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Palau A, Segerberg F, Lidschreiber M, Lidschreiber K, Naughton AJ, Needhamsen M, Jung LA, Jagodic M, Cramer P, Lehmann S, Carlsten M, Lennartsson A. Perturbed epigenetic transcriptional regulation in AML with IDH mutations causes increased susceptibility to NK cells. Leukemia 2023; 37:1830-1841. [PMID: 37495775 PMCID: PMC10457197 DOI: 10.1038/s41375-023-01972-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/05/2023] [Accepted: 07/10/2023] [Indexed: 07/28/2023]
Abstract
Isocitrate dehydrogenase (IDH) mutations are found in 20% of acute myeloid leukemia (AML) patients. However, only 30-40% of the patients respond to IDH inhibitors (IDHi). We aimed to identify a molecular vulnerability to tailor novel therapies for AML patients with IDH mutations. We characterized the transcriptional and epigenetic landscape with the IDH2i AG-221, using an IDH2 mutated AML cell line model and AML patient cohorts, and discovered a perturbed transcriptional regulatory network involving myeloid transcription factors that were partly restored after AG-221 treatment. In addition, hypermethylation of the HLA cluster caused a down-regulation of HLA class I genes, triggering an enhanced natural killer (NK) cell activation and an increased susceptibility to NK cell-mediated responses. Finally, analyses of DNA methylation data from IDHi-treated patients showed that non-responders still harbored hypermethylation in HLA class I genes. In conclusion, this study provides new insights suggesting that IDH mutated AML is particularly sensitive to NK cell-based personalized immunotherapy.
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Affiliation(s)
- Anna Palau
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Filip Segerberg
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Michael Lidschreiber
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Katja Lidschreiber
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Aonghus J Naughton
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Maria Needhamsen
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden
| | - Lisa Anna Jung
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden
| | - Patrick Cramer
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Sören Lehmann
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
- Hematology Centre, Karolinska University Hospital, Stockholm, Sweden.
- Hematology Unit, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
| | - Mattias Carlsten
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
- Center for Cell Therapy and Allogeneic Stem Cell Transplantation, Karolinska Comprehensive Cancer Center, Karolinska University Hospital, Stockholm, Sweden.
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.
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2
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Ramasamy S, Aljahani A, Karpinska MA, Cao TBN, Velychko T, Cruz JN, Lidschreiber M, Oudelaar AM. The Mediator complex regulates enhancer-promoter interactions. Nat Struct Mol Biol 2023:10.1038/s41594-023-01027-2. [PMID: 37430065 DOI: 10.1038/s41594-023-01027-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 05/30/2023] [Indexed: 07/12/2023]
Abstract
Enhancer-mediated gene activation generally requires physical proximity between enhancers and their target gene promoters. However, the molecular mechanisms by which interactions between enhancers and promoters are formed are not well understood. Here, we investigate the function of the Mediator complex in the regulation of enhancer-promoter interactions, by combining rapid protein depletion and high-resolution MNase-based chromosome conformation capture approaches. We show that depletion of Mediator leads to reduced enhancer-promoter interaction frequencies, which are associated with a strong decrease in gene expression. In addition, we find increased interactions between CTCF-binding sites upon Mediator depletion. These changes in chromatin architecture are associated with a redistribution of the Cohesin complex on chromatin and a reduction in Cohesin occupancy at enhancers. Together, our results indicate that the Mediator and Cohesin complexes contribute to enhancer-promoter interactions and provide insights into the molecular mechanisms by which communication between enhancers and promoters is regulated.
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Affiliation(s)
- Shyam Ramasamy
- Genome Organization and Regulation, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Abrar Aljahani
- Genome Organization and Regulation, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Magdalena A Karpinska
- Genome Organization and Regulation, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - T B Ngoc Cao
- Genome Organization and Regulation, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Taras Velychko
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - J Neos Cruz
- Genome Organization and Regulation, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Michael Lidschreiber
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - A Marieke Oudelaar
- Genome Organization and Regulation, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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3
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Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P. Structural basis of transcription reduction by a promoter-proximal +1 nucleosome. Mol Cell 2023:S1097-2765(23)00255-1. [PMID: 37148879 DOI: 10.1016/j.molcel.2023.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 01/31/2023] [Revised: 03/16/2023] [Accepted: 04/11/2023] [Indexed: 05/08/2023]
Abstract
At active human genes, the +1 nucleosome is located downstream of the RNA polymerase II (RNA Pol II) pre-initiation complex (PIC). However, at inactive genes, the +1 nucleosome is found further upstream, at a promoter-proximal location. Here, we establish a model system to show that a promoter-proximal +1 nucleosome can reduce RNA synthesis in vivo and in vitro, and we analyze its structural basis. We find that the PIC assembles normally when the edge of the +1 nucleosome is located 18 base pairs (bp) downstream of the transcription start site (TSS). However, when the nucleosome edge is located further upstream, only 10 bp downstream of the TSS, the PIC adopts an inhibited state. The transcription factor IIH (TFIIH) shows a closed conformation and its subunit XPB contacts DNA with only one of its two ATPase lobes, inconsistent with DNA opening. These results provide a mechanism for nucleosome-dependent regulation of transcription initiation.
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Affiliation(s)
- Julio Abril-Garrido
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Dienemann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Frauke Grabbe
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Taras Velychko
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Michael Lidschreiber
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Haibo Wang
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
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4
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Xiong L, Tolen EA, Choi J, Velychko S, Caizzi L, Velychko T, Adachi K, MacCarthy CM, Lidschreiber M, Cramer P, Schöler HR. Oct4 differentially regulates chromatin opening and enhancer transcription in pluripotent stem cells. eLife 2022; 11:71533. [PMID: 35621159 PMCID: PMC9142147 DOI: 10.7554/elife.71533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 06/22/2021] [Accepted: 05/17/2022] [Indexed: 12/21/2022] Open
Abstract
The transcription factor Oct4 is essential for the maintenance and induction of stem cell pluripotency, but its functional roles are not fully understood. Here, we investigate the functions of Oct4 by depleting and subsequently recovering it in mouse embryonic stem cells (ESCs) and conducting a time-resolved multiomics analysis. Oct4 depletion leads to an immediate loss of its binding to enhancers, accompanied by a decrease in mRNA synthesis from its target genes that are part of the transcriptional network that maintains pluripotency. Gradual decrease of Oct4 binding to enhancers does not immediately change the chromatin accessibility but reduces transcription of enhancers. Conversely, partial recovery of Oct4 expression results in a rapid increase in chromatin accessibility, whereas enhancer transcription does not fully recover. These results indicate different concentration-dependent activities of Oct4. Whereas normal ESC levels of Oct4 are required for transcription of pluripotency enhancers, low levels of Oct4 are sufficient to retain chromatin accessibility, likely together with other factors such as Sox2.
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Affiliation(s)
- Le Xiong
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Erik A Tolen
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Münster, Germany
| | - Jinmi Choi
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Sergiy Velychko
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Münster, Germany
| | - Livia Caizzi
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Taras Velychko
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Kenjiro Adachi
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Münster, Germany
| | - Caitlin M MacCarthy
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Münster, Germany
| | - Michael Lidschreiber
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Hans R Schöler
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Münster, Germany
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5
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Shao R, Kumar B, Lidschreiber K, Lidschreiber M, Cramer P, Elsässer SJ. Distinct transcription kinetics of pluripotent cell states. Mol Syst Biol 2022; 18:e10407. [PMID: 35020268 PMCID: PMC8754154 DOI: 10.15252/msb.202110407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 06/10/2021] [Revised: 12/12/2021] [Accepted: 12/14/2021] [Indexed: 12/20/2022] Open
Abstract
Mouse embryonic stem cells (mESCs) can adopt naïve, ground, and paused pluripotent states that give rise to unique transcriptomes. Here, we use transient transcriptome sequencing (TT-seq) to define both coding and non-coding transcription units (TUs) in these three pluripotent states and combine TT-seq with RNA polymerase II occupancy profiling to unravel the kinetics of RNA metabolism genome-wide. Compared to the naïve state (serum), RNA synthesis and turnover rates are globally reduced in the ground state (2i) and the paused state (mTORi). The global reduction in RNA synthesis goes along with a genome-wide decrease of polymerase elongation velocity, which is related to epigenomic features and alterations in the Pol II termination window. Our data suggest that transcription activity is the main determinant of steady state mRNA levels in the naïve state and that genome-wide changes in transcription kinetics invoke ground and paused pluripotent states.
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Affiliation(s)
- Rui Shao
- Science for Life LaboratoryDepartment of Medical Biochemistry and BiophysicsDivision of Genome BiologyKarolinska InstitutetStockholmSweden
- Ming Wai Lau Centre for Reparative MedicineStockholm nodeKarolinska InstitutetStockholmSweden
| | - Banushree Kumar
- Science for Life LaboratoryDepartment of Medical Biochemistry and BiophysicsDivision of Genome BiologyKarolinska InstitutetStockholmSweden
- Ming Wai Lau Centre for Reparative MedicineStockholm nodeKarolinska InstitutetStockholmSweden
| | - Katja Lidschreiber
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
- Department of Molecular BiologyMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Michael Lidschreiber
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
- Department of Molecular BiologyMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Patrick Cramer
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
- Department of Molecular BiologyMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Simon J Elsässer
- Science for Life LaboratoryDepartment of Medical Biochemistry and BiophysicsDivision of Genome BiologyKarolinska InstitutetStockholmSweden
- Ming Wai Lau Centre for Reparative MedicineStockholm nodeKarolinska InstitutetStockholmSweden
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6
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Caizzi L, Monteiro-Martins S, Schwalb B, Lysakovskaia K, Schmitzova J, Sawicka A, Chen Y, Lidschreiber M, Cramer P. Efficient RNA polymerase II pause release requires U2 snRNP function. Mol Cell 2021; 81:1920-1934.e9. [PMID: 33689748 DOI: 10.1016/j.molcel.2021.02.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 01/07/2021] [Accepted: 02/10/2021] [Indexed: 12/21/2022]
Abstract
Transcription by RNA polymerase II (Pol II) is coupled to pre-mRNA splicing, but the underlying mechanisms remain poorly understood. Co-transcriptional splicing requires assembly of a functional spliceosome on nascent pre-mRNA, but whether and how this influences Pol II transcription remains unclear. Here we show that inhibition of pre-mRNA branch site recognition by the spliceosome component U2 snRNP leads to a widespread and strong decrease in new RNA synthesis from human genes. Multiomics analysis reveals that inhibition of U2 snRNP function increases the duration of Pol II pausing in the promoter-proximal region, impairs recruitment of the pause release factor P-TEFb, and reduces Pol II elongation velocity at the beginning of genes. Our results indicate that efficient release of paused Pol II into active transcription elongation requires the formation of functional spliceosomes and that eukaryotic mRNA biogenesis relies on positive feedback from the splicing machinery to the transcription machinery.
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Affiliation(s)
- Livia Caizzi
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Sara Monteiro-Martins
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Björn Schwalb
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kseniia Lysakovskaia
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jana Schmitzova
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Anna Sawicka
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ying Chen
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Michael Lidschreiber
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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7
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Sawicka A, Villamil G, Lidschreiber M, Darzacq X, Dugast-Darzacq C, Schwalb B, Cramer P. Transcription activation depends on the length of the RNA polymerase II C-terminal domain. EMBO J 2021; 40:e107015. [PMID: 33555055 PMCID: PMC8090853 DOI: 10.15252/embj.2020107015] [Citation(s) in RCA: 11] [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: 10/12/2020] [Revised: 01/04/2021] [Accepted: 01/13/2021] [Indexed: 01/02/2023] Open
Abstract
Eukaryotic RNA polymerase II (Pol II) contains a tail‐like, intrinsically disordered carboxy‐terminal domain (CTD) comprised of heptad‐repeats, that functions in coordination of the transcription cycle and in coupling transcription to co‐transcriptional processes. The CTD repeat number varies between species and generally increases with genome size, but the reasons for this are unclear. Here, we show that shortening the CTD in human cells to half of its length does not generally change pre‐mRNA synthesis or processing in cells. However, CTD shortening decreases the duration of promoter‐proximal Pol II pausing, alters transcription of putative enhancer elements, and delays transcription activation after stimulation of the MAP kinase pathway. We suggest that a long CTD is required for efficient enhancer‐dependent recruitment of Pol II to target genes for their rapid activation.
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Affiliation(s)
- Anna Sawicka
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Gabriel Villamil
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Michael Lidschreiber
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.,CIRM Center of Excellence, University of California, Berkeley, CA, USA
| | - Claire Dugast-Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.,CIRM Center of Excellence, University of California, Berkeley, CA, USA
| | - Björn Schwalb
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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8
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Osman S, Mohammad E, Lidschreiber M, Stuetzer A, Bazsó FL, Maier KC, Urlaub H, Cramer P. The Cdk8 kinase module regulates interaction of the mediator complex with RNA polymerase II. J Biol Chem 2021; 296:100734. [PMID: 33933450 PMCID: PMC8191332 DOI: 10.1016/j.jbc.2021.100734] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 11/10/2020] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 11/17/2022] Open
Abstract
The Cdk8 kinase module (CKM) is a dissociable part of the coactivator complex mediator, which regulates gene transcription by RNA polymerase II. The CKM has both negative and positive functions in gene transcription that remain poorly understood at the mechanistic level. In order to reconstitute the role of the CKM in transcription initiation, we prepared recombinant CKM from the yeast Saccharomyces cerevisiae. We showed that CKM bound to the core mediator (cMed) complex, sterically inhibiting cMed from binding to the polymerase II preinitiation complex (PIC) in vitro. We further showed that the Cdk8 kinase activity of the CKM weakened CKM-cMed interaction, thereby facilitating dissociation of the CKM and enabling mediator to bind the PIC in order to stimulate transcription initiation. Finally, we report that the kinase activity of Cdk8 is required for gene activation during the stressful condition of heat shock in vivo but not under steady-state growth conditions. Based on these results, we propose a model in which the CKM negatively regulates mediator function at upstream-activating sequences by preventing mediator binding to the PIC at the gene promoter. However, during gene activation in response to stress, the Cdk8 kinase activity of the CKM may release mediator and allow its binding to the PIC, thereby accounting for the positive function of CKM. This may impart improved adaptability to stress by allowing a rapid transcriptional response to environmental changes, and we speculate that a similar mechanism in metazoans may allow the precise timing of developmental transcription programs.
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Affiliation(s)
- Sara Osman
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Eusra Mohammad
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Michael Lidschreiber
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Alexandra Stuetzer
- Bioanalytical Mass Spectrometry Group, Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics Research Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Fanni Laura Bazsó
- Bioanalytical Mass Spectrometry Group, Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics Research Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Kerstin C Maier
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics Research Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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9
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Lidschreiber K, Jung LA, von der Emde H, Dave K, Taipale J, Cramer P, Lidschreiber M. Transcriptionally active enhancers in human cancer cells. Mol Syst Biol 2021; 17:e9873. [PMID: 33502116 PMCID: PMC7838827 DOI: 10.15252/msb.20209873] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 07/17/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 12/30/2022] Open
Abstract
The growth of human cancer cells is driven by aberrant enhancer and gene transcription activity. Here, we use transient transcriptome sequencing (TT-seq) to map thousands of transcriptionally active putative enhancers in fourteen human cancer cell lines covering seven types of cancer. These enhancers were associated with cell type-specific gene expression, enriched for genetic variants that predispose to cancer, and included functionally verified enhancers. Enhancer-promoter (E-P) pairing by correlation of transcription activity revealed ~ 40,000 putative E-P pairs, which were depleted for housekeeping genes and enriched for transcription factors, cancer-associated genes, and 3D conformational proximity. The cell type specificity and transcription activity of target genes increased with the number of paired putative enhancers. Our results represent a rich resource for future studies of gene regulation by enhancers and their role in driving cancerous cell growth.
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Affiliation(s)
- Katja Lidschreiber
- Department of Molecular BiologyMax Planck Institute for Biophysical ChemistryGöttingenGermany
- Department of Biosciences and NutritionKarolinska InstitutetNEOHuddingeSweden
| | - Lisa A Jung
- Department of Biosciences and NutritionKarolinska InstitutetNEOHuddingeSweden
- Department of Cell and Molecular BiologyKarolinska InstitutetBiomedicumSolnaSweden
| | - Henrik von der Emde
- Department of Molecular BiologyMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Kashyap Dave
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetBiomedicumSolnaSweden
| | - Jussi Taipale
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetBiomedicumSolnaSweden
- Department of BiochemistryUniversity of CambridgeCambridgeUK
- Genome‐Scale Biology ProgramUniversity of HelsinkiHelsinkiFinland
| | - Patrick Cramer
- Department of Molecular BiologyMax Planck Institute for Biophysical ChemistryGöttingenGermany
- Department of Biosciences and NutritionKarolinska InstitutetNEOHuddingeSweden
| | - Michael Lidschreiber
- Department of Molecular BiologyMax Planck Institute for Biophysical ChemistryGöttingenGermany
- Department of Biosciences and NutritionKarolinska InstitutetNEOHuddingeSweden
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10
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Hendriks GJ, Jung LA, Larsson AJM, Lidschreiber M, Andersson Forsman O, Lidschreiber K, Cramer P, Sandberg R. NASC-seq monitors RNA synthesis in single cells. Nat Commun 2019; 10:3138. [PMID: 31316066 PMCID: PMC6637240 DOI: 10.1038/s41467-019-11028-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [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: 11/22/2018] [Accepted: 06/12/2019] [Indexed: 12/14/2022] Open
Abstract
Sequencing of newly synthesised RNA can monitor transcriptional dynamics with great sensitivity and high temporal resolution, but is currently restricted to populations of cells. Here, we develop new transcriptome alkylation-dependent single-cell RNA sequencing (NASC-seq), to monitor newly synthesised and pre-existing RNA simultaneously in single cells. We validate the method on pre-labelled RNA, and by demonstrating that more newly synthesised RNA was detected for genes with known high mRNA turnover. Monitoring RNA synthesis during Jurkat T-cell activation with NASC-seq reveals both rapidly up- and down-regulated genes, and that induced genes are almost exclusively detected as newly transcribed. Moreover, the newly synthesised and pre-existing transcriptomes after T-cell activation are distinct, confirming that NASC-seq simultaneously measures gene expression corresponding to two time points in single cells. Altogether, NASC-seq enables precise temporal monitoring of RNA synthesis at single-cell resolution during homoeostasis, perturbation responses and cellular differentiation.
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Affiliation(s)
- Gert-Jan Hendriks
- Department of Cell and Molecular Biology, Karolinska Instiutet, Biomedicum, Solnavägen 9, 171 65, Solna, Sweden
| | - Lisa A Jung
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Blickagången 16, 141 52, Huddinge, Sweden
| | - Anton J M Larsson
- Department of Cell and Molecular Biology, Karolinska Instiutet, Biomedicum, Solnavägen 9, 171 65, Solna, Sweden
| | - Michael Lidschreiber
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Blickagången 16, 141 52, Huddinge, Sweden
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Oscar Andersson Forsman
- Department of Cell and Molecular Biology, Karolinska Instiutet, Biomedicum, Solnavägen 9, 171 65, Solna, Sweden
| | - Katja Lidschreiber
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Patrick Cramer
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Blickagången 16, 141 52, Huddinge, Sweden.
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Instiutet, Biomedicum, Solnavägen 9, 171 65, Solna, Sweden.
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11
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Lidschreiber M, Easter AD, Battaglia S, Rodríguez-Molina JB, Casañal A, Carminati M, Baejen C, Grzechnik P, Maier KC, Cramer P, Passmore LA. The APT complex is involved in non-coding RNA transcription and is distinct from CPF. Nucleic Acids Res 2019; 46:11528-11538. [PMID: 30247719 PMCID: PMC6265451 DOI: 10.1093/nar/gky845] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 05/14/2018] [Accepted: 09/11/2018] [Indexed: 11/15/2022] Open
Abstract
The 3'-ends of eukaryotic pre-mRNAs are processed in the nucleus by a large multiprotein complex, the cleavage and polyadenylation factor (CPF). CPF cleaves RNA, adds a poly(A) tail and signals transcription termination. CPF harbors four enzymatic activities essential for these processes, but how these are coordinated remains poorly understood. Several subunits of CPF, including two protein phosphatases, are also found in the related 'associated with Pta1' (APT) complex, but the relationship between CPF and APT is unclear. Here, we show that the APT complex is physically distinct from CPF. The 21 kDa Syc1 protein is associated only with APT, and not with CPF, and is therefore the defining subunit of APT. Using ChIP-seq, PAR-CLIP and RNA-seq, we show that Syc1/APT has distinct, but possibly overlapping, functions from those of CPF. Syc1/APT plays a more important role in sn/snoRNA production whereas CPF processes the 3'-ends of protein-coding pre-mRNAs. These results define distinct protein machineries for synthesis of mature eukaryotic protein-coding and non-coding RNAs.
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Affiliation(s)
- Michael Lidschreiber
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Karolinska Institutet, Department of Biosciences and Nutrition, Center for Innovative Medicine and Science for Life Laboratory, Novum, Hälsovägen 7, 141 83 Huddinge, Sweden
| | | | - Sofia Battaglia
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | | | - Ana Casañal
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Carlo Baejen
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Pawel Grzechnik
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Kerstin C Maier
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Karolinska Institutet, Department of Biosciences and Nutrition, Center for Innovative Medicine and Science for Life Laboratory, Novum, Hälsovägen 7, 141 83 Huddinge, Sweden
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12
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Battaglia S, Lidschreiber M, Baejen C, Torkler P, Vos SM, Cramer P. RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases. eLife 2017; 6. [PMID: 28537551 PMCID: PMC5457138 DOI: 10.7554/elife.25637] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [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: 02/01/2017] [Accepted: 05/22/2017] [Indexed: 11/13/2022] Open
Abstract
For transcription through chromatin, RNA polymerase (Pol) II associates with elongation factors (EFs). Here we show that many EFs crosslink to RNA emerging from transcribing Pol II in the yeast Saccharomyces cerevisiae. Most EFs crosslink preferentially to mRNAs, rather than unstable non-coding RNAs. RNA contributes to chromatin association of many EFs, including the Pol II serine 2 kinases Ctk1 and Bur1 and the histone H3 methyltransferases Set1 and Set2. The Ctk1 kinase complex binds RNA in vitro, consistent with direct EF-RNA interaction. Set1 recruitment to genes in vivo depends on its RNA recognition motifs (RRMs). These results strongly suggest that nascent RNA contributes to EF recruitment to transcribing Pol II. We propose that EF-RNA interactions facilitate assembly of the elongation complex on transcribed genes when RNA emerges from Pol II, and that loss of EF-RNA interactions upon RNA cleavage at the polyadenylation site triggers disassembly of the elongation complex. DOI:http://dx.doi.org/10.7554/eLife.25637.001
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Affiliation(s)
- Sofia Battaglia
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Michael Lidschreiber
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Biosciences and Nutrition, Center for Innovative Medicine and Science for Life Laboratory, Novum, Karolinska Institutet, Huddinge, Sweden
| | - Carlo Baejen
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Phillipp Torkler
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Seychelle M Vos
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Biosciences and Nutrition, Center for Innovative Medicine and Science for Life Laboratory, Novum, Karolinska Institutet, Huddinge, Sweden
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13
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Baejen C, Andreani J, Torkler P, Battaglia S, Schwalb B, Lidschreiber M, Maier KC, Boltendahl A, Rus P, Esslinger S, Söding J, Cramer P. Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes. Mol Cell 2017; 66:38-49.e6. [PMID: 28318822 DOI: 10.1016/j.molcel.2017.02.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [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: 06/21/2016] [Revised: 10/06/2016] [Accepted: 02/09/2017] [Indexed: 01/09/2023]
Abstract
At the end of protein-coding genes, RNA polymerase (Pol) II undergoes a concerted transition that involves 3'-processing of the pre-mRNA and transcription termination. Here, we present a genome-wide analysis of the 3'-transition in budding yeast. We find that the 3'-transition globally requires the Pol II elongation factor Spt5 and factors involved in the recognition of the polyadenylation (pA) site and in endonucleolytic RNA cleavage. Pol II release from DNA occurs in a narrow termination window downstream of the pA site and requires the "torpedo" exonuclease Rat1 (XRN2 in human). The Rat1-interacting factor Rai1 contributes to RNA degradation downstream of the pA site. Defects in the 3'-transition can result in increased transcription at downstream genes.
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Affiliation(s)
- Carlo Baejen
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jessica Andreani
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Phillipp Torkler
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Sofia Battaglia
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Bjoern Schwalb
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Michael Lidschreiber
- Karolinska Institutet, Department of Biosciences and Nutrition, Center for Innovative Medicine and Science for Life Laboratory, Novum, Hälsovägen 7, 141 83 Huddinge, Sweden
| | - Kerstin C Maier
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Andrea Boltendahl
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Petra Rus
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stephanie Esslinger
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Johannes Söding
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Patrick Cramer
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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14
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Zacher B, Lidschreiber M, Cramer P, Gagneur J, Tresch A. Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle. Mol Syst Biol 2014; 10:768. [PMID: 25527639 PMCID: PMC4300491 DOI: 10.15252/msb.20145654] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [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: 02/02/2023] Open
Abstract
DNA replication, transcription and repair involve the recruitment of protein complexes that change their composition as they progress along the genome in a directed or strand-specific manner. Chromatin immunoprecipitation in conjunction with hidden Markov models (HMMs) has been instrumental in understanding these processes, as they segment the genome into discrete states that can be related to DNA-associated protein complexes. However, current HMM-based approaches are not able to assign forward or reverse direction to states or properly integrate strand-specific (e.g., RNA expression) with non-strand-specific (e.g., ChIP) data, which is indispensable to accurately characterize directed processes. To overcome these limitations, we introduce bidirectional HMMs which infer directed genomic states from occupancy profiles de novo. Application to RNA polymerase II-associated factors in yeast and chromatin modifications in human T cells recovers the majority of transcribed loci, reveals gene-specific variations in the yeast transcription cycle and indicates the existence of directed chromatin state patterns at transcribed, but not at repressed, regions in the human genome. In yeast, we identify 32 new transcribed loci, a regulated initiation–elongation transition, the absence of elongation factors Ctk1 and Paf1 from a class of genes, a distinct transcription mechanism for highly expressed genes and novel DNA sequence motifs associated with transcription termination. We anticipate bidirectional HMMs to significantly improve the analyses of genome-associated directed processes.
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Affiliation(s)
- Benedikt Zacher
- Gene Center and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany Institute for Genetics, University of Cologne, Cologne, Germany
| | - Michael Lidschreiber
- Gene Center and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Patrick Cramer
- Gene Center and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Julien Gagneur
- Gene Center and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Achim Tresch
- Gene Center and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany Institute for Genetics, University of Cologne, Cologne, Germany Max Planck Institute for Plant Breeding Research, Cologne, Germany
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15
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Schreieck A, Easter AD, Etzold S, Wiederhold K, Lidschreiber M, Cramer P, Passmore LA. RNA polymerase II termination involves C-terminal-domain tyrosine dephosphorylation by CPF subunit Glc7. Nat Struct Mol Biol 2014; 21:175-179. [PMID: 24413056 PMCID: PMC3917824 DOI: 10.1038/nsmb.2753] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [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: 06/25/2013] [Accepted: 12/04/2013] [Indexed: 02/07/2023]
Abstract
At the 3′ end of protein-coding genes, RNA polymerase (Pol) II is dephosphorylated at tyrosine (Tyr1) residues of its C-terminal domain (CTD). In addition, the associated cleavage and polyadenylation (pA) factor (CPF) cleaves the transcript and adds a polyA tail. Whether these events are coordinated and how they lead to transcription termination remains poorly understood. Here we show that CPF from Saccharomyces cerevisiae is a Pol II CTD phosphatase and that the CPF subunit Glc7 dephosphorylates Tyr1 in vitro. In vivo, the activity of Glc7 is required for normal Tyr1 dephosphorylation at the pA site, for recruitment of termination factors Pcf11 and Rtt103, and for normal Pol II termination. These results show that transcription termination involves Tyr1 dephosphorylation of the CTD and indicate that pre-mRNA processing by CPF and transcription termination are coupled via Glc7-dependent Pol II Tyr1 dephosphorylation.
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Affiliation(s)
- Amelie Schreieck
- Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ashley D Easter
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Stefanie Etzold
- Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Katrin Wiederhold
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Michael Lidschreiber
- Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Patrick Cramer
- Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lori A Passmore
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, United Kingdom
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16
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Heo DH, Yoo I, Kong J, Lidschreiber M, Mayer A, Choi BY, Hahn Y, Cramer P, Buratowski S, Kim M. The RNA polymerase II C-terminal domain-interacting domain of yeast Nrd1 contributes to the choice of termination pathway and couples to RNA processing by the nuclear exosome. J Biol Chem 2013; 288:36676-90. [PMID: 24196955 DOI: 10.1074/jbc.m113.508267] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RNA polymerase II (RNApII) C-terminal domain (CTD)-interacting domain (CID) proteins are involved in two distinct RNApII termination pathways and recognize different phosphorylated forms of CTD. To investigate the role of differential CTD-CID interactions in the choice of termination pathway, we altered the CTD-binding specificity of Nrd1 by domain swapping. Nrd1 with the CID from Rtt103 (Nrd1(CID(Rtt103))) causes read-through transcription at many genes, but can also trigger termination where multiple Nrd1/Nab3-binding sites and the Ser(P)-2 CTD co-exist. Therefore, CTD-CID interactions target specific termination complexes to help choose an RNApII termination pathway. Interactions of Nrd1 with both CTD and nascent transcripts contribute to efficient termination by the Nrd1 complex. Surprisingly, replacing the Nrd1 CID with that from Rtt103 reduces binding to Rrp6/Trf4, and RNA transcripts terminated by Nrd1(CID(Rtt103)) are predominantly processed by core exosome. Thus, the Nrd1 CID couples Ser(P)-5 CTD not only to termination, but also to RNA processing by the nuclear exosome.
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Affiliation(s)
- Dong-hyuk Heo
- From the Center for RNA Research, Institute for Basic Science and
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17
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Bohne AV, Schwarz C, Schottkowski M, Lidschreiber M, Piotrowski M, Zerges W, Nickelsen J. Reciprocal regulation of protein synthesis and carbon metabolism for thylakoid membrane biogenesis. PLoS Biol 2013; 11:e1001482. [PMID: 23424285 PMCID: PMC3570535 DOI: 10.1371/journal.pbio.1001482] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 01/04/2013] [Indexed: 11/19/2022] Open
Abstract
A subunit of the chloroplast pyruvate dehydrogenase complex, which serves as a metabolic enzyme, also has a dual function as an RNA-binding protein and influences mRNA translation. Metabolic control of gene expression coordinates the levels of specific gene products to meet cellular demand for their activities. This control can be exerted by metabolites acting as regulatory signals and/or a class of metabolic enzymes with dual functions as regulators of gene expression. However, little is known about how metabolic signals affect the balance between enzymatic and regulatory roles of these dual functional proteins. We previously described the RNA binding activity of a 63 kDa chloroplast protein from Chlamydomonas reinhardtii, which has been implicated in expression of the psbA mRNA, encoding the D1 protein of photosystem II. Here, we identify this factor as dihydrolipoamide acetyltransferase (DLA2), a subunit of the chloroplast pyruvate dehydrogenase complex (cpPDC), which is known to provide acetyl-CoA for fatty acid synthesis. Analyses of RNAi lines revealed that DLA2 is involved in the synthesis of both D1 and acetyl-CoA. Gel filtration analyses demonstrated an RNP complex containing DLA2 and the chloroplast psbA mRNA specifically in cells metabolizing acetate. An intrinsic RNA binding activity of DLA2 was confirmed by in vitro RNA binding assays. Results of fluorescence microscopy and subcellular fractionation experiments support a role of DLA2 in acetate-dependent localization of the psbA mRNA to a translation zone within the chloroplast. Reciprocally, the activity of the cpPDC was specifically affected by binding of psbA mRNA. Beyond that, in silico analysis and in vitro RNA binding studies using recombinant proteins support the possibility that RNA binding is an ancient feature of dihydrolipoamide acetyltransferases. Our results suggest a regulatory function of DLA2 in response to growth on reduced carbon energy sources. This raises the intriguing possibility that this regulation functions to coordinate the synthesis of lipids and proteins for the biogenesis of photosynthetic membranes. Metabolic control of gene expression coordinates the levels of specific gene products to meet cellular demand for their activities. This control can be exerted by metabolites acting as regulatory signals on a class of metabolic enzymes with dual functions as regulators of gene expression. However, little is known about how metabolic signals affect the balance between enzymatic and regulatory roles of these proteins. Here, we report an example of a protein with dual functions in gene expression and carbon metabolism. The chloroplast pyruvate dehydrogenase complex is well-known to produce activated di-carbon precursors for fatty acid, which is required for lipid synthesis. Our results show that a subunit of this enzyme forms ribonucleoprotein particles and influences chloroplast mRNA translation. Conversely, RNA binding affects pyruvate dehydrogenase (metabolic) activity. These findings offer insight into how intracellular metabolic signaling and gene expression are reciprocally regulated during membrane biogenesis. In addition, our results suggest that these dual roles of the protein might exist in evolutionary distant organisms ranging from cyanobacteria to humans.
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Affiliation(s)
- Alexandra-Viola Bohne
- Molecular Plant Sciences, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Christian Schwarz
- Molecular Plant Sciences, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Marco Schottkowski
- Biology Department and Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Michael Lidschreiber
- Molecular Plant Sciences, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Markus Piotrowski
- Department of Plant Physiology, Ruhr-University Bochum, Bochum, Germany
| | - William Zerges
- Biology Department and Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Jörg Nickelsen
- Molecular Plant Sciences, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
- * E-mail:
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18
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Mayer A, Heidemann M, Lidschreiber M, Schreieck A, Sun M, Hintermair C, Kremmer E, Eick D, Cramer P. CTD tyrosine phosphorylation impairs termination factor recruitment to RNA polymerase II. Science 2012; 336:1723-5. [PMID: 22745433 DOI: 10.1126/science.1219651] [Citation(s) in RCA: 192] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In different phases of the transcription cycle, RNA polymerase (Pol) II recruits various factors via its C-terminal domain (CTD), which consists of conserved heptapeptide repeats with the sequence Tyr(1)-Ser(2)-Pro(3)-Thr(4)-Ser(5)-Pro(6)-Ser(7). We show that the CTD of transcribing yeast Pol II is phosphorylated at Tyr(1), in addition to Ser(2), Thr(4), Ser(5), and Ser(7). Tyr(1) phosphorylation stimulates binding of elongation factor Spt6 and impairs recruitment of termination factors Nrd1, Pcf11, and Rtt103. Tyr(1) phosphorylation levels rise downstream of the transcription start site and decrease before the polyadenylation site, largely excluding termination factors from gene bodies. These results show that CTD modifications trigger and block factor recruitment and lead to an extended CTD code that explains transcription cycle coordination on the basis of differential phosphorylation of Tyr(1), Ser(2), and Ser(5).
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Affiliation(s)
- Andreas Mayer
- Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
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19
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Marcinowski L, Lidschreiber M, Windhager L, Rieder M, Bosse JB, Rädle B, Bonfert T, Györy I, de Graaf M, da Costa OP, Rosenstiel P, Friedel CC, Zimmer R, Ruzsics Z, Dölken L. Real-time transcriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection. PLoS Pathog 2012; 8:e1002908. [PMID: 22969428 PMCID: PMC3435240 DOI: 10.1371/journal.ppat.1002908] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [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: 02/22/2012] [Accepted: 08/01/2012] [Indexed: 01/08/2023] Open
Abstract
During viral infections cellular gene expression is subject to rapid alterations induced by both viral and antiviral mechanisms. In this study, we applied metabolic labeling of newly transcribed RNA with 4-thiouridine (4sU-tagging) to dissect the real-time kinetics of cellular and viral transcriptional activity during lytic murine cytomegalovirus (MCMV) infection. Microarray profiling on newly transcribed RNA obtained at different times during the first six hours of MCMV infection revealed discrete functional clusters of cellular genes regulated with distinct kinetics at surprising temporal resolution. Immediately upon virus entry, a cluster of NF-κB- and interferon-regulated genes was induced. Rapid viral counter-regulation of this coincided with a very transient DNA-damage response, followed by a delayed ER-stress response. Rapid counter-regulation of all three clusters indicated the involvement of novel viral regulators targeting these pathways. In addition, down-regulation of two clusters involved in cell-differentiation (rapid repression) and cell-cycle (delayed repression) was observed. Promoter analysis revealed all five clusters to be associated with distinct transcription factors, of which NF-κB and c-Myc were validated to precisely match the respective transcriptional changes observed in newly transcribed RNA. 4sU-tagging also allowed us to study the real-time kinetics of viral gene expression in the absence of any interfering virion-associated-RNA. Both qRT-PCR and next-generation sequencing demonstrated a sharp peak of viral gene expression during the first two hours of infection including transcription of immediate-early, early and even well characterized late genes. Interestingly, this was subject to rapid gene silencing by 5–6 hours post infection. Despite the rapid increase in viral DNA load during viral DNA replication, transcriptional activity of some viral genes remained remarkably constant until late-stage infection, or was subject to further continuous decline. In summary, this study pioneers real-time transcriptional analysis during a lytic herpesvirus infection and highlights numerous novel regulatory aspects of virus-host-cell interaction. Cytomegaloviruses are large DNA viruses, which establish life-long latent infections, leaving the infected individual at risk of reactivation and disease. Here, we applied 4-thiouridine-(4sU)-tagging of newly transcribed RNA to monitor the real-time kinetics of transcriptional activity of both cellular and viral genes during lytic murine CMV (MCMV) infection. We observed a cascade of MCMV-induced signaling events including a rapid inflammatory/interferon-response, a transient DNA-damage-response and a delayed ER-stress-response. All of these were heavily counter-regulated by viral gene expression. Besides dramatically increasing temporal resolution, our approach provides the unique opportunity to study viral transcriptional activity in absence of any interfering virion-associated-RNA. Virion-associated-RNA consists of transcripts that are unspecifically incorporated into the virus particles thereby resembling the cellular RNA profile of late stage infection. A clear picture of which viral genes are expressed, particularly at very early times of infection, could thus not be obtained. By overcoming this problem, we provide intriguing insights into the regulation of viral gene expression, namely 1) a peak of viral gene expression during the first two hours of infection including the expression of well-characterized late genes and 2) remarkably constant or even continuously declining expression of some viral genes despite the onset of rapid viral DNA replication.
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Affiliation(s)
- Lisa Marcinowski
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University, Munich, Germany
| | - Michael Lidschreiber
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University, Munich, Germany
| | - Lukas Windhager
- Institute for Informatics, Ludwig-Maximilians-University, Munich, Germany
| | - Martina Rieder
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University, Munich, Germany
| | - Jens B. Bosse
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Bernd Rädle
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University, Munich, Germany
| | - Thomas Bonfert
- Institute for Informatics, Ludwig-Maximilians-University, Munich, Germany
| | - Ildiko Györy
- School of Biomedical and Biological Sciences, Centre for Research in Translational Biomedicine, Plymouth University, Plymouth, United Kingdom
| | - Miranda de Graaf
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | | | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | | | - Ralf Zimmer
- Institute for Informatics, Ludwig-Maximilians-University, Munich, Germany
| | - Zsolt Ruzsics
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University, Munich, Germany
| | - Lars Dölken
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University, Munich, Germany
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
- * E-mail:
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20
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Niederberger T, Etzold S, Lidschreiber M, Maier KC, Martin DE, Fröhlich H, Cramer P, Tresch A. MC EMiNEM maps the interaction landscape of the Mediator. PLoS Comput Biol 2012; 8:e1002568. [PMID: 22737066 PMCID: PMC3380870 DOI: 10.1371/journal.pcbi.1002568] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 05/04/2012] [Indexed: 11/18/2022] Open
Abstract
The Mediator is a highly conserved, large multiprotein complex that is involved essentially in the regulation of eukaryotic mRNA transcription. It acts as a general transcription factor by integrating regulatory signals from gene-specific activators or repressors to the RNA Polymerase II. The internal network of interactions between Mediator subunits that conveys these signals is largely unknown. Here, we introduce MC EMiNEM, a novel method for the retrieval of functional dependencies between proteins that have pleiotropic effects on mRNA transcription. MC EMiNEM is based on Nested Effects Models (NEMs), a class of probabilistic graphical models that extends the idea of hierarchical clustering. It combines mode-hopping Monte Carlo (MC) sampling with an Expectation-Maximization (EM) algorithm for NEMs to increase sensitivity compared to existing methods. A meta-analysis of four Mediator perturbation studies in Saccharomyces cerevisiae, three of which are unpublished, provides new insight into the Mediator signaling network. In addition to the known modular organization of the Mediator subunits, MC EMiNEM reveals a hierarchical ordering of its internal information flow, which is putatively transmitted through structural changes within the complex. We identify the N-terminus of Med7 as a peripheral entity, entailing only local structural changes upon perturbation, while the C-terminus of Med7 and Med19 appear to play a central role. MC EMiNEM associates Mediator subunits to most directly affected genes, which, in conjunction with gene set enrichment analysis, allows us to construct an interaction map of Mediator subunits and transcription factors.
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Affiliation(s)
- Theresa Niederberger
- Gene Center Munich and Center for integrated Protein Science CiPSM, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Stefanie Etzold
- Gene Center Munich and Center for integrated Protein Science CiPSM, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Michael Lidschreiber
- Gene Center Munich and Center for integrated Protein Science CiPSM, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Kerstin C. Maier
- Gene Center Munich and Center for integrated Protein Science CiPSM, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Dietmar E. Martin
- Gene Center Munich and Center for integrated Protein Science CiPSM, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Holger Fröhlich
- Bonn-Aachen International Center for IT (B-IT) Algorithmic Bioinformatics, Rheinische Friedrich-Wilhelms-University Bonn, Bonn, Germany
| | - Patrick Cramer
- Gene Center Munich and Center for integrated Protein Science CiPSM, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Achim Tresch
- Gene Center Munich and Center for integrated Protein Science CiPSM, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
- * E-mail:
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