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Stixová L, Tichý V, Bártová E. RNA-related DNA damage and repair: The role of N7-methylguanosine in the cell nucleus exposed to UV light. Heliyon 2024; 10:e25599. [PMID: 38370261 PMCID: PMC10869776 DOI: 10.1016/j.heliyon.2024.e25599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/20/2024] Open
Abstract
Background Chemical modifications in mRNAs, tRNAs, rRNAs, and non-coding RNAs stabilize these nucleic acids and regulate their function. In addition to regulating the translation of genetic information from mRNA to proteins, it has been revealed that modifications in RNAs regulate repair processes in the genome. Methods Using local laser microirradiation, confocal microscopy, dot blots, and mass spectrometry we studied the role of N7-methylguanosine (m7G), which is co-transcriptionally installed in RNA. Results Here, we show that after UVC and UVA irradiation, the level of m7G RNA is increased initially in the cytoplasm, and after local laser microirradiation, m7G RNA is highly abundant in UVA-damaged chromatin. This process is poly(ADP-ribose) polymerase (PARP)-dependent, but not accompanied by changes in the level of m7G-writers, including methyltransferases RNMT, METTL1, and WBSCR22. We also observed that METTL1 deficiency does not affect the recruitment of m7G RNA to microirradiated chromatin. Analyzing the levels of mRNA, let-7e, and miR-203a in both the cytoplasm and the cell nucleus, we revealed that UVC irradiation changed the level of mRNA, and significantly increased the pool of both let-7e and miR-203a, which correlated with radiation-induced m7G RNA increase in the cytoplasm. Conclusions Irradiation by UV light increases the m7G RNA pool in the cytoplasm and in the microirradiated genome. Thus, epigenetically modified RNAslikely contribute to DNA damage responses or m7G signals the presence of RNA damage.
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Affiliation(s)
- Lenka Stixová
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, Czech Republic
| | - Vlastimil Tichý
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, Czech Republic
| | - Eva Bártová
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, Czech Republic
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Svobodová Kovaříková A, Stixová L, Kovařík A, Bártová E. PARP-dependent and NAT10-independent acetylation of N4-cytidine in RNA appears in UV-damaged chromatin. Epigenetics Chromatin 2023; 16:26. [PMID: 37322549 DOI: 10.1186/s13072-023-00501-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 06/06/2023] [Indexed: 06/17/2023] Open
Abstract
RNA modifications have been known for many years, but their function has not been fully elucidated yet. For instance, the regulatory role of acetylation on N4-cytidine (ac4C) in RNA can be explored not only in terms of RNA stability and mRNA translation but also in DNA repair. Here, we observe a high level of ac4C RNA at DNA lesions in interphase cells and irradiated cells in telophase. Ac4C RNA appears in the damaged genome from 2 to 45 min after microirradiation. However, RNA cytidine acetyltransferase NAT10 did not accumulate to damaged sites, and NAT10 depletion did not affect the pronounced recruitment of ac4C RNA to DNA lesions. This process was not dependent on the G1, S, and G2 cell cycle phases. In addition, we observed that the PARP inhibitor, olaparib, prevents the recruitment of ac4C RNA to damaged chromatin. Our data imply that the acetylation of N4-cytidine, especially in small RNAs, has an important role in mediating DNA damage repair. Ac4C RNA likely causes de-condensation of chromatin in the vicinity of DNA lesions, making it accessible for other DNA repair factors involved in the DNA damage response. Alternatively, RNA modifications, including ac4C, could be direct markers of damaged RNAs.
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Affiliation(s)
- Alena Svobodová Kovaříková
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, Czech Republic
| | - Lenka Stixová
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, Czech Republic
| | - Aleš Kovařík
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, Czech Republic
| | - Eva Bártová
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, Czech Republic.
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Legartová S, Svobodová Kovaříková A, Běhalová Suchánková J, Polášek-Sedláčková H, Bártová E. Early recruitment of PARP-dependent m 8A RNA methylation at DNA lesions is subsequently accompanied by active DNA demethylation. RNA Biol 2022; 19:1153-1171. [PMID: 36382943 PMCID: PMC9673957 DOI: 10.1080/15476286.2022.2139109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
RNA methylation, especially 6-methyladenosine (m6A)-modified RNAs, plays a specific role in DNA damage response (DDR). Here, we also observe that RNA modified at 8-methyladenosine (m8A) is recruited to UVA-damaged chromatin immediately after microirradiation. Interestingly, the level of m8A RNA at genomic lesions was reduced after inhibition of histone deacetylases and DNA methyltransferases. It appears in later phases of DNA damage response, accompanied by active DNA demethylation. Also, PARP inhibitor (PARPi), Olaparib, prevented adenosine methylation at microirradiated chromatin. PARPi abrogated not only m6A and m8A RNA positivity at genomic lesions, but also XRCC1, the factor of base excision repair (BER), did not recognize lesions in DNA. To this effect, Olaparib enhanced the genome-wide level of γH2AX. This histone modification interacted with m8A RNAs to a similar extent as m8A RNAs with DNA. Pronounced interaction properties we did not observe for m6A RNAs and DNA; however, m6A RNA interacted with XRCC1 with the highest efficiency, especially in microirradiated cells. Together, we show that the recruitment of m6A RNA and m8A RNA to DNA lesions is PARP dependent. We suggest that modified RNAs likely play a role in the BER mechanism accompanied by active DNA demethylation. In this process, γH2AX stabilizes m6A/m8A-positive RNA-DNA hybrid loops via its interaction with m8A RNAs. R-loops could represent basic three-stranded structures recognized by PARP-dependent non-canonical m6A/m8A-mediated DNA repair pathway.
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Affiliation(s)
- Soňa Legartová
- Department of Cell Biology and Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Alena Svobodová Kovaříková
- Department of Cell Biology and Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Jana Běhalová Suchánková
- Department of Cell Biology and Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Hana Polášek-Sedláčková
- Department of Cell Biology and Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Eva Bártová
- Department of Cell Biology and Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic,CONTACT Eva Bártová Department of Cell Biology and Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
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Legartová S, Fagherazzi P, Stixová L, Kovařík A, Raška I, Bártová E. The SC-35 Splicing Factor Interacts with RNA Pol II and A-Type Lamin Depletion Weakens This Interaction. Cells 2021; 10:cells10020297. [PMID: 33535591 PMCID: PMC7912905 DOI: 10.3390/cells10020297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/22/2021] [Accepted: 01/28/2021] [Indexed: 11/17/2022] Open
Abstract
The essential components of splicing are the splicing factors accumulated in nuclear speckles; thus, we studied how DNA damaging agents and A-type lamin depletion affect the properties of these regions, positive on the SC-35 protein. We observed that inhibitor of PARP (poly (ADP-ribose) polymerase), and more pronouncedly inhibitors of RNA polymerases, caused DNA damage and increased the SC-35 protein level. Interestingly, nuclear blebs, induced by PARP inhibitor and observed in A-type lamin-depleted or senescent cells, were positive on both the SC-35 protein and another component of the spliceosome, SRRM2. In the interphase cell nuclei, SC-35 interacted with the phosphorylated form of RNAP II, which was A-type lamin-dependent. In mitotic cells, especially in telophase, the SC-35 protein formed a well-visible ring in the cytoplasmic fraction and colocalized with β-catenin, associated with the plasma membrane. The antibody against the SRRM2 protein showed that nuclear speckles are already established in the cytoplasm of the late telophase and at the stage of early cytokinesis. In addition, we observed the occurrence of splicing factors in the nuclear blebs and micronuclei, which are also sites of both transcription and splicing. This conclusion supports the fact that splicing proceeds transcriptionally. According to our data, this process is A-type lamin-dependent. Lamin depletion also reduces the interaction between SC-35 and β-catenin in mitotic cells.
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Affiliation(s)
- Soňa Legartová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic; (S.L.); (P.F.); (L.S.); (A.K.)
| | - Paolo Fagherazzi
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic; (S.L.); (P.F.); (L.S.); (A.K.)
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Lenka Stixová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic; (S.L.); (P.F.); (L.S.); (A.K.)
| | - Aleš Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic; (S.L.); (P.F.); (L.S.); (A.K.)
| | - Ivan Raška
- 1st Faculty of Medicine, Charles University, Albertov 4, 128 00 Praha, Czech Republic;
| | - Eva Bártová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic; (S.L.); (P.F.); (L.S.); (A.K.)
- Correspondence:
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N 6-Adenosine Methylation in RNA and a Reduced m 3G/TMG Level in Non-Coding RNAs Appear at Microirradiation-Induced DNA Lesions. Cells 2020; 9:cells9020360. [PMID: 32033081 PMCID: PMC7072662 DOI: 10.3390/cells9020360] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/28/2020] [Accepted: 01/30/2020] [Indexed: 12/12/2022] Open
Abstract
The DNA damage response is mediated by both DNA repair proteins and epigenetic markers. Here, we observe that N6-methyladenosine (m6A), a mark of the epitranscriptome, was common in RNAs accumulated at UV-damaged chromatin; however, inhibitors of RNA polymerases I and II did not affect the m6A RNA level at the irradiated genomic regions. After genome injury, m6A RNAs either diffused to the damaged chromatin or appeared at the lesions enzymatically. DNA damage did not change the levels of METTL3 and METTL14 methyltransferases. In a subset of irradiated cells, only the METTL16 enzyme, responsible for m6A in non-coding RNAs as well as for splicing regulation, was recruited to microirradiated sites. Importantly, the levels of the studied splicing factors were not changed by UVA light. Overall, if the appearance of m6A RNAs at DNA lesions is regulated enzymatically, this process must be mediated via the coregulatory function of METTL-like enzymes. This event is additionally accompanied by radiation-induced depletion of 2,2,7-methylguanosine (m3G/TMG) in RNA. Moreover, UV-irradiation also decreases the global cellular level of N1-methyladenosine (m1A) in RNAs. Based on these results, we prefer a model in which m6A RNAs rapidly respond to radiation-induced stress and diffuse to the damaged sites. The level of both (m1A) RNAs and m3G/TMG in RNAs is reduced as a consequence of DNA damage, recognized by the nucleotide excision repair mechanism.
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DNA Damage Changes Distribution Pattern and Levels of HP1 Protein Isoforms in the Nucleolus and Increases Phosphorylation of HP1β-Ser88. Cells 2019; 8:cells8091097. [PMID: 31533340 PMCID: PMC6770535 DOI: 10.3390/cells8091097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/10/2019] [Accepted: 09/10/2019] [Indexed: 12/28/2022] Open
Abstract
The family of heterochromatin protein 1 (HP1) isoforms is essential for chromatin packaging, regulation of gene expression, and repair of damaged DNA. Here we document that γ-radiation reduced the number of HP1α-positive foci, but not HP1β and HP1γ foci, located in the vicinity of the fibrillarin-positive region of the nucleolus. The additional analysis confirmed that γ-radiation has the ability to significantly decrease the level of HP1α in rDNA promoter and rDNA encoding 28S rRNA. By mass spectrometry, we showed that treatment by γ-rays enhanced the HP1β serine 88 phosphorylation (S88ph), but other analyzed modifications of HP1β, including S161ph/Y163ph, S171ph, and S174ph, were not changed in cells exposed to γ-rays or treated by the HDAC inhibitor (HDACi). Interestingly, a combination of HDACi and γ-radiation increased the level of HP1α and HP1γ. The level of HP1β remained identical before and after the HDACi/γ-rays treatment, but HDACi strengthened HP1β interaction with the KRAB-associated protein 1 (KAP1) protein. Conversely, HP1γ did not interact with KAP1, although approximately 40% of HP1γ foci co-localized with accumulated KAP1. Especially HP1γ foci at the periphery of nucleoli were mostly absent of KAP1. Together, DNA damage changed the morphology, levels, and interaction properties of HP1 isoforms. Also, γ-irradiation-induced hyperphosphorylation of the HP1β protein; thus, HP1β-S88ph could be considered as an important marker of DNA damage.
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Stixová L, Komůrková D, Svobodová Kovaříková A, Bártová E. UVA irradiation strengthened an interaction between UBF1/2 proteins and H4K20 di-/tri-methylation. Chromosome Res 2019; 27:41-55. [PMID: 30610403 DOI: 10.1007/s10577-018-9596-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 12/29/2022]
Abstract
Repair of ribosomal DNA (rDNA) is a very important nuclear process due to the most active transcription of ribosomal genes. Proper repair of rDNA is required for physiological biogenesis of ribosomes. Here, we analyzed the epigenetics of the DNA damage response in a nucleolar compartment, thus in the ribosomal genes studied in nonirradiated and UVA-irradiated mouse embryonic fibroblasts (MEFs). We found that the promoter of ribosomal genes is not abundant on H4K20me2, but it is densely occupied by H4K20me3. Ribosomal genes, regulated via UBF1/2 proteins, were characterized by an interaction between UBF1/2 and H4K20me2/me3. This interaction was strengthened by UVA irradiation that additionally causes a focal accumulation of H4K20me3 in the nucleolus. No interaction has been found between UBF1/2 and H3K9me3. Interestingly, UVA irradiation decreases the levels of H3K9me3 and H4K20me3 at 28S rDNA. Altogether, the UVA light affects the epigenetic status of ribosomal genes at 28S rDNA and strengthens an interaction between UBF1/2 proteins and H4K20me2/me3.
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Affiliation(s)
- Lenka Stixová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-612 65, Brno, Czech Republic
| | - Denisa Komůrková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-612 65, Brno, Czech Republic
| | - Alena Svobodová Kovaříková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-612 65, Brno, Czech Republic
| | - Eva Bártová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-612 65, Brno, Czech Republic.
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Svobodová Kovaříková A, Legartová S, Krejčí J, Bártová E. H3K9me3 and H4K20me3 represent the epigenetic landscape for 53BP1 binding to DNA lesions. Aging (Albany NY) 2018; 10:2585-2605. [PMID: 30312172 PMCID: PMC6224238 DOI: 10.18632/aging.101572] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/24/2018] [Indexed: 04/21/2023]
Abstract
Methylation of histones H4 at lysine 20 position (H4K20me), which is functional in DNA repair, represents a binding site for the 53BP1 protein. Here, we show a radiation-induced increase in the level of H4K20me3 while the levels of H4K20me1 and H4K20me2 remained intact. H4K20me3 was significantly pronounced at DNA lesions in only the G1 phase of the cycle, while this histone mark was reduced in very late S and G2 phases when PCNA was recruited to locally micro-irradiated chromatin. H4K20me3 was diminished in locally irradiated Suv39h1/h2 double knockout (dn) fibroblasts, and the same phenomenon was observed for H3K9me3 and its binding partner, the HP1β protein. Immunoprecipitation showed the existence of an interaction between H3K9me3-53BP1 and H4K20me3-53BP1; however, HP1β did not interact with 53BP1. Together, H3K9me3 and H4K20me3 represent epigenetic markers that are important for the function of the 53BP1 protein in non-homologous end joining (NHEJ) repair. The very late S phase represents the cell cycle breakpoint when a DDR function of the H4K20me3-53BP1 complex is abrogated due to recruitment of the PCNA protein and other DNA repair factors of homologous recombination to DNA lesions.
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Affiliation(s)
| | - Soňa Legartová
- Institute of Biophysics of the Czech Academy of Sciences, Brno, 61265, Czech Republic
| | - Jana Krejčí
- Institute of Biophysics of the Czech Academy of Sciences, Brno, 61265, Czech Republic
| | - Eva Bártová
- Institute of Biophysics of the Czech Academy of Sciences, Brno, 61265, Czech Republic
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Legartová S, Suchánková J, Krejčí J, Kovaříková A, Bártová E. Advanced Confocal Microscopy Techniques to Study Protein-protein Interactions and Kinetics at DNA Lesions. J Vis Exp 2017. [PMID: 29155761 DOI: 10.3791/55999] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Local microirradiation with lasers represents a useful tool for studies of DNA-repair-related processes in live cells. Here, we describe a methodological approach to analyzing protein kinetics at DNA lesions over time or protein-protein interactions on locally microirradiated chromatin. We also show how to recognize individual phases of the cell cycle using the Fucci cellular system to study cell-cycle-dependent protein kinetics at DNA lesions. A methodological description of the use of two UV lasers (355 nm and 405 nm) to induce different types of DNA damage is also presented. Only the cells microirradiated by the 405-nm diode laser proceeded through mitosis normally and were devoid of cyclobutane pyrimidine dimers (CPDs). We also show how microirradiated cells can be fixed at a given time point to perform immunodetection of the endogenous proteins of interest. For the DNA repair studies, we additionally describe the use of biophysical methods including FRAP (Fluorescence Recovery After Photobleaching) and FLIM (Fluorescence Lifetime Imaging Microscopy) in cells with spontaneously occurring DNA damage foci. We also show an application of FLIM-FRET (Fluorescence Resonance Energy Transfer) in experimental studies of protein-protein interactions.
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Affiliation(s)
- Soňa Legartová
- Institute of Biophysics of the Czech Academy of Sciences
| | | | - Jana Krejčí
- Institute of Biophysics of the Czech Academy of Sciences
| | | | - Eva Bártová
- Institute of Biophysics of the Czech Academy of Sciences;
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Bártová E, Malyšková B, Komůrková D, Legartová S, Suchánková J, Krejčí J, Kozubek S. Function of heterochromatin protein 1 during DNA repair. PROTOPLASMA 2017; 254:1233-1240. [PMID: 28236007 DOI: 10.1007/s00709-017-1090-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/14/2017] [Indexed: 05/04/2023]
Abstract
This review focuses on the function of heterochromatin protein HP1 in response to DNA damage. We specifically outline the regulatory mechanisms in which HP1 and its interacting partners are involved. HP1 protein subtypes (HP1α, HP1β, and HP1γ) are the main components of constitutive heterochromatin, and HP1α and HP1β in particular are responsible for heterochromatin maintenance. The recruitment of these proteins to DNA lesions is also important from the perspective of proper DNA repair mechanisms. For example, HP1α is necessary for the binding of the main DNA damage-related protein 53BP1 at DNA repair foci, which are positive not only for the HP1α protein but also for the RAD51 protein, a component of DNA repair machinery. The HP1β protein also appears in monomeric form in DNA lesions together with the evolutionarily well-conserved protein called proliferating cell nuclear antigen (PCNA). The role of HP1 in DNA lesions is also mediated via the Kap1 transcription repressor. Taken together, these results indicate that the function of HP1 after DNA injury depends strongly on the kinetics of other DNA repair-related factors and their post-translational modifications, such as the phosphorylation of Kap-1.
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Affiliation(s)
- Eva Bártová
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic.
| | - Barbora Malyšková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Denisa Komůrková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Soňa Legartová
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Jana Suchánková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Jana Krejčí
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Stanislav Kozubek
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
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Suchánková J, Legartová S, Ručková E, Vojtěšek B, Kozubek S, Bártová E. Mutations in the TP53 gene affected recruitment of 53BP1 protein to DNA lesions, but level of 53BP1 was stable after γ-irradiation that depleted MDC1 protein in specific TP53 mutants. Histochem Cell Biol 2017; 148:239-255. [PMID: 28397142 DOI: 10.1007/s00418-017-1567-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2017] [Indexed: 11/30/2022]
Abstract
53BP1 is a very well-known protein that is recruited to DNA lesions. The focal accumulation of p53 binding protein, 53BP1, is a main feature indicating the repair of spontaneous or irradiation-induced foci (IRIF). Thus, here, we addressed the question of whether mutations in the TP53 gene, which often affect the level of p53 protein, can change the recruitment of 53BP1 to γ- or UVA-irradiated chromatin. In various TP53 mutants, we observed a distinct accumulation of 53BP1 protein to UV-induced DNA lesions: in R273C mutants, 53BP1 appeared transiently at DNA lesions, during 10-30 min after irradiation; the mutation R282W was responsible for accumulation of 53BP1 immediately after UVA-damage; and in L194F mutants, the first appearance of 53BP1 protein at the lesions occurred during 60-70 min. These results showed that specific mutations in the TP53 gene stand behind not only different levels of p53 protein, but also affect the localized kinetics of 53BP1 protein in UVA-damaged chromatin. However, after γ-irradiation, only G245S mutation in TP53 gene was associated with surprisingly decreased level of 53BP1 protein. In other mutant cell lines, levels of 53BP1 were not affected by γ-rays. To these effects, we conversely found a distinct number of 53BP1-positive irradiation-induced foci in various TP53 mutants. The R280K, G245S, L194F mutations, or TP53 deletion were also characterized by radiation-induced depletion in MDC1 protein. Moreover, in mutant cells, an interaction between MDC1 and 53BP1 proteins was abrogated when compared with wild-type counterpart. Together, the kinetics of 53BP1 accumulation at UV-induced DNA lesions is different in various TP53 mutant cells. After γ-irradiation, despite changes in a number and a volume of 53BP1-positive foci, levels of 53BP1 protein were relatively stable. Here, we showed a link between the status of MDC1 protein and TP53 gene, which specific mutations caused radiation-induced MDC1 down-regulation. This observation is significant, especially with regard to radiotherapy of tumors with abrogated function of TP53 gene.
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Affiliation(s)
- Jana Suchánková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 00, Brno, Czech Republic
| | - Soňa Legartová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 00, Brno, Czech Republic
| | - Eva Ručková
- Masaryk Memorial Cancer Institute, Žlutý kopec 543/7, 656 53, Brno, Czech Republic
| | - Bořivoj Vojtěšek
- Masaryk Memorial Cancer Institute, Žlutý kopec 543/7, 656 53, Brno, Czech Republic
| | - Stanislav Kozubek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 00, Brno, Czech Republic
| | - Eva Bártová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 00, Brno, Czech Republic.
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Neural Differentiation in HDAC1-Depleted Cells Is Accompanied by Coilin Downregulation and the Accumulation of Cajal Bodies in Nucleoli. Stem Cells Int 2017; 2017:1021240. [PMID: 28337219 PMCID: PMC5350323 DOI: 10.1155/2017/1021240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 01/12/2017] [Accepted: 01/26/2017] [Indexed: 12/23/2022] Open
Abstract
Cajal bodies (CBs) are important compartments containing accumulated proteins that preferentially regulate RNA-related nuclear events, including splicing. Here, we studied the nuclear distribution pattern of CBs in neurogenesis. In adult brains, coilin was present at a high density, but CB formation was absent in the nuclei of the choroid plexus of the lateral ventricles. Cells of the adult hippocampus were characterized by a crescent-like morphology of coilin protein. We additionally observed a 70 kDa splice variant of coilin in adult mouse brains, which was different to embryonic brains and mouse pluripotent embryonic stem cells (mESCs), characterized by the 80 kDa standard variant of coilin. Here, we also showed that depletion of coilin is induced during neural differentiation and HDAC1 deficiency in mESCs caused coilin accumulation inside the fibrillarin-positive region of the nucleoli. A similar distribution pattern was observed in adult brain hippocampi, characterized by lower levels of both coilin and HDAC1. In summary, we observed that neural differentiation and HDAC1 deficiency lead to coilin depletion and coilin accumulation in body-like structures inside the nucleoli.
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Franek M, Kovaříková A, Bártová E, Kozubek S. Nucleolar Reorganization Upon Site-Specific Double-Strand Break Induction. J Histochem Cytochem 2016; 64:669-686. [PMID: 27680669 PMCID: PMC5084524 DOI: 10.1369/0022155416668505] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/09/2016] [Indexed: 12/20/2022] Open
Abstract
DNA damage response (DDR) in ribosomal genes and mechanisms of DNA repair in embryonic stem cells (ESCs) are less explored nuclear events. DDR in ESCs should be unique due to their high proliferation rate, expression of pluripotency factors, and specific chromatin signature. Given short population doubling time and fast progress through G1 phase, ESCs require a sustained production of rRNA, which leads to the formation of large and prominent nucleoli. Although transcription of rRNA in the nucleolus is relatively well understood, little is known about DDR in this nuclear compartment. Here, we directed formation of double-strand breaks in rRNA genes with I- PpoI endonuclease, and we studied nucleolar morphology, DDR, and chromatin modifications. We observed a pronounced formation of I- PpoI-induced nucleolar caps, positive on BRCA1, NBS1, MDC1, γH2AX, and UBF1 proteins. We showed interaction of nucleolar protein TCOF1 with HDAC1 and TCOF1 with CARM1 after DNA injury. Moreover, H3R17me2a modification mediated by CARM1 was found in I- PpoI-induced nucleolar caps. Finally, we report that heterochromatin protein 1 is not involved in DNA repair of nucleolar caps.
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Affiliation(s)
- Michal Franek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic (MF, AK, EB, SK)
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14
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Legartová S, Sehnalová P, Malyšková B, Küntziger T, Collas P, Cmarko D, Raška I, Sorokin DV, Kozubek S, Bártová E. Localized Movement and Levels of 53BP1 Protein Are Changed by γ-irradiation in PML Deficient Cells. J Cell Biochem 2016; 117:2583-96. [PMID: 27526954 DOI: 10.1002/jcb.25551] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 03/23/2016] [Indexed: 01/07/2023]
Abstract
We studied epigenetics, distribution pattern, kinetics, and diffusion of proteins recruited to spontaneous and γ-radiation-induced DNA lesions. We showed that PML deficiency leads to an increased number of DNA lesions, which was accompanied by changes in histone signature. In PML wt cells, we observed two mobile fractions of 53BP1 protein with distinct diffusion in spontaneous lesions. These protein fractions were not detected in PML-deficient cells, characterized by slow-diffusion of 53BP1. Single particle tracking analysis revealed limited local motion of 53BP1 foci in PML double null cells and local motion 53BP1 foci was even more reduced after γ-irradiation. However, radiation did not change co-localization between 53BP1 nuclear bodies and interchromatin granule-associated zones (IGAZs), nuclear speckles, or chromocenters. This newly observed interaction pattern imply that 53BP1 protein could be a part of not only DNA repair, but also process mediated via components accumulated in IGAZs, nuclear speckles, or paraspeckles. Together, PML deficiency affected local motion of 53BP1 nuclear bodies and changed composition and a number of irradiation-induced foci. J. Cell. Biochem. 117: 2583-2596, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Soňa Legartová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Petra Sehnalová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Barbora Malyšková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno, 612 65, Czech Republic
| | | | - Philippe Collas
- Department of Biochemistry, Institute of Basic Medical Sciences, University of Oslo, Norwegian Center for Stem Cell Research, Oslo, Norway
| | - Dušan Cmarko
- Institute of Cellular Biology and Pathology, the First Faculty of Medicine, Charles University in Prague, Albertov 4, Prague, 128 01, Czech Republic
| | - Ivan Raška
- Institute of Cellular Biology and Pathology, the First Faculty of Medicine, Charles University in Prague, Albertov 4, Prague, 128 01, Czech Republic
| | - Dmitry V Sorokin
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno, 612 65, Czech Republic.,Faculty of Informatics, Masaryk University, Botanická 68a, Brno, 602 00, Czech Republic
| | - Stanislav Kozubek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Eva Bártová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno, 612 65, Czech Republic. .,Institute of Cellular Biology and Pathology, the First Faculty of Medicine, Charles University in Prague, Albertov 4, Prague, 128 01, Czech Republic.
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15
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Franek M, Suchánková J, Sehnalová P, Krejčí J, Legartová S, Kozubek S, Večeřa J, Sorokin DV, Bártová E. Advanced Image Acquisition and Analytical Techniques for Studies of Living Cells and Tissue Sections. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2016; 22:326-341. [PMID: 26903193 DOI: 10.1017/s1431927616000052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Studies on fixed samples or genome-wide analyses of nuclear processes are useful for generating snapshots of a cell population at a particular time point. However, these experimental approaches do not provide information at the single-cell level. Genome-wide studies cannot assess variability between individual cells that are cultured in vitro or originate from different pathological stages. Immunohistochemistry and immunofluorescence are fundamental experimental approaches in clinical laboratories and are also widely used in basic research. However, the fixation procedure may generate artifacts and prevents monitoring of the dynamics of nuclear processes. Therefore, live-cell imaging is critical for studying the kinetics of basic nuclear events, such as DNA replication, transcription, splicing, and DNA repair. This review is focused on the advanced microscopy analyses of the cells, with a particular focus on live cells. We note some methodological innovations and new options for microscope systems that can also be used to study tissue sections. Cornerstone methods for the biophysical research of living cells, such as fluorescence recovery after photobleaching and fluorescence resonance energy transfer, are also discussed, as are studies on the effects of radiation at the individual cellular level.
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Affiliation(s)
- Michal Franek
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | - Jana Suchánková
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | - Petra Sehnalová
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | - Jana Krejčí
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | - Soňa Legartová
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | - Stanislav Kozubek
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | | | | | - Eva Bártová
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
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16
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Bártová E, Večeřa J, Krejčí J, Legartová S, Pacherník J, Kozubek S. The level and distribution pattern of HP1β in the embryonic brain correspond to those of H3K9me1/me2 but not of H3K9me3. Histochem Cell Biol 2016; 145:447-61. [PMID: 26794325 DOI: 10.1007/s00418-015-1402-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2015] [Indexed: 01/13/2023]
Abstract
We studied the histone signature of embryonic and adult brains to strengthen existing evidence of the importance of the histone code in mouse brain development. We analyzed the levels and distribution patterns of H3K9me1, H3K9me2, H3K9me3, and HP1β in both embryonic and adult brains. Western blotting showed that during mouse brain development, the levels of H3K9me1, H3K9me2, and HP1β exhibited almost identical trends, with the highest protein levels occurring at E15 stage. These trends differed from the relatively stable level of H3K9me3 at developmental stages E8, E13, E15, and E18. Compared with embryonic brains, adult brains were characterized by very low levels of H3K9me1/me2/me3 and HP1β. Manipulation of the embryonic epigenome through histone deacetylase inhibitor treatment did not affect the distribution patterns of the studied histone markers in embryonic ventricular ependyma. Similarly, Hdac3 depletion in adult animals had no effect on histone methylation in the adult hippocampus. Our results indicate that the distribution of HP1β in the embryonic mouse brain is related to that of H3K9me1/me2 but not to that of H3K9me3. The unique status of H3K9me3 in the brain was confirmed by its pronounced accumulation in the granular layer of the adult olfactory bulb. Moreover, among the studied proteins, H3K9me3 was the only posttranslational histone modification that was highly abundant at clusters of centromeric heterochromatin, called chromocenters. When we focused on the hippocampus, we found this region to be rich in H3K9me1 and H3K9me3, whereas H3K9me2 and HP1β were present at a very low level or even absent in the hippocampal blade. Taken together, these results revealed differences in the epigenome of the embryonic and adult mouse brain and showed that the adult hippocampus, the granular layer of the adult olfactory bulb, and the ventricular ependyma of the embryonic brain are colonized by specific epigenetic marks.
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Affiliation(s)
- Eva Bártová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic.
| | - Josef Večeřa
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, Brno, Czech Republic
| | - Jana Krejčí
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Soňa Legartová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Jiří Pacherník
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, Brno, Czech Republic
| | - Stanislav Kozubek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
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Sorokin DV, Stixová L, Sehnalová P, Legartová S, Suchánková J, Šimara P, Kozubek S, Matula P, Skalníková M, Raška I, Bártová E. Localized movement and morphology of UBF1-positive nucleolar regions are changed by γ-irradiation in G2 phase of the cell cycle. Nucleus 2015. [PMID: 26208041 DOI: 10.1080/19491034.2015.1075111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The nucleolus is a well-organized site of ribosomal gene transcription. Moreover, many DNA repair pathway proteins, including ATM, ATR kinases, MRE11, PARP1 and Ku70/80, localize to the nucleolus (Moore et al., 2011 ). We analyzed the consequences of DNA damage in nucleoli following ultraviolet A (UVA), C (UVC), or γ-irradiation in order to test whether and how radiation-mediated genome injury affects local motion and morphology of nucleoli. Because exposure to radiation sources can induce changes in the pattern of UBF1-positive nucleolar regions, we visualized nucleoli in living cells by GFP-UBF1 expression for subsequent morphological analyses and local motion studies. UVA radiation, but not 5 Gy of γ-rays, induced apoptosis as analyzed by an advanced computational method. In non-apoptotic cells, we observed that γ-radiation caused nucleolar re-positioning over time and changed several morphological parameters, including the size of the nucleolus and the area of individual UBF1-positive foci. Radiation-induced nucleoli re-arrangement was observed particularly in G2 phase of the cell cycle, indicating repair of ribosomal genes in G2 phase and implying that nucleoli are less stable, thus sensitive to radiation, in G2 phase.
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Affiliation(s)
- Dmitry V Sorokin
- a Institute of Biophysics ; Academy of Sciences of the Czech Republic ; Brno , Czech Republic
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