reproduce and possibly inaccurate. Using cutting-edge neural networks, we have developed a fully automated pipeline for colony segmentation and classification, which speeds up white/red colony quantification 100-fold over manual counting by an experienced researcher. Our approach uses readily available training data and can be smoothly integrated into existing protocols, vastly speeding up screening assays and increasing the statistical power of experiments that employ adenine auxotrophy.
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Affiliation(s)
- Sarah H Carl
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics Quartier Sorge - Batiment Amphipole 1015, Lausanne, Switzerland
| | - Lea Duempelmann
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
- University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Yukiko Shimada
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
- University of Basel, Petersplatz 10, 4003 Basel, Switzerland
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9
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Kaaij LJT, Mohn F, van der Weide RH, de Wit E, Bühler M. The ChAHP Complex Counteracts Chromatin Looping at CTCF Sites that Emerged from SINE Expansions in Mouse. Cell 2020; 178:1437-1451.e14. [PMID: 31491387 DOI: 10.1016/j.cell.2019.08.007] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/29/2019] [Accepted: 08/02/2019] [Indexed: 12/27/2022]
Abstract
CCCTC-binding factor (CTCF) and cohesin are key players in three-dimensional chromatin organization. The topologically associating domains (TADs) demarcated by CTCF are remarkably well conserved between species, although genome-wide CTCF binding has diverged substantially following transposon-mediated motif expansions. Therefore, the CTCF consensus motif poorly predicts TADs, and additional factors must modulate CTCF binding and subsequent TAD formation. Here, we demonstrate that the ChAHP complex (CHD4, ADNP, HP1) competes with CTCF for a common set of binding motifs. In Adnp knockout cells, novel insulated regions are formed at sites normally bound by ChAHP, whereas proximal canonical boundaries are weakened. These data reveal that CTCF-mediated loop formation is modulated by a distinct zinc-finger protein complex. Strikingly, ChAHP-bound loci are mainly situated within less diverged SINE B2 transposable elements. This implicates ChAHP in maintenance of evolutionarily conserved spatial chromatin organization by buffering novel CTCF binding sites that emerged through SINE expansions.
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Affiliation(s)
- Lucas J T Kaaij
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.
| | - Fabio Mohn
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.
| | - Robin H van der Weide
- Division of Gene Regulation, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland.
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10
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Tuck AC, Rankova A, Arpat AB, Liechti LA, Hess D, Iesmantavicius V, Castelo-Szekely V, Gatfield D, Bühler M. Mammalian RNA Decay Pathways Are Highly Specialized and Widely Linked to Translation. Mol Cell 2020; 77:1222-1236.e13. [PMID: 32048998 PMCID: PMC7083229 DOI: 10.1016/j.molcel.2020.01.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/11/2019] [Accepted: 01/07/2020] [Indexed: 12/24/2022]
Abstract
RNA decay is crucial for mRNA turnover and surveillance and misregulated in many diseases. This complex system is challenging to study, particularly in mammals, where it remains unclear whether decay pathways perform specialized versus redundant roles. Cytoplasmic pathways and links to translation are particularly enigmatic. By directly profiling decay factor targets and normal versus aberrant translation in mouse embryonic stem cells (mESCs), we uncovered extensive decay pathway specialization and crosstalk with translation. XRN1 (5'-3') mediates cytoplasmic bulk mRNA turnover whereas SKIV2L (3'-5') is universally recruited by ribosomes, tackling aberrant translation and sometimes modulating mRNA abundance. Further exploring translation surveillance revealed AVEN and FOCAD as SKIV2L interactors. AVEN prevents ribosome stalls at structured regions, which otherwise require SKIV2L for clearance. This pathway is crucial for histone translation, upstream open reading frame (uORF) regulation, and counteracting ribosome arrest on small ORFs. In summary, we uncovered key targets, components, and functions of mammalian RNA decay pathways and extensive coupling to translation.
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Affiliation(s)
- Alex Charles Tuck
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Aneliya Rankova
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Alaaddin Bulak Arpat
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Luz Angelica Liechti
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Vytautas Iesmantavicius
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | | | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland.
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11
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Welte T, Tuck AC, Papasaikas P, Carl SH, Flemr M, Knuckles P, Rankova A, Bühler M, Großhans H. The RNA hairpin binder TRIM71 modulates alternative splicing by repressing MBNL1. Genes Dev 2019; 33:1221-1235. [PMID: 31371437 PMCID: PMC6719626 DOI: 10.1101/gad.328492.119] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/19/2019] [Indexed: 01/19/2023]
Abstract
In this study, Welte et al. investigated the dual roles of mammalian TRIM71, a phylogenetically conserved regulator of development, in the control of stem cell fate. They demonstrate that TRIM71 shapes the transcriptome of mESCs predominantly through its RNA-binding activity and identify a set of primary targets consistently regulated in various human and mouse cell lines, including MBNL1/Muscleblind. TRIM71/LIN-41, a phylogenetically conserved regulator of development, controls stem cell fates. Mammalian TRIM71 exhibits both RNA-binding and protein ubiquitylation activities, but the functional contribution of either activity and relevant primary targets remain poorly understood. Here, we demonstrate that TRIM71 shapes the transcriptome of mouse embryonic stem cells (mESCs) predominantly through its RNA-binding activity. We reveal that TRIM71 binds targets through 3′ untranslated region (UTR) hairpin motifs and that it acts predominantly by target degradation. TRIM71 mutations implicated in etiogenesis of human congenital hydrocephalus impair target silencing. We identify a set of primary targets consistently regulated in various human and mouse cell lines, including MBNL1 (Muscleblind-like protein 1). MBNL1 promotes cell differentiation through regulation of alternative splicing, and we demonstrate that TRIM71 promotes embryonic splicing patterns through MBNL1 repression. Hence, repression of MBNL1-dependent alternative splicing may contribute to TRIM71's function in regulating stem cell fates.
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Affiliation(s)
- Thomas Welte
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Alex C Tuck
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Panagiotis Papasaikas
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, 4058 Basel, Switzerland.,These authors contributed equally to this work
| | - Sarah H Carl
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, 4058 Basel, Switzerland.,These authors contributed equally to this work
| | - Matyas Flemr
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Philip Knuckles
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Aneliya Rankova
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, 4056 Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, 4056 Basel, Switzerland
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, 4056 Basel, Switzerland
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12
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Duempelmann L, Mohn F, Shimada Y, Oberti D, Andriollo A, Lochs S, Bühler M. Inheritance of a Phenotypically Neutral Epimutation Evokes Gene Silencing in Later Generations. Mol Cell 2019; 74:534-541.e4. [PMID: 30898439 PMCID: PMC6509282 DOI: 10.1016/j.molcel.2019.02.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/18/2019] [Accepted: 02/06/2019] [Indexed: 01/16/2023]
Abstract
Small RNAs trigger the formation of epialleles that are silenced across generations. Consequently, RNA-directed epimutagenesis is associated with persistent gene repression. Here, we demonstrate that small interfering RNA-induced epimutations in fission yeast are still inherited even when the silenced gene is reactivated, and descendants can reinstate the silencing phenotype that only occurred in their ancestors. This process is mediated by the deposition of a phenotypically neutral molecular mark composed of tri-methylated histone H3 lysine 9 (H3K9me3). Its stable propagation is coupled to RNAi and requires maximal binding affinity of the Clr4/Suvar39 chromodomain to H3K9me3. In wild-type cells, this mark has no visible impact on transcription but causes gene silencing if RNA polymerase-associated factor 1 complex (Paf1C) activity is impaired. In sum, our results reveal a distinct form of epigenetic memory in which cells acquire heritable, transcriptionally active epialleles that confer gene silencing upon modulation of Paf1C. S. pombe remembers and reinstates silencing that occurred in a previous generation Paf1 modulation enables acquisition of a new trait that is plastic and inheritable H3K9me3 functions as an epigenetic mark that is not repressive per se Paf1C facilitates transcription elongation through H3K9-methylated nucleosomes
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Affiliation(s)
- Lea Duempelmann
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Fabio Mohn
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Yukiko Shimada
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Daniele Oberti
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Aude Andriollo
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Silke Lochs
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Centre Utrecht, Uppsalalaan 8, 3584 Utrecht, the Netherlands
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland.
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13
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Tuck AC, Natarajan KN, Rice GM, Borawski J, Mohn F, Rankova A, Flemr M, Wenger A, Nutiu R, Teichmann S, Bühler M. Distinctive features of lincRNA gene expression suggest widespread RNA-independent functions. Life Sci Alliance 2018; 1:e201800124. [PMID: 30456373 PMCID: PMC6238598 DOI: 10.26508/lsa.201800124] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 07/13/2018] [Accepted: 07/13/2018] [Indexed: 02/06/2023] Open
Abstract
Eukaryotic genomes produce RNAs lacking protein-coding potential, with enigmatic roles. We integrated three approaches to study large intervening noncoding RNA (lincRNA) gene functions. First, we profiled mouse embryonic stem cells and neural precursor cells at single-cell resolution, revealing lincRNAs expressed in specific cell types, cell subpopulations, or cell cycle stages. Second, we assembled a transcriptome-wide atlas of nuclear lincRNA degradation by identifying targets of the exosome cofactor Mtr4. Third, we developed a reversible depletion system to separate the role of a lincRNA gene from that of its RNA. Our approach distinguished lincRNA loci functioning in trans from those modulating local gene expression. Some genes express stable and/or abundant lincRNAs in single cells, but many prematurely terminate transcription and produce lincRNAs rapidly degraded by the nuclear exosome. This suggests that besides RNA-dependent functions, lincRNA loci act as DNA elements or through transcription. Our integrative approach helps distinguish these mechanisms.
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Affiliation(s)
- Alex C Tuck
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Kedar Nath Natarajan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Danish Institute of Advanced Study and Functional Genomics and Metabolism Unit, University of Southern Denmark, Denmark
| | - Greggory M Rice
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jason Borawski
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Fabio Mohn
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Aneliya Rankova
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Matyas Flemr
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Alice Wenger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Razvan Nutiu
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Sarah Teichmann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
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14
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Knuckles P, Bühler M. Adenosine methylation as a molecular imprint defining the fate of RNA. FEBS Lett 2018; 592:2845-2859. [PMID: 29782652 PMCID: PMC6175371 DOI: 10.1002/1873-3468.13107] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 11/12/2022]
Abstract
Multiple lines of evidence suggest the RNA modification N6‐methyladonsine (m6A), which is installed in the nucleus cotranscriptionally and, thereafter, serves as a reversible chemical imprint that influences several steps of mRNA metabolism. This includes but is not limited to RNA folding, splicing, stability, transport and translation. In this Review we focus on the current view of the nuclear installation of m6A as well as the molecular players involved, the so called m6A writers. We also explore the effector proteins, or m6A readers, that decode the imprint in different cellular contexts and compartments, and ultimately, the way the modification influences the lifecycle of an RNA molecule. The wide evolutionary conservation of m6A and its critical role in physiology and disease warrants further studies into this burgeoning and exciting field.
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Affiliation(s)
- Philip Knuckles
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Switzerland
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15
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Knuckles P, Lence T, Haussmann IU, Jacob D, Kreim N, Carl SH, Masiello I, Hares T, Villaseñor R, Hess D, Andrade-Navarro MA, Biggiogera M, Helm M, Soller M, Bühler M, Roignant JY. Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m 6A machinery component Wtap/Fl(2)d. Genes Dev 2018. [PMID: 29535189 PMCID: PMC5900714 DOI: 10.1101/gad.309146.117] [Citation(s) in RCA: 371] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
In this study, Knuckles et al. identified Flacc/Zc3h13 as a novel interactor of m6A methyltransferase complex components in Drosophila and mice. They show that Flacc promotes the recruitment of the methyltransferase to mRNA by bridging Fl(2)d to the mRNA-binding factor Nito, providing novel insights into the conservation and regulation of the m6A machinery. N6-methyladenosine (m6A) is the most abundant mRNA modification in eukaryotes, playing crucial roles in multiple biological processes. m6A is catalyzed by the activity of methyltransferase-like 3 (Mettl3), which depends on additional proteins whose precise functions remain poorly understood. Here we identified Zc3h13 (zinc finger CCCH domain-containing protein 13)/Flacc [Fl(2)d-associated complex component] as a novel interactor of m6A methyltransferase complex components in Drosophila and mice. Like other components of this complex, Flacc controls m6A levels and is involved in sex determination in Drosophila. We demonstrate that Flacc promotes m6A deposition by bridging Fl(2)d to the mRNA-binding factor Nito. Altogether, our work advances the molecular understanding of conservation and regulation of the m6A machinery.
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Affiliation(s)
- Philip Knuckles
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, Basel 4002, Switzerland
| | - Tina Lence
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Irmgard U Haussmann
- School of Life Science, Faculty of Health and Life Sciences, Coventry University, Coventry CV1 5FB, United Kingdom.,School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Dominik Jacob
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Nastasja Kreim
- Bioinformatics Core Facility, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Sarah H Carl
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel 4058, Switzerland
| | - Irene Masiello
- Institute of Molecular Biology, 55128 Mainz, Germany.,Laboratory of Cell Biology and Neurobiology, Department of Animal Biology, University of Pavia, Pavia 27100, Italy
| | - Tina Hares
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Rodrigo Villaseñor
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, Basel 4002, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Miguel A Andrade-Navarro
- Institute of Molecular Biology, 55128 Mainz, Germany.,Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Marco Biggiogera
- Laboratory of Cell Biology and Neurobiology, Department of Animal Biology, University of Pavia, Pavia 27100, Italy
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Matthias Soller
- School of Life Science, Faculty of Health and Life Sciences, Coventry University, Coventry CV1 5FB, United Kingdom
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, Basel 4002, Switzerland
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16
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Knuckles P, Lence T, Haussmann IU, Jacob D, Kreim N, Carl SH, Masiello I, Hares T, Villaseñor R, Hess D, Andrade-Navarro MA, Biggiogera M, Helm M, Soller M, Bühler M, Roignant JY. Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m 6A machinery component Wtap/Fl(2)d. Genes Dev 2018. [PMID: 29535189 DOI: 10.1101/gad.309146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
N6-methyladenosine (m6A) is the most abundant mRNA modification in eukaryotes, playing crucial roles in multiple biological processes. m6A is catalyzed by the activity of methyltransferase-like 3 (Mettl3), which depends on additional proteins whose precise functions remain poorly understood. Here we identified Zc3h13 (zinc finger CCCH domain-containing protein 13)/Flacc [Fl(2)d-associated complex component] as a novel interactor of m6A methyltransferase complex components in Drosophila and mice. Like other components of this complex, Flacc controls m6A levels and is involved in sex determination in Drosophila We demonstrate that Flacc promotes m6A deposition by bridging Fl(2)d to the mRNA-binding factor Nito. Altogether, our work advances the molecular understanding of conservation and regulation of the m6A machinery.
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Affiliation(s)
- Philip Knuckles
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- University of Basel, Basel 4002, Switzerland
| | - Tina Lence
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Irmgard U Haussmann
- School of Life Science, Faculty of Health and Life Sciences, Coventry University, Coventry CV1 5FB, United Kingdom
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Dominik Jacob
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Nastasja Kreim
- Bioinformatics Core Facility, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Sarah H Carl
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel 4058, Switzerland
| | - Irene Masiello
- Institute of Molecular Biology, 55128 Mainz, Germany
- Laboratory of Cell Biology and Neurobiology, Department of Animal Biology, University of Pavia, Pavia 27100, Italy
| | - Tina Hares
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Rodrigo Villaseñor
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- University of Basel, Basel 4002, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Miguel A Andrade-Navarro
- Institute of Molecular Biology, 55128 Mainz, Germany
- Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Marco Biggiogera
- Laboratory of Cell Biology and Neurobiology, Department of Animal Biology, University of Pavia, Pavia 27100, Italy
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Matthias Soller
- School of Life Science, Faculty of Health and Life Sciences, Coventry University, Coventry CV1 5FB, United Kingdom
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- University of Basel, Basel 4002, Switzerland
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17
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Berry S, Rosa S, Howard M, Bühler M, Dean C. Disruption of an RNA-binding hinge region abolishes LHP1-mediated epigenetic repression. Genes Dev 2017; 31:2115-2120. [PMID: 29212661 PMCID: PMC5749160 DOI: 10.1101/gad.305227.117] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/07/2017] [Indexed: 12/24/2022]
Abstract
In this study, Berry et al. investigated the functions of the different domains of LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) in Arabidopsis. They show that LHP1 binds RNA in vitro through the intrinsically disordered hinge region and show that both the hinge region and H3K27me3 recognition facilitate LHP1 localization and H3K27me3 maintenance. Epigenetic maintenance of gene repression is essential for development. Polycomb complexes are central to this memory, but many aspects of the underlying mechanism remain unclear. LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) binds Polycomb-deposited H3K27me3 and is required for repression of many Polycomb target genes in Arabidopsis. Here we show that LHP1 binds RNA in vitro through the intrinsically disordered hinge region. By independently perturbing the RNA-binding hinge region and H3K27me3 (trimethylation of histone H3 at Lys27) recognition, we found that both facilitate LHP1 localization and H3K27me3 maintenance. Disruption of the RNA-binding hinge region also prevented formation of subnuclear foci, structures potentially important for epigenetic repression.
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Affiliation(s)
- Scott Berry
- John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Stefanie Rosa
- Institute of Biochemistry and Biology, University of Potsdam, DE-14476 Potsdam-Golm, Germany
| | | | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
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18
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Zhang L, Pereira Mestre R, Bihl F, Bühler M, Vannata B, Stathis A. A Rare Case of Classical Hodgkin Lymphoma Diagnosed 10 Years after Liver Transplant. Case Rep Oncol 2017; 10:923-927. [PMID: 29279693 PMCID: PMC5731166 DOI: 10.1159/000481452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 09/13/2017] [Indexed: 12/20/2022] Open
Abstract
Posttransplant lymphoproliferative disorders (PTLD) represent a rare and potentially life-threatening complication after liver transplantation. Classical Hodgkin lymphoma (cHL), with an incidence of approximately 1.8-3.4% of all PTLD cases, represents a minority of PTLD, mainly presenting as a late transplant complication. The main risk factors for the development of PTLD are Epstein-Barr virus (EBV) infection and intensive immunosuppression. However, other risk factors like hepatitis C virus may, together with EBV infection, contribute to the development of PTLD. Here we present a case of late-onset EBV-positive cHL that occurred 10 years after an unrelated donor liver transplantation. To our knowledge, this is the first report of cHL occurring with such a long interval after liver transplantation. Given the low incidence of cHL PTLD, there is little information regarding pathology, clinical characteristics, and management of this disease. The development of individual, risk-adapted treatments may improve the long-term outcome of cHL PTLD.
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Affiliation(s)
- L Zhang
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - R Pereira Mestre
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - F Bihl
- Cantonal Hepatology Service, Cantonal Hospital Ticino, Bellinzona, Switzerland.,Department of Gastroenterology and Hepatology, University Hospital Geneva, Geneva, Switzerland
| | - M Bühler
- Cantonal Institute of Pathology, Locarno, Switzerland
| | - B Vannata
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - A Stathis
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
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19
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Flury V, Georgescu PR, Iesmantavicius V, Shimada Y, Kuzdere T, Braun S, Bühler M. The Histone Acetyltransferase Mst2 Protects Active Chromatin from Epigenetic Silencing by Acetylating the Ubiquitin Ligase Brl1. Mol Cell 2017. [PMID: 28648780 PMCID: PMC5526834 DOI: 10.1016/j.molcel.2017.05.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Faithful propagation of functionally distinct chromatin states is crucial for maintaining cellular identity, and its breakdown can lead to diseases such as cancer. Whereas mechanisms that sustain repressed states have been intensely studied, regulatory circuits that protect active chromatin from inactivating signals are not well understood. Here we report a positive feedback loop that preserves the transcription-competent state of RNA polymerase II-transcribed genes. We found that Pdp3 recruits the histone acetyltransferase Mst2 to H3K36me3-marked chromatin. Thereby, Mst2 binds to all transcriptionally active regions genome-wide. Besides acetylating histone H3K14, Mst2 also acetylates Brl1, a component of the histone H2B ubiquitin ligase complex. Brl1 acetylation increases histone H2B ubiquitination, which positively feeds back on transcription and prevents ectopic heterochromatin assembly. Our work uncovers a molecular pathway that secures epigenome integrity and highlights the importance of opposing feedback loops for the partitioning of chromatin into transcriptionally active and inactive states.
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Affiliation(s)
- Valentin Flury
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Paula Raluca Georgescu
- Biomedical Center Munich, Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Vytautas Iesmantavicius
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Yukiko Shimada
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Tahsin Kuzdere
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Sigurd Braun
- Biomedical Center Munich, Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany.
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland.
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20
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Knuckles P, Carl SH, Musheev M, Niehrs C, Wenger A, Bühler M. RNA fate determination through cotranscriptional adenosine methylation and microprocessor binding. Nat Struct Mol Biol 2017; 24:561-569. [PMID: 28581511 DOI: 10.1038/nsmb.3419] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/09/2017] [Indexed: 02/07/2023]
Abstract
Eukaryotic gene expression is heavily regulated at the transcriptional and post-transcriptional levels. An additional layer of regulation occurs co-transcriptionally through processing and decay of nascent transcripts physically associated with chromatin. This process involves RNA interference (RNAi) machinery and is well documented in yeast, but little is known about its conservation in mammals. Here we show that Dgcr8 and Drosha physically associate with chromatin in murine embryonic stem cells (mES), specifically with a subset of transcribed coding and noncoding genes. Dgcr8 recruitment to chromatin is dependent on transcription as well as methyltransferase-like 3 (Mettl3), which catalyzes RNA N6-methyladenosine (m6A). Intriguingly, we found that acute temperature stress causes radical relocalization of Dgcr8 and Mettl3 to heat-shock genes, where they act to co-transcriptionally mark mRNAs for subsequent RNA degradation. Together, our findings elucidate a novel mode of co-transcriptional gene regulation, in which m6A serves as a chemical mark that instigates subsequent post-transcriptional RNA-processing events.
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Affiliation(s)
- Philip Knuckles
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sarah H Carl
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Michael Musheev
- Faculty of Science, Institute of Molecular Biology, Mainz, Germany
| | - Christof Niehrs
- Faculty of Science, Institute of Molecular Biology, Mainz, Germany.,Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Alice Wenger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
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21
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Shimada Y, Mohn F, Bühler M. The RNA-induced transcriptional silencing complex targets chromatin exclusively via interacting with nascent transcripts. Genes Dev 2016; 30:2571-2580. [PMID: 27941123 PMCID: PMC5204350 DOI: 10.1101/gad.292599.116] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 11/21/2016] [Indexed: 01/24/2023]
Abstract
Small RNAs regulate chromatin modification and transcriptional gene silencing across the eukaryotic kingdom. Although these processes have been well studied, fundamental mechanistic aspects remain obscure. Specifically, it is unclear exactly how small RNA-loaded Argonaute protein complexes target chromatin to mediate silencing. Here, using fission yeast, we demonstrate that transcription of the target locus is essential for RNA-directed formation of heterochromatin. However, high transcriptional activity is inhibitory; thus, a transcriptional window exists that is optimal for silencing. We further found that pre-mRNA splicing is compatible with RNA-directed heterochromatin formation. However, the kinetics of pre-mRNA processing is critical. Introns close to the 5' end of a transcript that are rapidly spliced result in a bistable response whereby the target either remains euchromatic or becomes fully silenced. Together, our results discount siRNA-DNA base pairing in RNA-mediated heterochromatin formation, and the mechanistic insights further reveal guiding paradigms for the design of small RNA-directed chromatin silencing studies in multicellular organisms.
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Affiliation(s)
- Yukiko Shimada
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, 4003 Basel, Switzerland
| | - Fabio Mohn
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, 4003 Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, 4003 Basel, Switzerland
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22
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Stunnenberg R, Kulasegaran-Shylini R, Keller C, Kirschmann MA, Gelman L, Bühler M. H3K9 methylation extends across natural boundaries of heterochromatin in the absence of an HP1 protein. EMBO J 2015; 34:2789-803. [PMID: 26438724 PMCID: PMC4682641 DOI: 10.15252/embj.201591320] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 09/03/2015] [Indexed: 12/13/2022] Open
Abstract
Proteins of the conserved HP1 family are elementary components of heterochromatin and are generally assumed to play a central role in the creation of a rigid, densely packed heterochromatic network that is inaccessible to the transcription machinery. Here, we demonstrate that the fission yeast HP1 protein Swi6 exists as a single highly dynamic population that rapidly exchanges in cis and in trans between different heterochromatic regions. Binding to methylated H3K9 or to heterochromatic RNA decelerates Swi6 mobility. We further show that Swi6 is largely dispensable to the maintenance of heterochromatin domains. In the absence of Swi6, H3K9 methylation levels are maintained by a mechanism that depends on polymeric self‐association properties of Tas3, a subunit of the RNA‐induced transcriptional silencing complex. Our results disclose a surprising role for Swi6 dimerization in demarcating constitutive heterochromatin from neighboring euchromatin. Thus, rather than promoting maintenance and spreading of heterochromatin, Swi6 appears to limit these processes and appropriately confine heterochromatin.
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Affiliation(s)
- Rieka Stunnenberg
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland University of Basel, Basel, Switzerland
| | | | - Claudia Keller
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland University of Basel, Basel, Switzerland
| | | | - Laurent Gelman
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland University of Basel, Basel, Switzerland
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23
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Kolodziejczyk AA, Kim JK, Tsang JCH, Ilicic T, Henriksson J, Natarajan KN, Tuck AC, Gao X, Bühler M, Liu P, Marioni JC, Teichmann SA. Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation. Cell Stem Cell 2015; 17:471-85. [PMID: 26431182 PMCID: PMC4595712 DOI: 10.1016/j.stem.2015.09.011] [Citation(s) in RCA: 341] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 03/07/2015] [Accepted: 09/15/2015] [Indexed: 01/27/2023]
Abstract
Embryonic stem cell (ESC) culture conditions are important for maintaining long-term self-renewal, and they influence cellular pluripotency state. Here, we report single cell RNA-sequencing of mESCs cultured in three different conditions: serum, 2i, and the alternative ground state a2i. We find that the cellular transcriptomes of cells grown in these conditions are distinct, with 2i being the most similar to blastocyst cells and including a subpopulation resembling the two-cell embryo state. Overall levels of intercellular gene expression heterogeneity are comparable across the three conditions. However, this masks variable expression of pluripotency genes in serum cells and homogeneous expression in 2i and a2i cells. Additionally, genes related to the cell cycle are more variably expressed in the 2i and a2i conditions. Mining of our dataset for correlations in gene expression allowed us to identify additional components of the pluripotency network, including Ptma and Zfp640, illustrating its value as a resource for future discovery.
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Affiliation(s)
- Aleksandra A Kolodziejczyk
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jong Kyoung Kim
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jason C H Tsang
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Tomislav Ilicic
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Johan Henriksson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kedar N Natarajan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Alex C Tuck
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Xuefei Gao
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Pentao Liu
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK; University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK.
| | - Sarah A Teichmann
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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Flemr M, Bühler M. Single-Step Generation of Conditional Knockout Mouse Embryonic Stem Cells. Cell Rep 2015; 12:709-16. [PMID: 26190102 DOI: 10.1016/j.celrep.2015.06.051] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/02/2015] [Accepted: 06/11/2015] [Indexed: 10/23/2022] Open
Abstract
Induction of double-strand DNA breaks (DSBs) by engineered nucleases, such as CRISPR/Cas9 or transcription activator-like effector nucleases (TALENs), stimulates knockin of exogenous DNA fragments via homologous recombination (HR). However, the knockin efficiencies reported so far have not allowed more complex in vitro genome modifications such as, for instance, simultaneous integration of a DNA fragment at two distinct genomic sites. We developed a reporter system to enrich for cells with engineered nuclease-assisted HR events. Using this system in mouse embryonic stem cells (mESCs), we achieve single-step biallelic and seamless integration of two loxP sites for Cre recombinase-mediated inducible gene knockout, as well as biallelic endogenous gene tagging with high efficiency. Our approach reduces the time and resources required for conditional knockout mESC generation dramatically.
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Affiliation(s)
- Matyas Flemr
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland.
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25
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Schmid M, Marti-Jaun J, Bühler M, Herová M, Hersberger M. Polymorphisms in SOCS 1 and 3 and human coronary artery disease. Atherosclerosis 2015. [DOI: 10.1016/j.atherosclerosis.2015.04.329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Kowalik KM, Shimada Y, Flury V, Stadler MB, Batki J, Bühler M. The Paf1 complex represses small-RNA-mediated epigenetic gene silencing. Nature 2015; 520:248-252. [PMID: 25807481 PMCID: PMC4398878 DOI: 10.1038/nature14337] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 02/16/2015] [Indexed: 01/26/2023]
Abstract
RNA interference (RNAi) refers to the ability of exogenously introduced double-stranded RNA (dsRNA) to silence expression of homologous sequences. Silencing is initiated when the enzyme Dicer processes the dsRNA into small interfering RNAs (siRNAs). Small RNA molecules are incorporated into Argonaute protein-containing effector complexes, which they guide to complementary targets to mediate different types of gene silencing, specifically post-transcriptional gene silencing (PTGS) and chromatin-dependent gene silencing1. Although endogenous small RNAs play critical roles in chromatin-mediated processes across kingdoms, efforts to initiate chromatin modifications in trans by using siRNAs have been inherently difficult to achieve in all eukaryotic cells. Using fission yeast, we show that RNAi-directed heterochromatin formation is negatively controlled by the highly conserved RNA polymerase-associated factor 1 complex (Paf1C). Temporary expression of a synthetic hairpin RNA in Paf1C mutants triggers stable heterochromatin formation at homologous loci, effectively silencing genes in trans. This repressed state is propagated across generations by continual production of secondary siRNAs, independently of the synthetic hairpin RNA. Our data support a model where Paf1C prevents targeting of nascent transcripts by the siRNA-containing RNA-induced transcriptional silencing (RITS) complex and thereby epigenetic gene silencing, by promoting efficient transcription termination and rapid release of the RNA from the site of transcription. We show that although compromised transcription termination is sufficient to initiate the formation of bi-stable heterochromatin by trans-acting siRNAs, impairment of both transcription termination and nascent transcript release is imperative to confer stability to the repressed state. Our work uncovers a novel mechanism for small RNA- mediated epigenome regulation and highlights fundamental roles for Paf1C and the RNAi machinery in building epigenetic memory.
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Affiliation(s)
- Katarzyna Maria Kowalik
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.,University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Yukiko Shimada
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.,University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Valentin Flury
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.,University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Michael Beda Stadler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.,University of Basel, Petersplatz 10, 4003 Basel, Switzerland.,Swiss Institute of Bioinformatics, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Julia Batki
- Eötvös Loránd University, Faculty of Sciences, Institute of Chemistry, 1/A Pázmány Péter sétány, Budapest, 1117, Hungary
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.,University of Basel, Petersplatz 10, 4003 Basel, Switzerland
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27
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Villaseñor R, Miraglia L, Romero A, Tu B, Punga T, Knuckles P, Duss S, Orth T, Bühler M. Genome-Engineering Tools to Establish Accurate Reporter Cell Lines That Enable Identification of Therapeutic Strategies to Treat Friedreich's Ataxia. J Biomol Screen 2015; 20:760-7. [PMID: 25616511 DOI: 10.1177/1087057114568071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 12/18/2014] [Indexed: 11/15/2022]
Abstract
Friedreich's ataxia is a neurodegenerative disease caused by deficiency of the mitochondrial protein frataxin. This deficiency results from expansion of a trinucleotide repeat in the first intron of the frataxin gene. Because this repeat expansion resides in an intron and hence does not alter the amino acid sequence of the frataxin protein, gene reactivation could be of therapeutic benefit. High-throughput screening for frataxin activators has so far met with limited success because current cellular models may not accurately assess endogenous frataxin gene regulation. Here we report the design and validation of genome-engineering tools that enable the generation of human cell lines that express the frataxin gene fused to a luciferase reporter gene from its endogenous locus. Performing a pilot high-throughput genomic screen in a newly established reporter cell line, we uncovered novel negative regulators of frataxin expression. Rational design of small-molecule inhibitors of the identified frataxin repressors and/or high-throughput screening of large siRNA or compound libraries with our system may yield treatments for Friedreich's ataxia.
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Affiliation(s)
- Rodrigo Villaseñor
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland University of Basel, Basel, Switzerland
| | - Loren Miraglia
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Angelica Romero
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Buu Tu
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Tanel Punga
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland University of Basel, Basel, Switzerland Uppsala University, Department of Medical Biochemistry and Microbiology, BMC Uppsala, Sweden
| | - Philip Knuckles
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland University of Basel, Basel, Switzerland
| | - Stephan Duss
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland University of Basel, Basel, Switzerland
| | - Tony Orth
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland University of Basel, Basel, Switzerland
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Schmidt HGK, Diefenbeck M, Krenn V, Abitzsch D, Militz M, Tiemann AH, Haustedt N, Gückel P, Bühler M, Gerlach UJ. [Classification of haematogenous and post-traumatic osteomyelitis]. Z Orthop Unfall 2014; 152:334-42. [PMID: 25144842 DOI: 10.1055/s-0034-1368620] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A classification of osteomyelitis must reflect the complexity of the disease and, moreover, provide conclusions for the treatment. The classification is based on the following eight parameters: source of infection (OM [osteomyelitis]/OT [post-traumatic OM]), anatomic region, stability of affected bone (continuity of bone), foreign material (internal fixation, prosthesis), range of infection (involved structures), activity of infection (acute, chronic, quiescent), causative microbes (unspecific and specific bacteria, fungi) and comorbidity (immunosuppressive diseases, general and local). In the long version of the classification, which was designed for scientific studies, the parameters are named by capital letters and specified by Arabic numbers, e.g., an acute, haematogenous osteomyelitis of a femur in an adolescent with diabetes mellitus, caused by Staphylococcus aureus, multi-sensible is coded as: OM2 Lo33 S1a M1 In1d Aa1 Ba2a K2a. The letters and numbers can be found in clearly arranged tables or calculated by a freely available grouper on the internet (www.osteomyelitis.exquit.net). An equally composed compact version of the classification for clinical use includes all eight parameters, but without further specification. The above-mentioned example in the compact version is: OM 3 S a Ba2 K2. The short version of the classification uses only the first six parameters and excludes causative microbes and comorbidity. The above mentioned example in the short version is: OM 3 S a. The long version of the classification describes an osteomyelitis in every detail. The complexity of the patient's disease is clearly reproducible and can be used for scientific comparisons. The for clinical use suggested compact and short versions of the classification include all important characteristics of an osteomyelitis, can be composed quickly and distinctly with the help of tables and provide conclusions for the individual treatment. The freely available grouper (www.osteomyelitis.exquit.net) creates all three versions of the classification in one step.
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Affiliation(s)
- H G K Schmidt
- Septische Knochen- u. Weichteilchirurgie, Schön Klinik Hamburg-Eilbek
| | - M Diefenbeck
- Septische Knochen- u. Weichteilchirurgie, Schön Klinik Hamburg-Eilbek
| | - V Krenn
- Zentrum f. Histologie, Zytologie u. Molekulare Diagnostik, Pathologie Trier
| | - D Abitzsch
- Klinik f. spezialisierte septische Chirurgie, Traumazentrum, Sankt Georg Klinikum, Leipzig
| | - M Militz
- Septische Chirurgie, BG Unfallklinik Murnau
| | - A H Tiemann
- Septische u. rekonstruktive Chirurgie, BG-Klinik Halle
| | - N Haustedt
- Septische Knochen- u. Weichteilchirurgie, Schön Klinik Hamburg-Eilbek
| | | | - M Bühler
- Septische Unfallchirurgie u. Orthopädie, Klinikum Ingolstadt
| | - U-J Gerlach
- Septische Unfallchirugie u. Orthopädie, BG-Unfallkrankenhaus Hamburg
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Abstract
RNA transcripts that do not code for proteins have been long known to lie at the heart of many biological processes, such as splicing and translation. Yet their full potential has only been appreciated recently and non-coding RNAs (ncRNAs) are now attracting increasing attention. Pioneering work in yeast and plant systems has revealed that non-coding RNAs can have a major influence on the deposition of histone and DNA modifications. This can introduce heritable variation into gene expression and, thus, be the basis of epigenetic phenomena. Mechanistically, such processes have been studied extensively in the fission yeast Schizosaccharomyces pombe, providing an important conceptual framework for possible modes of action of ncRNAs also in other organisms. In this review, we highlight mechanistic insights into chromatin-associated ncRNA activities gained from work with fission yeast, and we draw parallels to studies in other eukaryotes that indicate evolutionary conservation.
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Affiliation(s)
- Claudia Keller
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
- University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
- University of Basel, Petersplatz 10, 4003 Basel, Switzerland
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30
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Bühler M, Fürst A, Lewis FI, Kummer M, Ohlerth S. Computed tomographic features of apical infection of equine maxillary cheek teeth: A retrospective study of 49 horses. Equine Vet J 2013; 46:468-73. [DOI: 10.1111/evj.12174] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Accepted: 08/21/2013] [Indexed: 11/29/2022]
Affiliation(s)
- M. Bühler
- Section of Equine Surgery; Vetsuisse Faculty; University of Zurich; Zurich Switzerland
| | - A. Fürst
- Section of Equine Surgery; Vetsuisse Faculty; University of Zurich; Zurich Switzerland
| | - F. I. Lewis
- Equine Department; Section of Epidemiology; Vetsuisse Faculty; University of Zurich; Zurich Switzerland
| | - M. Kummer
- Section of Equine Surgery; Vetsuisse Faculty; University of Zurich; Zurich Switzerland
| | - S. Ohlerth
- Section of Diagnostic Imaging; Vetsuisse Faculty; University of Zurich; Zurich Switzerland
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31
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Woolcock KJ, Bühler M. Nuclear organisation and RNAi in fission yeast. Curr Opin Cell Biol 2013; 25:372-7. [DOI: 10.1016/j.ceb.2013.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 02/05/2013] [Indexed: 12/20/2022]
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Abstract
In this issue of Molecular Cell, Ye et al. (2012) show an unexpected cytoplasmic assembly of Arabidopsis ARGONAUTE4/siRNA complexes and that siRNA binding could facilitate the nuclear import of mature AGO4/siRNA complexes, revealing a key regulatory process during RNA-directed DNA methylation (RdDM).
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Affiliation(s)
- Rieka Stunnenberg
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
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33
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34
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Shimada Y, Bühler M. Schizosaccharomyces pombe reporter strains for relative quantitative assessment of heterochromatin silencing. Yeast 2012; 29:335-41. [DOI: 10.1002/yea.2913] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 06/12/2012] [Accepted: 06/26/2012] [Indexed: 11/08/2022] Open
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Keller C, Adaixo R, Stunnenberg R, Woolcock KJ, Hiller S, Bühler M. HP1(Swi6) mediates the recognition and destruction of heterochromatic RNA transcripts. Mol Cell 2012; 47:215-27. [PMID: 22683269 DOI: 10.1016/j.molcel.2012.05.009] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 03/21/2012] [Accepted: 05/03/2012] [Indexed: 10/28/2022]
Abstract
HP1 proteins are major components of heterochromatin, which is generally perceived to be an inert and transcriptionally inactive chromatin structure. Yet, HP1 binding to chromatin is highly dynamic and robust silencing of heterochromatic genes can involve RNA processing. Here, we demonstrate by a combination of in vivo and in vitro experiments that the fission yeast HP1(Swi6) protein guarantees tight repression of heterochromatic genes through RNA sequestration and degradation. Stimulated by positively charged residues in the hinge region, RNA competes with methylated histone H3K9 for binding to the chromodomain of HP1(Swi6). Hence, HP1(Swi6) binding to RNA is incompatible with stable heterochromatin association. We propose a model in which an ensemble of HP1(Swi6) proteins functions as a heterochromatin-specific checkpoint, capturing and priming heterochromatic RNAs for the RNA degradation machinery. Sustaining a functional checkpoint requires continuous exchange of HP1(Swi6) within heterochromatin, which explains the dynamic localization of HP1 proteins on heterochromatin.
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Affiliation(s)
- Claudia Keller
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
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36
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Woolcock KJ, Stunnenberg R, Gaidatzis D, Hotz HR, Emmerth S, Barraud P, Bühler M. RNAi keeps Atf1-bound stress response genes in check at nuclear pores. Genes Dev 2012; 26:683-92. [PMID: 22431512 DOI: 10.1101/gad.186866.112] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
RNAi pathways are prevalent throughout the eukaryotic kingdom and are well known to regulate gene expression on a post-transcriptional level in the cytoplasm. Less is known about possible functions of RNAi in the nucleus. In the fission yeast Schizosaccharomyces pombe, RNAi is crucial to establish and maintain centromeric heterochromatin and functions to repress genome activity by a chromatin silencing mechanism referred to as cotranscriptional gene silencing (CTGS). Mechanistic details and the physiological relevance of CTGS are unknown. Here we show that RNAi components interact with chromatin at nuclear pores to keep stress response genes in check. We demonstrate that RNAi-mediated CTGS represses stress-inducible genes by degrading mRNAs under noninduced conditions. Under chronic heat stress conditions, a Dicer thermoswitch deports Dicer to the cytoplasm, thereby disrupting CTGS and enabling expression of genes implicated in the acquisition of thermotolerance. Taken together, our work highlights a role for nuclear pores and the stress response transcription factor Atf1 in coordinating the interplay between the RNAi machinery and the S. pombe genome and uncovers a novel mode of RNAi regulation in response to an environmental cue.
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Affiliation(s)
- Katrina J Woolcock
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
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37
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Schmidt HGK, Tiemann AH, Braunschweig R, Diefenbeck M, Bühler M, Abitzsch D, Haustedt N, Walter G, Schoop R, Heppert V, Hofmann GO, Glombitza M, Grimme C, Gerlach UJ, Flesch I. [Definition of the Diagnosis Osteomyelitis-Osteomyelitis Diagnosis Score (ODS)]. Z Orthop Unfall 2011; 149:449-60. [PMID: 21544785 DOI: 10.1055/s-0030-1270970] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AIM The disease "osteomyelitis" is characterised by different symptoms and parameters. Decisive roles in the development of the disease are played by the causative bacteria, the route of infection and the individual defense mechanisms of the host. The diagnosis is based on different symptoms and findings from the clinical history, clinical symptoms, laboratory results, diagnostic imaging, microbiological and histopathological analyses. While different osteomyelitis classifications have been published, there is to the best of our knowledge no score that gives information how sure the diagnosis "osteomyelitis" is in general. METHOD For any scientific study of a disease a valid definition is essential. We have developed a special osteomyelitis diagnosis score for the reliable classification of clinical, laboratory and technical findings. The score is based on five diagnostic procedures: 1) clinical history and risk factors, 2) clinical examination and laboratory results, 3) diagnostic imaging (ultrasound, radiology, CT, MRI, nuclear medicine and hybrid methods), 4) microbiology, and 5) histopathology. RESULTS Each diagnostic procedure is related to many individual findings, which are weighted by a score system, in order to achieve a relevant value for each assessment. If the sum of the five diagnostic criteria is 18 or more points, the diagnosis of osteomyelitis can be viewed as "safe" (diagnosis class A). Between 8-17 points the diagnosis is "probable" (diagnosis class B). Less than 8 points means that the diagnosis is "possible, but unlikely" (class C diagnosis). Since each parameter can score six points at a maximum, a reliable diagnosis can only be achieved if at least 3 parameters are scored with 6 points. CONCLUSION The osteomyelitis diagnosis score should help to avoid the false description of a clinical presentation as "osteomyelitis". A safe diagnosis is essential for the aetiology, treatment and outcome studies of osteomyelitis.
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Affiliation(s)
- H G K Schmidt
- Septische Knochen- und Weichteilchirurgie, Schön Klinik HH Eilbek, Dehnhaide 120, Hamburg.
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Bühler M, Jackson M, Fürst A. Successful reduction and internal fixation of an open tibial fracture in an adult Icelandic horse. PFERDEHEILKUNDE 2011. [DOI: 10.21836/pem20110616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Woolcock KJ, Gaidatzis D, Punga T, Bühler M. Dicer associates with chromatin to repress genome activity in Schizosaccharomyces pombe. Nat Struct Mol Biol 2010; 18:94-9. [PMID: 21151114 DOI: 10.1038/nsmb.1935] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 09/20/2010] [Indexed: 01/06/2023]
Abstract
In the fission yeast S. pombe, the RNA interference (RNAi) pathway is required to generate small interfering RNAs (siRNAs) that mediate heterochromatic silencing of centromeric repeats. Here, we demonstrate that RNAi also functions to repress genomic elements other than constitutive heterochromatin. Using DNA adenine methyltransferase identification (DamID), we show that the RNAi proteins Dcr1 and Rdp1 physically associate with some euchromatic genes, noncoding RNA genes and retrotransposon long terminal repeats, and that this association is independent of the Clr4 histone methyltransferase. Physical association of RNAi with chromatin is sufficient to trigger a silencing response but not to assemble heterochromatin. The mode of silencing at the newly identified RNAi targets is consistent with a co-transcriptional gene silencing model, as proposed earlier, and functions with trace amounts of siRNAs. We anticipate that similar mechanisms could also be operational in other eukaryotes.
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Affiliation(s)
- Katrina J Woolcock
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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40
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Keller C, Woolcock K, Hess D, Bühler M. Proteomic and functional analysis of the noncanonical poly(A) polymerase Cid14. RNA 2010; 16:1124-1129. [PMID: 20403971 PMCID: PMC2874164 DOI: 10.1261/rna.2053710] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 02/19/2010] [Indexed: 05/29/2023]
Abstract
The fission yeast Cid14 protein belongs to a family of noncanonical poly(A) polymerases which have been implicated in a broad range of biological functions. Here we describe an extensive Cid14 protein-protein interaction network and its biochemical dissection. Cid14 most stably interacts with the zinc-knuckle protein Air1 to form the Cid14-Air1 complex (CAC). Providing a link to ribosomal RNA processing, Cid14 sediments with 60S ribosomal subunits and copurifies with 60S assembly factors. In contrast, no physical link to chromatin has been identified, although gene expression profiling revealed that efficient silencing of a few heterochromatic genes depends on Cid14 and/or Air1.
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Affiliation(s)
- Claudia Keller
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
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41
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Punga T, Bühler M. Long intronic GAA repeats causing Friedreich ataxia impede transcription elongation. EMBO Mol Med 2010; 2:120-9. [PMID: 20373285 PMCID: PMC3377279 DOI: 10.1002/emmm.201000064] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 01/08/2010] [Accepted: 02/02/2010] [Indexed: 12/31/2022] Open
Abstract
Friedreich ataxia is a degenerative disease caused by deficiency of the protein frataxin (FXN). An intronic expansion of GAA triplets in the FXN-encoding gene, FXN, causes gene silencing and thus reduced FXN protein levels. Although it is widely assumed that GAA repeats block transcription via the assembly of an inaccessible chromatin structure marked by methylated H3K9, direct proof for this is lacking. In this study, we analysed different histone modification patterns along the human FXN gene in FRDA patient-derived lymphoblastoid cell lines. We show that FXN mRNA synthesis, but not turnover rates are affected by an expanded GAA repeat tract. Importantly, rather than preventing transcription initiation, long GAA repeat tracts affect transcription at the elongation step and this can occur independently of H3K9 methylation. Our data demonstrate that finding novel strategies to overcome the transcription elongation problem may develop into promising new treatments for FRDA.
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Affiliation(s)
- Tanel Punga
- Friedrich Miescher Institute for Biomedical ResearchBasel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical ResearchBasel, Switzerland
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42
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Emmerth S, Schober H, Gaidatzis D, Roloff T, Jacobeit K, Bühler M. Nuclear retention of fission yeast dicer is a prerequisite for RNAi-mediated heterochromatin assembly. Dev Cell 2010; 18:102-13. [PMID: 20152181 DOI: 10.1016/j.devcel.2009.11.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 10/24/2009] [Accepted: 11/25/2009] [Indexed: 12/20/2022]
Abstract
RNaseIII ribonucleases act at the heart of RNA silencing pathways by processing precursor RNAs into mature microRNAs and siRNAs. In the fission yeast Schizosaccharomyces pombe, siRNAs are generated by the RNaseIII enzyme Dcr1 and are required for heterochromatin formation at centromeres. In this study, we have analyzed the subcellular localization of Dcr1 and found that it accumulates in the nucleus and is enriched at the nuclear periphery. Nuclear accumulation of Dcr1 depends on a short motif that impedes nuclear export promoted by the double-stranded RNA binding domain of Dcr1. Absence of this motif renders Dcr1 mainly cytoplasmic and is accompanied by remarkable changes in gene expression and failure to assemble heterochromatin. Our findings suggest that Dicer proteins are shuttling proteins and that the steady-state subcellular levels can be shifted toward either compartment.
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Affiliation(s)
- Stephan Emmerth
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
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Pitton B, Grewatta PJ, Bühler M, Schneider J, Achenbach T, Otto G, Düber C. Pfortaderembolisation versus intraoperative Pfortaderligatur zur Induktion einer linksseitigen Leberhypertrophie vor rechtsseitiger Hemihepatektomie. ROFO-FORTSCHR RONTG 2010. [DOI: 10.1055/s-0030-1252784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Mutschler J, Grosshans M, Bühler M, Diehl A, Kiefer F. Disulfiram in the treatment of pathological gambling? Pharmacopsychiatry 2009. [DOI: 10.1055/s-0029-1240182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Bühler M. RNA turnover and chromatin-dependent gene silencing. Chromosoma 2008; 118:141-51. [DOI: 10.1007/s00412-008-0195-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2008] [Revised: 10/31/2008] [Accepted: 11/03/2008] [Indexed: 12/31/2022]
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Bühler M, Spies N, Bartel DP, Moazed D. TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway. Nat Struct Mol Biol 2008; 15:1015-23. [PMID: 18776903 PMCID: PMC3240669 DOI: 10.1038/nsmb.1481] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Accepted: 07/24/2008] [Indexed: 12/27/2022]
Abstract
In the fission yeast Schizosaccharomyces pombe, the RNA interference (RNAi) machinery is required to generate small interfering RNAs (siRNAs) that mediate heterochromatic gene silencing. Efficient silencing also requires the TRAMP complex, which contains the noncanonical Cid14 poly(A) polymerase and targets aberrant RNAs for degradation. Here we use high-throughput sequencing to analyze Argonaute-associated small RNAs (sRNAs) in both the presence and absence of Cid14. Most sRNAs in fission yeast start with a 5′ uracil, and we argue these are loaded most efficiently into Argonaute. In wild-type cells most sRNAs match to repeated regions of the genome, whereas in cid14Δ cells the sRNA profile changes to include major new classes of sRNAs originating from ribosomal RNAs and a tRNA. Thus, Cid14 prevents certain abundant RNAs from becoming substrates for the RNAi machinery, thereby freeing the RNAi machinery to act on its proper targets.
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Affiliation(s)
- Marc Bühler
- Department of Cell Biology, 240 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115 USA
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Walter G, Bühler M, Hoffmann R. [Two-stage procedure to exchange septic total hip arthroplasties with late periprosthetic infection. Early results after implantation of a reverse modular hybrid endoprosthesis]. Unfallchirurg 2008; 110:537-46. [PMID: 17361449 DOI: 10.1007/s00113-007-1238-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND Between January 2001 and January 2005 we performed the exchange of infected total hip arthroplasties in 40 cases. MATERIAL AND METHODS We applied a two-stage procedure when implant salvage was not possible. Our treatment algorithm included complete removal of the infected material, thorough débridement, and repeated revisions until cultures were negative. We then implanted a cemented acetabular polyethylene cup with specific antibiotic addition and a cementless modular stem (reverse modular hybrid endoprosthesis). Appropriate intravenous and oral antibiotic therapy was prescribed. RESULTS A total of 18 women and 22 men (age 48-86 years) were followed up for 4-48 months (mean: 12 months). Up to now 38 have remained infection free; in two cases the treatment failed and a resection arthroplasty had to be performed. There were eight complications intraoperatively (shaft fractures); four of them were treated conservatively and four needed additional stabilization. The mean hip score improved from 21 points initially to 81 points at the last examination. All details are listed in table form. Two-stage revision hip arthroplasty for infection using the inverse modular hybrid technique seems to be a safe and reliable method. Further investigation and a larger number of patients are necessary to confirm these preliminary results.
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Affiliation(s)
- G Walter
- Abteilung für Septische Chirurgie, BG-Unfallklinik, Friedberger Landstrasse 430, 60389 Frankfurt/M.
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Bühler M, Haas W, Gygi SP, Moazed D. RNAi-dependent and -independent RNA turnover mechanisms contribute to heterochromatic gene silencing. Cell 2007; 129:707-21. [PMID: 17512405 DOI: 10.1016/j.cell.2007.03.038] [Citation(s) in RCA: 199] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Revised: 02/14/2007] [Accepted: 03/16/2007] [Indexed: 01/06/2023]
Abstract
In fission yeast, the RNAi pathway is required for heterochromatin-dependent silencing of transgene insertions at centromeric repeats and acts together with other pathways to silence transgenes at the silent mating-type locus. Here, we show that transgene transcripts at centromeric repeats are processed into siRNAs and are therefore direct targets of RNAi. Furthermore, we show that Cid14, a member of the Trf4/5 family of poly(A) polymerases, has poly(A) polymerase activity that is required for heterochromatic gene silencing. Surprisingly, while siRNA levels in cid14Delta cells are dramatically reduced, the structural integrity of heterochromatin appears to be preserved. Cid14 resides in a complex similar to the TRAMP complex found in budding yeast, which is part of a nuclear surveillance mechanism that degrades aberrant transcripts. Our findings indicate that polyadenylation by a TRAMP-like complex contributes to robust silencing of heterochromatic genes in fission yeast via the recruitment of the exosome and/or the RNAi machinery.
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Affiliation(s)
- Marc Bühler
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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Moazed D, Bühler M, Buker SM, Colmenares SU, Gerace EL, Gerber SA, Hong EJE, Motamedi MR, Verdel A, Villén J, Gygi SP. Studies on the mechanism of RNAi-dependent heterochromatin assembly. Cold Spring Harb Symp Quant Biol 2007; 71:461-71. [PMID: 17381328 DOI: 10.1101/sqb.2006.71.044] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Assembly of heterochromatin at centromeric DNA regions in the fission yeast Schizosaccharomyces pombe involves an intimate interplay between chromatin modifying complexes and components of the RNAi pathway. The RNA-induced transcriptional silencing (RITS) complex, containing Chp1, Ago1, Tas3, and centromeric siRNAs, localizes to centromeric DNA repeats and is required for the assembly and maintenance of heterochromatin. RITS brings together two types of molecular recognition modules: a chromodomain protein, which binds to lysine 9 methylated histone H3 (H3K9), and Argonaute, which binds to specific sequences by siRNA-directed base-pairing interactions. The RNA-directed RNA polymerase complex (RDRC), composed of Rdp1, the Hrr1 helicase, and the Cid12 Poly(A) polymerase family member, synthesizes double-stranded RNA and creates the substrate for Dicer to generate siRNAs. RDRC physically associates with RITS, and both complexes localize to noncoding centromeric RNAs and centromeric DNA repeats, suggesting that recognition of nascent RNA transcripts may be involved in localization of these complexes to specific chromosome regions. In support of this possibility, tethering of the RITS complex to the transcript of the normally euchromatic ura4 (+) gene results in siRNA generation and RNAi- and heterochromatin-dependent silencing of the ura4 (+) gene. Finally, silencing of a subset of endogenous and transgene promoters within heterochromatic DNA domains occurs by RNAi-dependent degradation of nascent transcripts by a mechanism that we have termed co-transcriptional gene silencing (CTGS).
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Affiliation(s)
- D Moazed
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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