1
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Ohtsuka H, Ohara K, Shimasaki T, Hatta Y, Maekawa Y, Aiba H. A novel transcription factor Sdr1 involving sulfur depletion response in fission yeast. Genes Cells 2024; 29:667-680. [PMID: 39105351 DOI: 10.1111/gtc.13136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 08/07/2024]
Abstract
In the fission yeast Schizosaccharomyces pombe, the response to sulfur depletion has been less studied compared to the response to nitrogen depletion. Our study reveals that the fission yeast gene, SPCC417.09c, plays a significant role in the sulfur depletion response. This gene encodes a protein with a Zn2Cys6 fungal-type DNA-binding domain and a transcription factor domain, and we have named it sdr1+ (sulfur depletion response 1). Interestingly, while sulfur depletion typically induces autophagy akin to nitrogen depletion, we found that autophagy was not induced under sulfur depletion in the absence of sdr1+. This suggests that sdr1+ is necessary for the induction of autophagy under conditions of sulfur depletion. Although sdr1+ is not essential for the growth of fission yeast, its overexpression, driven by the nmt1 promoter, inhibits growth. This implies that Sdr1 may possess cell growth-inhibitory capabilities. In addition, our analysis of Δsdr1 cells revealed that sdr1+ also plays a role in regulating the expression of genes associated with the phosphate depletion response. In conclusion, our study introduces Sdr1 as a novel transcription factor that contributes to an appropriate cellular nutrient starvation response. It does so by inhibiting inappropriate cell growth and inducing autophagy in response to sulfur depletion.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Kotaro Ohara
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Yoshiko Hatta
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Yasukichi Maekawa
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
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2
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Cohen A, Lubenski L, Mouzon A, Kupiec M, Weisman R. TORC2 is required for the accumulation of γH2A in response to DNA damage. J Biol Chem 2024; 300:107531. [PMID: 38971312 DOI: 10.1016/j.jbc.2024.107531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 06/16/2024] [Accepted: 06/17/2024] [Indexed: 07/08/2024] Open
Abstract
TOR protein kinases serve as the catalytic subunit of the TORC1 and TORC2 complexes, which regulate cellular growth, proliferation, and survival. In the fission yeast, Schizosaccharomyces pombe, cells lacking TORC2 or its downstream kinase Gad8 (AKT or SGK1 in human cells) exhibit sensitivity to a wide range of stress conditions, including DNA damage stress. One of the first responses to DNA damage is the phosphorylation of C-terminal serine residues within histone H2AX in human cells (γH2AX), or histone H2A in yeast cells (γH2A). The kinases responsible for γH2A in S. pombe are the two DNA damage checkpoint kinases Rad3 and Tel1 (ATR and ATM, respectively, in human cells). Here we report that TORC2-Gad8 signaling is required for accumulation of γH2A in response to DNA damage and during quiescence. Using the TOR-specific inhibitor, Torin1, we demonstrate that the effect of TORC2 on γH2A in response to DNA damage is immediate, rather than adaptive. The lack of γH2A is restored by deletion mutations of transcription and chromatin modification factors, including loss of components of Paf1C, SAGA, Mediator, and the bromo-domain proteins Bdf1/Bdf2. Thus, we suggest that TORC2-Gad8 may affect the accumulation of γH2A by regulating chromatin structure and function.
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Affiliation(s)
- Adiel Cohen
- Department of Natural Sciences, The Open University of Israel, Ranana, Israel
| | - Lea Lubenski
- The Shmunis School of Biomedicine & Cancer Research, Tel Aviv University, Tel Aviv, Israel
| | - Ava Mouzon
- The Shmunis School of Biomedicine & Cancer Research, Tel Aviv University, Tel Aviv, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine & Cancer Research, Tel Aviv University, Tel Aviv, Israel
| | - Ronit Weisman
- Department of Natural Sciences, The Open University of Israel, Ranana, Israel.
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3
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Francette AM, Arndt KM. Multiple direct and indirect roles of Paf1C in elongation, splicing, and histone post-translational modifications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591159. [PMID: 38712269 PMCID: PMC11071476 DOI: 10.1101/2024.04.25.591159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Paf1C is a highly conserved protein complex with critical functions during eukaryotic transcription. Previous studies have shown that Paf1C is multi-functional, controlling specific aspects of transcription, ranging from RNAPII processivity to histone modifications. However, it is unclear how specific Paf1C subunits directly impact transcription and coupled processes. We have compared conditional depletion to steady-state deletion for each Paf1C subunit to determine the direct and indirect contributions to gene expression in Saccharomyces cerevisiae. Using nascent transcript sequencing, RNAPII profiling, and modeling of transcription elongation dynamics, we have demonstrated direct effects of Paf1C subunits on RNAPII processivity and elongation rate and indirect effects on transcript splicing and repression of antisense transcripts. Further, our results suggest that the direct transcriptional effects of Paf1C cannot be readily assigned to any particular histone modification. This work comprehensively analyzes both the immediate and extended roles of each Paf1C subunit in transcription elongation and transcript regulation.
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Affiliation(s)
- Alex M. Francette
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Karen M. Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
- Lead contact
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4
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Laurent M, Cordeddu L, Zahedi Y, Ekwall K. LEO1 Is Required for Efficient Entry into Quiescence, Control of H3K9 Methylation and Gene Expression in Human Fibroblasts. Biomolecules 2023; 13:1662. [PMID: 38002344 PMCID: PMC10668985 DOI: 10.3390/biom13111662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/08/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
(1) Background: The LEO1 (Left open reading frame 1) protein is a conserved subunit of the PAF1C complex (RNA polymerase II-associated factor 1 complex). PAF1C has well-established mechanistic functions in elongation of transcription and RNA processing. We previously showed, in fission yeast, that LEO1 controls histone H3K9 methylation levels by affecting the turnover of histone H3 in chromatin, and that it is essential for the proper regulation of gene expression during cellular quiescence. Human fibroblasts enter a reversible quiescence state upon serum deprivation in the growth media. Here we investigate the function of LEO1 in human fibroblasts. (2) Methods: We knocked out the LEO1 gene using CRISPR/Cas9 methodology in human fibroblasts and verified that the LEO1 protein was undetectable by Western blot. We characterized the phenotype of the ΔLEO1 knockout cells with FACS analysis and cell growth assays. We used RNA-sequencing using spike-in controls to measure gene expression and spike-in controlled ChIP-sequencing experiments to measure the histone modification H3K9me2 genome-wide. (3) Results: Gene expression levels are altered in quiescent cells, however factors controlling chromatin and gene expression changes in quiescent human cells are largely unknown. The ΔLEO1 knockout fibroblasts are viable but have reduced metabolic activity compared to wild-type cells. ΔLEO1 cells showed a slower entry into quiescence and a different morphology compared to wild-type cells. Gene expression was generally reduced in quiescent wild-type cells. The downregulated genes included genes involved in cell proliferation. A small number of genes were upregulated in quiescent wild-type cells including several genes involved in ERK1/ERK2 and Wnt signaling. In quiescent ΔLEO1 cells, many genes were mis-regulated compared to wild-type cells. This included genes involved in Calcium ion transport and cell morphogenesis. Finally, spike-in controlled ChIP-sequencing experiments demonstrated that the histone modification H3K9me2 levels are globally increased in quiescent ΔLEO1 cells. (4) Conclusions: Thus, LEO1 is important for proper entry into cellular quiescence, control of H3K9me2 levels, and gene expression in human fibroblasts.
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Affiliation(s)
| | | | | | - Karl Ekwall
- Department of Biosciences and Nutrition, Neo Building, Karolinska Institutet, SE-141 83 Huddinge, Sweden; (M.L.); (L.C.); (Y.Z.)
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5
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Dobbs OG, Wilson RHC, Newling K, Ainscough JFX, Coverley D. Epigenetic instability caused by absence of CIZ1 drives transformation during quiescence cycles. BMC Biol 2023; 21:175. [PMID: 37580709 PMCID: PMC10426085 DOI: 10.1186/s12915-023-01671-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/31/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Cip1-interacting zinc finger protein 1 (CIZ1) forms RNA-dependent protein assemblies that stabilise epigenetic state, notable at the inactive X chromosome in females. CIZ1 has been linked with a range of human cancers and in mice genetic deletion of CIZ1 manifests as hyperproliferative lymphoid lineages in females. This suggests that its role in maintenance of epigenetic stability is linked with disease. RESULTS Here, we show that male and female CIZ1-null primary murine fibroblasts have reduced H4K20me1 and that this compromises nuclear condensation on entry to quiescence. Global transcriptional repression remains intact in condensation-deficient CIZ1-null cells; however, a subset of genes linked with chromatin condensation and homology-directed DNA repair are perturbed. Failure to condense is phenotypically mimicked by manipulation of the H4K20me1 methyltransferase, SET8, in WT cells and partially reverted in CIZ1-null cells upon re-expression of CIZ1. Crucially, during exit from quiescence, nuclear decondensation remains active, so that repeated entry and exit cycles give rise to expanded nuclei susceptible to mechanical stress, DNA damage checkpoint activation, and downstream emergence of transformed proliferative colonies. CONCLUSIONS Our results demonstrate a role for CIZ1 in chromatin condensation on entry to quiescence and explore the consequences of this defect in CIZ1-null cells. Together, the data show that CIZ1's protection of the epigenome guards against genome instability during quiescence cycles. This identifies loss of CIZ1 as a potentially devastating vulnerability in cells that undergo cycles of quiescence entry and exit.
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Affiliation(s)
- Olivia G Dobbs
- Department of Biology, University of York, York, YO10 5DD, UK.
- York Biomedical Research Institute, University of York, York, UK.
| | - Rosemary H C Wilson
- Department of Biology, University of York, York, YO10 5DD, UK
- Exact Sciences Innovation, The Sherard Building, Oxford Science Park, Edmund Halley Rd, Oxford, OX4 4DQ, UK
| | - Katherine Newling
- Department of Biology, University of York, York, YO10 5DD, UK
- Genomics and Bioinformatics Laboratory, Bioscience Technology Facility, University of York, York, YO10 5DD, UK
| | | | - Dawn Coverley
- Department of Biology, University of York, York, YO10 5DD, UK
- York Biomedical Research Institute, University of York, York, UK
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6
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Zahedi Y, Zeng S, Ekwall K. An essential role for the Ino80 chromatin remodeling complex in regulation of gene expression during cellular quiescence. Chromosome Res 2023; 31:14. [PMID: 37043046 PMCID: PMC10097750 DOI: 10.1007/s10577-023-09723-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 03/15/2023] [Accepted: 03/31/2023] [Indexed: 04/13/2023]
Abstract
Cellular quiescence is an important physiological state both in unicellular and multicellular eukaryotes. Quiescent cells are halted for proliferation and stop the cell cycle at the G0 stage. Using fission yeast as a model organism, we have previously found that several subunits of a conserved chromatin remodeling complex, Ino80C (INOsitol requiring nucleosome remodeling factor), are required for survival in quiescence. Here, we demonstrate that Ino80C has a key function in the regulation of gene expression in G0 cells. We show that null mutants for two Ino80C subunits, Iec1 and Ies2, a putative subunit Arp42, a null mutant for the histone variant H2A.Z, and a null mutant for the Inositol kinase Asp1 have very similar phenotypes in quiescence. These mutants show reduced transcription genome-wide and specifically fail to activate 149 quiescence genes, of which many are localized to the subtelomeric regions. Using spike in normalized ChIP-seq experiments, we show that there is a global reduction of H2A.Z levels in quiescent wild-type cells but not in iec1∆ cells and that a subtelomeric chromosome boundary element is strongly affected by Ino80C. Based on these observations, we propose a model in which Ino80C is evicting H2A.Z from chromatin in quiescent cells, thereby inactivating the subtelomeric boundary element, leading to a reorganization of the chromosome structure and activation of genes required to survive in quiescence.
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Affiliation(s)
- Yasaman Zahedi
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo Building, 141 83, Huddinge, Sweden
| | - Shengyuan Zeng
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo Building, 141 83, Huddinge, Sweden
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo Building, 141 83, Huddinge, Sweden.
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7
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Yaseen I, White SA, Torres-Garcia S, Spanos C, Lafos M, Gaberdiel E, Yeboah R, El Karoui M, Rappsilber J, Pidoux AL, Allshire RC. Proteasome-dependent truncation of the negative heterochromatin regulator Epe1 mediates antifungal resistance. Nat Struct Mol Biol 2022; 29:745-758. [PMID: 35879419 PMCID: PMC7613290 DOI: 10.1038/s41594-022-00801-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 06/06/2022] [Indexed: 12/03/2022]
Abstract
Epe1 histone demethylase restricts H3K9-methylation-dependent heterochromatin, preventing it from spreading over, and silencing, gene-containing regions in fission yeast. External stress induces an adaptive response allowing heterochromatin island formation that confers resistance on surviving wild-type lineages. Here we investigate the mechanism by which Epe1 is regulated in response to stress. Exposure to caffeine or antifungals results in Epe1 ubiquitylation and proteasome-dependent removal of the N-terminal 150 residues from Epe1, generating truncated Epe1 (tEpe1) which accumulates in the cytoplasm. Constitutive tEpe1 expression increases H3K9 methylation over several chromosomal regions, reducing expression of underlying genes and enhancing resistance. Reciprocally, constitutive non-cleavable Epe1 expression decreases resistance. tEpe1-mediated resistance requires a functional JmjC demethylase domain. Moreover, caffeine-induced Epe1-to-tEpe1 cleavage is dependent on an intact cell integrity MAP kinase stress signaling pathway, mutations in which alter resistance. Thus, environmental changes elicit a mechanism that curtails the function of this key epigenetic modifier, allowing heterochromatin to reprogram gene expression, thereby bestowing resistance to some cells within a population. H3K9me-heterochromatin components are conserved in human and crop-plant fungal pathogens for which a limited number of antifungals exist. Our findings reveal how transient heterochromatin-dependent antifungal resistant epimutations develop and thus inform on how they might be countered.
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Affiliation(s)
- Imtiyaz Yaseen
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- CSIR Indian Institute of Integrative Medicine, Jammu, India
| | - Sharon A White
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Sito Torres-Garcia
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Christos Spanos
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Marcel Lafos
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Elisabeth Gaberdiel
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Rebecca Yeboah
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Meriem El Karoui
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- SynthSys, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Alison L Pidoux
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Robin C Allshire
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK.
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK.
- SynthSys, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK.
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8
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Cohen A, Pataki E, Kupiec M, Weisman R. TOR complex 2 contributes to regulation of gene expression via inhibiting Gcn5 recruitment to subtelomeric and DNA replication stress genes. PLoS Genet 2022; 18:e1010061. [PMID: 35157728 PMCID: PMC8880919 DOI: 10.1371/journal.pgen.1010061] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 02/25/2022] [Accepted: 01/28/2022] [Indexed: 11/18/2022] Open
Abstract
The fission yeast TOR complex 2 (TORC2) is required for gene silencing at subtelomeric regions and for the induction of gene transcription in response to DNA replication stress. Thus, TORC2 affects transcription regulation both negatively and positively. Whether these two TORC2-dependent functions share a common molecular mechanism is currently unknown. Here, we show that Gad8 physically interacts with proteins that regulate transcription, including subunits of the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex and the BET bromodomain protein Bdf2. We demonstrate that in the absence of TORC2, Gcn5, the histone acetyltransferase subunit of SAGA, accumulates at subtelomeric genes and at non-induced promoters of DNA replication genes. Remarkably, the loss of Gcn5 in TORC2 mutant cells restores gene silencing as well as transcriptional induction in response to DNA replication stress. Loss of Bdf2 alleviates excess of Gcn5 binding in TORC2 mutant cells and also rescues the aberrant regulation of transcription in these cells. Furthermore, the loss of either SAGA or Bdf2 suppresses the sensitivity of TORC2 mutant cells to a variety of stresses, including DNA replication, DNA damage, temperature and nutrient stresses. We suggest a role of TORC2 in transcriptional regulation that is critical for gene silencing and gene induction in response to stress and involves the binding of Gcn5 to the chromatin. A fundamental characteristic of signaling pathways is their role in the regulation of gene expression. Target of rapamycin (TOR), an atypical protein kinase, is a component of two highly conserved TOR complexes: TORC1 and TORC2. These complexes affect nuclear functions through their activity in the cytoplasm as well as directly, through nuclear TOR pools. We previously showed that in fission yeast, TORC2 and its downstream substrate Gad8 associate with the chromatin fraction. We have also demonstrated that TORC2-Gad8 is required for gene silencing and transcriptional induction in response to stresses. Here, we demonstrate that Gad8 physically associates with proteins of the transcriptional machinery. We found that the loss of two positive transcriptional regulators, the SAGA complex and the bromodomain protein Bdf2, restored gene silencing as well as stress-induced transcriptional induction in TORC2 mutant cells. Our data suggests that TORC2-Gad8 contributes to gene regulation through a mechanism involving the inhibition of the accumulation of Gcn5 at the chromatin. These findings suggest a novel and possibly conserved functional relationship between TORC2, Gcn5 and Bdf2. These proteins and protein complexes are key targets in cancer therapies, thus, deciphering their functional relationship may be valuable for combination therapy in personalized medicine.
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Affiliation(s)
- Adiel Cohen
- Department of Natural and Life Sciences, The Open University of Israel, Ra’anana, Israel
| | - Emese Pataki
- Department of Natural and Life Sciences, The Open University of Israel, Ra’anana, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine & Cancer Research, Tel Aviv University, Tel Aviv, Israel
| | - Ronit Weisman
- Department of Natural and Life Sciences, The Open University of Israel, Ra’anana, Israel
- * E-mail:
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9
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Bonitto K, Sarathy K, Atai K, Mitra M, Coller HA. Is There a Histone Code for Cellular Quiescence? Front Cell Dev Biol 2021; 9:739780. [PMID: 34778253 PMCID: PMC8586460 DOI: 10.3389/fcell.2021.739780] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/17/2021] [Indexed: 12/14/2022] Open
Abstract
Many of the cells in our bodies are quiescent, that is, temporarily not dividing. Under certain physiological conditions such as during tissue repair and maintenance, quiescent cells receive the appropriate stimulus and are induced to enter the cell cycle. The ability of cells to successfully transition into and out of a quiescent state is crucial for many biological processes including wound healing, stem cell maintenance, and immunological responses. Across species and tissues, transcriptional, epigenetic, and chromosomal changes associated with the transition between proliferation and quiescence have been analyzed, and some consistent changes associated with quiescence have been identified. Histone modifications have been shown to play a role in chromatin packing and accessibility, nucleosome mobility, gene expression, and chromosome arrangement. In this review, we critically evaluate the role of different histone marks in these processes during quiescence entry and exit. We consider different model systems for quiescence, each of the most frequently monitored candidate histone marks, and the role of their writers, erasers and readers. We highlight data that support these marks contributing to the changes observed with quiescence. We specifically ask whether there is a quiescence histone “code,” a mechanism whereby the language encoded by specific combinations of histone marks is read and relayed downstream to modulate cell state and function. We conclude by highlighting emerging technologies that can be applied to gain greater insight into the role of a histone code for quiescence.
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Affiliation(s)
- Kenya Bonitto
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kirthana Sarathy
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kaiser Atai
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Mithun Mitra
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Hilary A Coller
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
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10
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Tiwari V, Kulikowicz T, Wilson DM, Bohr VA. LEO1 is a partner for Cockayne syndrome protein B (CSB) in response to transcription-blocking DNA damage. Nucleic Acids Res 2021; 49:6331-6346. [PMID: 34096589 DOI: 10.1093/nar/gkab458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/04/2021] [Accepted: 06/03/2021] [Indexed: 12/25/2022] Open
Abstract
Cockayne syndrome (CS) is an autosomal recessive genetic disorder characterized by photosensitivity, developmental defects, neurological abnormalities, and premature aging. Mutations in CSA (ERCC8), CSB (ERCC6), XPB, XPD, XPG, XPF (ERCC4) and ERCC1 can give rise to clinical phenotypes resembling classic CS. Using a yeast two-hybrid (Y2H) screening approach, we identified LEO1 (Phe381-Ser568 region) as an interacting protein partner of full-length and C-terminal (Pro1010-Cys1493) CSB in two independent screens. LEO1 is a member of the RNA polymerase associated factor 1 complex (PAF1C) with roles in transcription elongation and chromatin modification. Supportive of the Y2H results, purified, recombinant LEO1 and CSB directly interact in vitro, and the two proteins exist in a common complex within human cells. In addition, fluorescently tagged LEO1 and CSB are both recruited to localized DNA damage sites in human cells. Cell fractionation experiments revealed a transcription-dependent, coordinated association of LEO1 and CSB to chromatin following either UVC irradiation or cisplatin treatment of HEK293T cells, whereas the response to menadione was distinct, suggesting that this collaboration occurs mainly in the context of bulky transcription-blocking lesions. Consistent with a coordinated interaction in DNA repair, LEO1 knockdown or knockout resulted in reduced CSB recruitment to chromatin, increased sensitivity to UVC light and cisplatin damage, and reduced RNA synthesis recovery and slower excision of cyclobutane pyrimidine dimers following UVC irradiation; the absence of CSB resulted in diminished LEO1 recruitment. Our data indicate a reciprocal communication between CSB and LEO1 in the context of transcription-associated DNA repair and RNA transcription recovery.
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Affiliation(s)
- Vinod Tiwari
- Section on DNA repair, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Tomasz Kulikowicz
- Section on DNA repair, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - David M Wilson
- Hasselt University, Biomedical Research Institute, 3590 Diepenbeek, Belgium
| | - Vilhelm A Bohr
- Section on DNA repair, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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11
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Francette AM, Tripplehorn SA, Arndt KM. The Paf1 Complex: A Keystone of Nuclear Regulation Operating at the Interface of Transcription and Chromatin. J Mol Biol 2021; 433:166979. [PMID: 33811920 PMCID: PMC8184591 DOI: 10.1016/j.jmb.2021.166979] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 12/14/2022]
Abstract
The regulation of transcription by RNA polymerase II is closely intertwined with the regulation of chromatin structure. A host of proteins required for the disassembly, reassembly, and modification of nucleosomes interacts with Pol II to aid its movement and counteract its disruptive effects on chromatin. The highly conserved Polymerase Associated Factor 1 Complex, Paf1C, travels with Pol II and exerts control over transcription elongation and chromatin structure, while broadly impacting the transcriptome in both single cell and multicellular eukaryotes. Recent studies have yielded exciting new insights into the mechanisms by which Paf1C regulates transcription elongation, epigenetic modifications, and post-transcriptional steps in eukaryotic gene expression. Importantly, these functional studies are now supported by an extensive foundation of high-resolution structural information, providing intimate views of Paf1C and its integration into the larger Pol II elongation complex. As a global regulatory factor operating at the interface between chromatin and transcription, the impact of Paf1C is broad and its influence reverberates into other domains of nuclear regulation, including genome stability, telomere maintenance, and DNA replication.
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Affiliation(s)
- Alex M Francette
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Sarah A Tripplehorn
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Karen M Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States.
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12
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Halova L, Cobley D, Franz-Wachtel M, Wang T, Morrison KR, Krug K, Nalpas N, Maček B, Hagan IM, Humphrey SJ, Petersen J. A TOR (target of rapamycin) and nutritional phosphoproteome of fission yeast reveals novel targets in networks conserved in humans. Open Biol 2021; 11:200405. [PMID: 33823663 PMCID: PMC8025308 DOI: 10.1098/rsob.200405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/05/2021] [Indexed: 12/21/2022] Open
Abstract
Fluctuations in TOR, AMPK and MAP-kinase signalling maintain cellular homeostasis and coordinate growth and division with environmental context. We have applied quantitative, SILAC mass spectrometry to map TOR and nutrient-controlled signalling in the fission yeast Schizosaccharomyces pombe. Phosphorylation levels at more than 1000 sites were altered following nitrogen stress or Torin1 inhibition of the TORC1 and TORC2 networks that comprise TOR signalling. One hundred and thirty of these sites were regulated by both perturbations, and the majority of these (119) new targets have not previously been linked to either nutritional or TOR control in either yeasts or humans. Elimination of AMPK inhibition of TORC1, by removal of AMPKα (ssp2::ura4+), identified phosphosites where nitrogen stress-induced changes were independent of TOR control. Using a yeast strain with an ATP analogue-sensitized Cdc2 kinase, we excluded sites that were changed as an indirect consequence of mitotic control modulation by nitrogen stress or TOR signalling. Nutritional control of gene expression was reflected in multiple targets in RNA metabolism, while significant modulation of actin cytoskeletal components points to adaptations in morphogenesis and cell integrity networks. Reduced phosphorylation of the MAPKK Byr1, at a site whose human equivalent controls docking between MEK and ERK, prevented sexual differentiation when resources were sparse but not eliminated.
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Affiliation(s)
- Lenka Halova
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
- Cancer Research UK Manchester Institute, Alderley Park, Macclesfield SK10 4TG, UK
| | - David Cobley
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Mirita Franz-Wachtel
- Proteome Center Tuebingen, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | - Tingting Wang
- Flinders Health and Medical Research Institute, Flinders Centre for Innovation in Cancer, Flinders University, Adelaide, South Australia 5042, Australia
| | - Kaitlin R. Morrison
- Flinders Health and Medical Research Institute, Flinders Centre for Innovation in Cancer, Flinders University, Adelaide, South Australia 5042, Australia
| | - Karsten Krug
- Proteome Center Tuebingen, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | - Nicolas Nalpas
- Proteome Center Tuebingen, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | - Boris Maček
- Proteome Center Tuebingen, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | - Iain M. Hagan
- Cancer Research UK Manchester Institute, Alderley Park, Macclesfield SK10 4TG, UK
| | - Sean J. Humphrey
- Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Camperdown, New South Wales, Australia
| | - Janni Petersen
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
- Flinders Health and Medical Research Institute, Flinders Centre for Innovation in Cancer, Flinders University, Adelaide, South Australia 5042, Australia
- Nutrition and Metabolism, South Australia Health and Medical Research Institute, North Terrace, Adelaide, South Australia 5000, Australia
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13
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High-Throughput Flow Cytometry Combined with Genetic Analysis Brings New Insights into the Understanding of Chromatin Regulation of Cellular Quiescence. Int J Mol Sci 2020; 21:ijms21239022. [PMID: 33260998 PMCID: PMC7729564 DOI: 10.3390/ijms21239022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 11/21/2022] Open
Abstract
Cellular quiescence is a reversible differentiation state when cells are changing the gene expression program to reduce metabolic functions and adapt to a new cellular environment. When fission yeast cells are deprived of nitrogen in the absence of any mating partner, cells can reversibly arrest in a differentiated G0-like cellular state, called quiescence. This change is accompanied by a marked alteration of nuclear organization and a global reduction of transcription. Using high-throughput flow cytometry combined with genetic analysis, we describe the results of a comprehensive screen for genes encoding chromatin components and regulators that are required for the entry and the maintenance of cellular quiescence. We show that the histone acetylase and deacetylase complexes, SAGA and Rpd3, have key roles both for G0 entry and survival during quiescence. We reveal a novel function for the Ino80 nucleosome remodeling complex in cellular quiescence. Finally, we demonstrate that components of the MRN complex, Rad3, the nonhomologous end-joining, and nucleotide excision DNA repair pathways are essential for viability in G0.
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14
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Ohtsuka H, Shimasaki T, Aiba H. Genes affecting the extension of chronological lifespan in Schizosaccharomyces pombe (fission yeast). Mol Microbiol 2020; 115:623-642. [PMID: 33064911 PMCID: PMC8246873 DOI: 10.1111/mmi.14627] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/17/2020] [Accepted: 10/11/2020] [Indexed: 02/06/2023]
Abstract
So far, more than 70 genes involved in the chronological lifespan (CLS) of Schizosaccharomyces pombe (fission yeast) have been reported. In this mini‐review, we arrange and summarize these genes based on the reported genetic interactions between them and the physical interactions between their products. We describe the signal transduction pathways that affect CLS in S. pombe: target of rapamycin complex 1, cAMP‐dependent protein kinase, Sty1, and Pmk1 pathways have important functions in the regulation of CLS extension. Furthermore, the Php transcription complex, Ecl1 family proteins, cyclin Clg1, and the cyclin‐dependent kinase Pef1 are important for the regulation of CLS extension in S. pombe. Most of the known genes involved in CLS extension are related to these pathways and genes. In this review, we focus on the individual genes regulating CLS extension in S. pombe and discuss the interactions among them.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
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15
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Pataki E, Simhaev L, Engel H, Cohen A, Kupiec M, Weisman R. TOR Complex 2- independent mutations in the regulatory PIF pocket of Gad8AKT1/SGK1 define separate branches of the stress response mechanisms in fission yeast. PLoS Genet 2020; 16:e1009196. [PMID: 33137119 PMCID: PMC7660925 DOI: 10.1371/journal.pgen.1009196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/12/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
The Target of rapamycin (TOR) protein kinase forms part of TOR complex 1 (TORC1) and TOR complex 2 (TORC2), two multi-subunit protein complexes that regulate growth, proliferation, survival and developmental processes by phosphorylation and activation of AGC-family kinases. In the fission yeast, Schizosaccharomyces pombe, TORC2 and its target, the AGC kinase Gad8 (an orthologue of human AKT or SGK1) are required for viability under stress conditions and for developmental processes in response to starvation cues. In this study, we describe the isolation of gad8 mutant alleles that bypass the requirement for TORC2 and reveal a separation of function of TORC2 and Gad8 under stress conditions. In particular, osmotic and nutritional stress responses appear to form a separate branch from genotoxic stress responses downstream of TORC2-Gad8. Interestingly, TORC2-independent mutations map into the regulatory PIF pocket of Gad8, a highly conserved motif in AGC kinases that regulates substrate binding in PDK1 (phosphoinositide dependent kinase-1) and kinase activity in several AGC kinases. Gad8 activation is thought to require a two-step mechanism, in which phosphorylation by TORC2 allows further phosphorylation and activation by Ksg1 (an orthologue of PDK1). We focus on the Gad8-K263C mutation and demonstrate that it renders the Gad8 kinase activity independent of TORC2 in vitro and independent of the phosphorylation sites of TORC2 in vivo. Molecular dynamics simulations of Gad8-K263C revealed abnormal high flexibility at T387, the phosphorylation site for Ksg1, suggesting a mechanism for the TORC2-independent Gad8 activity. Significantly, the K263 residue is highly conserved in the family of AGC-kinases, which may suggest a general way of keeping their activity in check when acting downstream of TOR complexes. Protein kinases catalyze the transfer of phosphate from high-energy, phosphate-donating molecules, such as ATP, to their substrates. This process is pivotal for regulation of almost any aspect of cellular biology. Many human diseases are associated with aberrant functions of protein kinases due to mutations. Accordingly, there is a growing number of kinase inhibitors that have been approved for clinical use. A better understanding of how protein kinases become active and how their activity is relayed to regulate their cellular functions is much needed for rational design of kinase inhibitors and for their optimal use in the clinic. The AGC-family of protein kinases play key roles in regulating cellular growth, proliferation and survival. In human cells, as well as in the fission yeast, our cellular model system, a subgroup of the AGC kinases is activated by the TOR protein kinases. Here we report the isolation of mutations in the AGC kinase Gad8 (AKT or SGK1 in human) that bypass the requirement for activation by TOR. Analyses of how these mutations affect cellular growth revealed separate branches of stress response mechanisms downstream of Gad8, while computer simulation methods suggested a molecular mechanism that keeps the activity of Gad8 in check.
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Affiliation(s)
- Emese Pataki
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana, Israel
| | - Luba Simhaev
- Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv, Israel
| | - Hamutal Engel
- Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv, Israel
| | - Adiel Cohen
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine & Cancer Research, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
| | - Ronit Weisman
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana, Israel
- * E-mail:
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16
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Coulon S, Vaurs M. Telomeric Transcription and Telomere Rearrangements in Quiescent Cells. J Mol Biol 2020; 432:4220-4231. [PMID: 32061930 DOI: 10.1016/j.jmb.2020.01.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 02/07/2023]
Abstract
Despite the condensed nature of terminal sequences, the telomeres are transcribed into a group of noncoding RNAs, including the TElomeric Repeat-containing RNA (TERRA). Since the discovery of TERRA, its evolutionary conserved function has been confirmed, and its involvement in telomere length regulation, heterochromatin establishment, and telomere recombination has been demonstrated. We previously reported that TERRA is upregulated in quiescent fission yeast cells, although the global transcription is highly reduced. Elevated telomeric transcription was also detected when telomeres detach from the nuclear periphery. These intriguing observations unveil unexpected facets of telomeric transcription in arrested cells. In this review, we present the different aspects of TERRA transcription during quiescence and discuss their implications for telomere maintenance and cell fate.
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Affiliation(s)
- Stéphane Coulon
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue contre le Cancer, Marseille, F-13009, France.
| | - Mélina Vaurs
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue contre le Cancer, Marseille, F-13009, France
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17
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Laribee RN, Weisman R. Nuclear Functions of TOR: Impact on Transcription and the Epigenome. Genes (Basel) 2020; 11:E641. [PMID: 32532005 PMCID: PMC7349558 DOI: 10.3390/genes11060641] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/04/2020] [Accepted: 06/09/2020] [Indexed: 12/15/2022] Open
Abstract
The target of rapamycin (TOR) protein kinase is at the core of growth factor- and nutrient-dependent signaling pathways that are well-known for their regulation of metabolism, growth, and proliferation. However, TOR is also involved in the regulation of gene expression, genomic and epigenomic stability. TOR affects nuclear functions indirectly through its activity in the cytoplasm, but also directly through active nuclear TOR pools. The mechanisms by which TOR regulates its nuclear functions are less well-understood compared with its cytoplasmic activities. TOR is an important pharmacological target for several diseases, including cancer, metabolic and neurological disorders. Thus, studies of the nuclear functions of TOR are important for our understanding of basic biological processes, as well as for clinical implications.
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Affiliation(s)
- R. Nicholas Laribee
- Department of Pathology and Laboratory Medicine, College of Medicine and Center for Cancer Research, University of Tennessee Health Science Center, 19 South Manassas, Cancer Research Building Rm 318, Memphis, TN 38163, USA
| | - Ronit Weisman
- Department of Natural and Life Sciences, The Open University of Israel, University Road 1, Ra’anana 4353701, Israel
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18
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Maestroni L, Reyes C, Vaurs M, Gachet Y, Tournier S, Géli V, Coulon S. Nuclear envelope attachment of telomeres limits TERRA and telomeric rearrangements in quiescent fission yeast cells. Nucleic Acids Res 2020; 48:3029-3041. [PMID: 31980821 PMCID: PMC7102995 DOI: 10.1093/nar/gkaa043] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 01/13/2020] [Accepted: 01/16/2020] [Indexed: 11/12/2022] Open
Abstract
Telomere anchoring to nuclear envelope (NE) is a key feature of nuclear genome architecture. Peripheral localization of telomeres is important for chromatin silencing, telomere replication and for the control of inappropriate recombination. Here, we report that fission yeast quiescent cells harbor predominantly a single telomeric cluster anchored to the NE. Telomere cluster association to the NE relies on Rap1-Bqt4 interaction, which is impacted by the length of telomeric sequences. In quiescent cells, reducing telomere length or deleting bqt4, both result in an increase in transcription of the telomeric repeat-containing RNA (TERRA). In the absence of Bqt4, telomere shortening leads to deep increase in TERRA level and the concomitant formation of subtelomeric rearrangements (STEEx) that accumulate massively in quiescent cells. Taken together, our data demonstrate that Rap1-Bqt4-dependent telomere association to NE preserves telomere integrity in post-mitotic cells, preventing telomeric transcription and recombination. This defines the nuclear periphery as an area where recombination is restricted, creating a safe zone for telomeres of post-mitotic cells.
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Affiliation(s)
- Laetitia Maestroni
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe labellisée Ligue contre le Cancer, France
| | - Céline Reyes
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31062 Toulouse Cedex, France
| | - Mélina Vaurs
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe labellisée Ligue contre le Cancer, France
| | - Yannick Gachet
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31062 Toulouse Cedex, France
| | - Sylvie Tournier
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31062 Toulouse Cedex, France
| | - Vincent Géli
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe labellisée Ligue contre le Cancer, France
| | - Stéphane Coulon
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe labellisée Ligue contre le Cancer, France
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19
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Hocher A, Taddei A. Subtelomeres as Specialized Chromatin Domains. Bioessays 2020; 42:e1900205. [PMID: 32181520 DOI: 10.1002/bies.201900205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/19/2020] [Indexed: 12/26/2022]
Abstract
Specificities associated with chromosomal linearity are not restricted to telomeres. Here, recent results obtained on fission and budding yeast are summarized and an attempt is made to define subtelomeres using chromatin features extending beyond the heterochromatin emanating from telomeres. Subtelomeres, the chromosome domains adjacent to telomeres, differ from the rest of the genome by their gene content, rapid evolution, and chromatin features that together contribute to organism adaptation. However, current definitions of subtelomeres are generally based on synteny and are largely gene-centered. Taking into consideration both the peculiar gene content and dynamics as well as the chromatin properties of those domains, it is discussed how chromatin features can contribute to subtelomeric properties and functions, and play a pivotal role in the emergence of subtelomeres.
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Affiliation(s)
- Antoine Hocher
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Angela Taddei
- Institut Curie, PSL Research University, CNRS, UMR3664, Paris, F-75005, France.,Sorbonne Université, UPMC University Paris 06, CNRS, UMR3664, Paris, F-75005, France
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