Publications by authors named "Weihua Qin"

20 Publications

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HP1β carries an acidic linker domain and requires H3K9me3 for phase separation.

Nucleus 2021 Dec;12(1):44-57

Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany.

Liquid-liquid phase separation (LLPS) mediated formation of membraneless organelles has been proposed to coordinate biological processes in space and time. Previously, the formation of phase-separated droplets was described as a unique property of HP1α. Here, we demonstrate that the positive net charge of the intrinsically disordered hinge region (IDR-H) of HP1 proteins is critical for phase separation and that the exchange of four acidic amino acids is sufficient to confer LLPS properties to HP1β. Surprisingly, the addition of mono-nucleosomes promoted H3K9me3-dependent LLPS of HP1β which could be specifically disrupted with methylated but not acetylated H3K9 peptides. HP1β mutants defective in H3K9me3 binding were less efficient in phase separationand failed to accumulate at heterochromatin . We propose that multivalent interactions of HP1β with H3K9me3-modified nucleosomes via its chromodomain and dimerization via its chromoshadow domain enable phase separation and contribute to the formation of heterochromatin compartments .
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http://dx.doi.org/10.1080/19491034.2021.1889858DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7939559PMC
December 2021

Chemical characteristics, oxidative potential, and sources of PM in wintertime in Lahore and Peshawar, Pakistan.

J Environ Sci (China) 2021 Apr 1;102:148-158. Epub 2020 Oct 1.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing 100875, China.

The chemical characteristics, oxidative potential, and sources of PM were analyzed at the urban sites of Lahore and Peshawar, Pakistan in February 2019. Carbonaceous species, water soluble ions, and metal elements were measured to investigate the chemical composition and sources of PM. The dithiothreitol (DTT) consumption rate was measured to evaluate the oxidative potential of PM. Both cities showed a high exposure risk of PM regarding its oxidative potential (DTT). Carbonaceous and some of the elemental species of PM correlated well with DTT in both Lahore and Peshawar. Besides, the DTT of PM in Lahore showed significant positive correlation with most of the measured water soluble ions, however, ions were DTT-inactive in Peshawar. Due to the higher proportions of carbonaceous species and metal elements, Peshawar showed higher mass-normalized DTT activity of PM compared to Lahore although the average PM concentration in Peshawar was lower. The high concentrations of toxic metals also posed serious non-carcinogenic and carcinogenic risks to the residents of both cities. Principle component analysis coupled with multiple linear regression was applied to investigate different source contributions to PM and its oxidative potential. Mixed sources of traffic and road dust resuspension and coal combustion, direct vehicle emission, and biomass burning and formation of secondary aerosol were identified as the major sources of PM in both cities. The findings of this study provide important data for evaluation of the potential health risks of PM and for formulation of efficient control strategies in major cities of Pakistan.
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http://dx.doi.org/10.1016/j.jes.2020.09.014DOI Listing
April 2021

Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals.

Nat Commun 2020 11 24;11(1):5972. Epub 2020 Nov 24.

Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.

Genome-wide DNA demethylation is a unique feature of mammalian development and naïve pluripotent stem cells. Here, we describe a recently evolved pathway in which global hypomethylation is achieved by the coupling of active and passive demethylation. TET activity is required, albeit indirectly, for global demethylation, which mostly occurs at sites devoid of TET binding. Instead, TET-mediated active demethylation is locus-specific and necessary for activating a subset of genes, including the naïve pluripotency and germline marker Dppa3 (Stella, Pgc7). DPPA3 in turn drives large-scale passive demethylation by directly binding and displacing UHRF1 from chromatin, thereby inhibiting maintenance DNA methylation. Although unique to mammals, we show that DPPA3 alone is capable of inducing global DNA demethylation in non-mammalian species (Xenopus and medaka) despite their evolutionary divergence from mammals more than 300 million years ago. Our findings suggest that the evolution of Dppa3 facilitated the emergence of global DNA demethylation in mammals.
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http://dx.doi.org/10.1038/s41467-020-19603-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7686362PMC
November 2020

Seasonal variation of dicarboxylic acids in PM in Beijing: Implications for the formation and aging processes of secondary organic aerosols.

Sci Total Environ 2021 Apr 15;763:142964. Epub 2020 Oct 15.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing 100875, China.

Dicarboxylic acids are a group of highly oxidized components, which can provide insights into the formation mechanism and aging process of secondary organic aerosols (SOA). Based on the 12-h day and night PM samples collected in downtown Beijing in January, April, July and October of 2017, dicarboxylic acids and relevant components were measured to investigate their seasonal variation pattern and sources. High concentrations of the identified organic acids were observed, following the decreasing order of July > January > October > April. The high fractions of phthalic acid and maleic acid in January indicated severe aromatic SOA pollution during the sampling period in winter, and the high malonic acid to succinic acid and malic acid to succinic acid ratios in July suggested strong photochemical formation over the sampling period in summer. Based on the calculation of principle component analysis and multiple linear regression, water-soluble organic acids were mainly formed from the aerosol aging process during the sampling periods except for January, while water-soluble organic carbon (WSOC) mostly originated from combustion sources. Correlation analysis was conducted between the CO-normalized concentrations of organic acids and PM, O, as well as the meteorological parameters. The results suggested that gas-phase photooxidation contributed significantly to the formation of these organic acids during the entire sampling period, and the aqueous-phase process played an important role over the severe haze event in January. Our results also suggested that the intensity of photooxidation and the aging degree of SOA were enhanced along with the reduction of PM in Beijing in recent years.
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http://dx.doi.org/10.1016/j.scitotenv.2020.142964DOI Listing
April 2021

Two distinct modes of DNMT1 recruitment ensure stable maintenance DNA methylation.

Nat Commun 2020 03 6;11(1):1222. Epub 2020 Mar 6.

Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan.

Stable inheritance of DNA methylation is critical for maintaining differentiated phenotypes in multicellular organisms. We have recently identified dual mono-ubiquitylation of histone H3 (H3Ub2) by UHRF1 as an essential mechanism to recruit DNMT1 to chromatin. Here, we show that PCNA-associated factor 15 (PAF15) undergoes UHRF1-dependent dual mono-ubiquitylation (PAF15Ub2) on chromatin in a DNA replication-coupled manner. This event will, in turn, recruit DNMT1. During early S-phase, UHRF1 preferentially ubiquitylates PAF15, whereas H3Ub2 predominates during late S-phase. H3Ub2 is enhanced under PAF15 compromised conditions, suggesting that H3Ub2 serves as a backup for PAF15Ub2. In mouse ES cells, loss of PAF15Ub2 results in DNA hypomethylation at early replicating domains. Together, our results suggest that there are two distinct mechanisms underlying replication timing-dependent recruitment of DNMT1 through PAF15Ub2 and H3Ub2, both of which are prerequisite for high fidelity DNA methylation inheritance.
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http://dx.doi.org/10.1038/s41467-020-15006-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7060239PMC
March 2020

Characteristics and secondary formation of water-soluble organic acids in PM, PM and PM in Beijing during haze episodes.

Sci Total Environ 2019 Jun 10;669:175-184. Epub 2019 Mar 10.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing 100875, China; Center of Atmospheric Environmental Studies, Beijing Normal University, Beijing 100875, China.

Water-soluble organic acids are widely involved in various atmospheric physicochemical processes and appear as an important fraction of atmospheric aerosols. Nineteen water-soluble organic acids in 12-h PM, PM and PM samples collected in urban Beijing during haze episodes in winter and spring of 2017 were identified to investigate their characteristics and secondary formation mechanism. The molecular distributions of water-soluble organic acids as well as the high ratio of phthalic acid (Ph)/azelaic acid (C) indicated severe aromatic secondary organic aerosol pollution during the haze episodes, especially in winter. The diurnal patterns, size distributions, and concentration ratios of specific organic acids were investigated to reveal the pollution characteristics and possible sources of major organic acids in particulate matter in Beijing during haze events. Multiple linear regression was used to tentatively quantify the relative contributions of photochemical oxidation and aqueous-phase oxidation to the formation of total water-soluble organic acids in PM, PM and PM during haze episodes. The formation mechanism of sulfate and nitrate was also investigated for comparison. Different from the secondary formation of sulfate, the secondary formation of water-soluble organic acids showed enhanced contribution of gas-phase photochemical oxidation though the aqueous-phase oxidation was the dominant process. CAPSULE: Molecular analyses of organic acids in PM, PM and PM in Beijing during haze periods revealed their pollution characteristics, possible sources and formation mechanism.
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http://dx.doi.org/10.1016/j.scitotenv.2019.03.131DOI Listing
June 2019

Variation, sources and historical trend of black carbon in Beijing, China based on ground observation and MERRA-2 reanalysis data.

Environ Pollut 2019 Feb 23;245:853-863. Epub 2018 Nov 23.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing, 100875, China; Center of Atmospheric Environmental Studies, Beijing Normal University, Beijing, 100875, China.

Based on the ground-measurements and MERRA-2 (Modern-Era Retrospective Analysis for Research and Applications, Version 2) reanalysis data, the temporal-spatial variation of black carbon (BC) in Beijing and the affecting factors were investigated. According to the ground-measured BC concentration in November months of 2014, 2015 and 2016, the before-heating period in November 2014 showed the lowest BC concentration as a result of the efficient emission controls for the Asia-Pacific Economic Cooperation (APEC) meeting. Except for November 2014, the BC mass concentration during the heating periods was notably lower than the before-heating periods in November 2015 and 2016. Wind speed and relative humidity appeared to be two important meteorological parameters affecting BC pollution. The MERRA-2 BC concentration was validated through comparison with the continuous ground BC measurements in 2015 and 2016, affirming its reliability in demonstrating the large scale and long term variations of the ground BC concentration. The MERRA-2 BC spatial distribution, the potential source regions determined by concentration weighted trajectory (CWT) analysis, and the regional emission inventories were combined to reveal the potential source regions and source types of BC in Beijing. Transportation emission in Beijing and residential emissions in the neighboring regions such as Hebei appeared to be important sources of BC in Beijing. According to the historical trends of MERRA-2 BC concentration and typical fossil fuel consumption (1980-2017), local coal and coke are no longer the major factor affecting the BC concentration, instead, liquid fuels such as gasoline, kerosene, and diesel may highly contribute to the BC pollution in Beijing in recent years. Regional transport of BC may have also contributed to the loading of BC in Beijing. Open biomass burning may be a non-negligible factor for the short-term variation of BC in the atmosphere.
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http://dx.doi.org/10.1016/j.envpol.2018.11.063DOI Listing
February 2019

Ubiquitome Analysis Reveals PCNA-Associated Factor 15 (PAF15) as a Specific Ubiquitination Target of UHRF1 in Embryonic Stem Cells.

J Mol Biol 2017 12 18;429(24):3814-3824. Epub 2017 Oct 18.

Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany. Electronic address:

Ubiquitination is a multifunctional posttranslational modification controlling the activity, subcellular localization and stability of proteins. The E3 ubiquitin ligase ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1) is an essential epigenetic factor that recognizes repressive histone marks as well as hemi-methylated DNA and recruits DNA methyltransferase 1. To explore enzymatic functions of UHRF1 beyond epigenetic regulation, we conducted a comprehensive screen in mouse embryonic stem cells to identify novel ubiquitination targets of UHRF1 and its paralogue UHRF2. We found differentially ubiquitinated peptides associated with a variety of biological processes such as transcriptional regulation and DNA damage response. Most prominently, we identified PCNA-associated factor 15 (PAF15; also known as Pclaf, Ns5atp9, KIAA0101 and OEATC-1) as a specific ubiquitination target of UHRF1. Although the function of PAF15 ubiquitination in translesion DNA synthesis is well characterized, the respective E3 ligase had been unknown. We could show that UHRF1 ubiquitinates PAF15 at Lys 15 and Lys 24 and promotes its binding to PCNA during late S-phase. In summary, we identified novel ubiquitination targets that link UHRF1 to transcriptional regulation and DNA damage response.
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http://dx.doi.org/10.1016/j.jmb.2017.10.014DOI Listing
December 2017

CDK9-dependent RNA polymerase II pausing controls transcription initiation.

Elife 2017 10 10;6. Epub 2017 Oct 10.

Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.

Gene transcription can be activated by decreasing the duration of RNA polymerase II pausing in the promoter-proximal region, but how this is achieved remains unclear. Here we use a 'multi-omics' approach to demonstrate that the duration of polymerase pausing generally limits the productive frequency of transcription initiation in human cells ('pause-initiation limit'). We further engineer a human cell line to allow for specific and rapid inhibition of the P-TEFb kinase CDK9, which is implicated in polymerase pause release. CDK9 activity decreases the pause duration but also increases the productive initiation frequency. This shows that CDK9 stimulates release of paused polymerase and activates transcription by increasing the number of transcribing polymerases and thus the amount of mRNA synthesized per time. CDK9 activity is also associated with long-range chromatin interactions, suggesting that enhancers can influence the pause-initiation limit to regulate transcription.
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http://dx.doi.org/10.7554/eLife.29736DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5669633PMC
October 2017

DNMT1 mutations found in HSANIE patients affect interaction with UHRF1 and neuronal differentiation.

Hum Mol Genet 2017 04;26(8):1522-1534

DNMT1 is recruited to substrate sites by PCNA and UHRF1 to maintain DNA methylation after replication. The cell cycle dependent recruitment of DNMT1 is mediated by the PCNA-binding domain (PBD) and the targeting sequence (TS) within the N-terminal regulatory domain. The TS domain was found to be mutated in patients suffering from hereditary sensory and autonomic neuropathies with dementia and hearing loss (HSANIE) and autosomal dominant cerebellar ataxia deafness and narcolepsy (ADCA-DN) and is associated with global hypomethylation and site specific hypermethylation. With functional complementation assays in mouse embryonic stem cells, we showed that DNMT1 mutations P496Y and Y500C identified in HSANIE patients not only impair DNMT1 heterochromatin association, but also UHRF1 interaction resulting in hypomethylation. Similar DNA methylation defects were observed when DNMT1 interacting domains in UHRF1, the UBL and the SRA domain, were deleted. With cell-based assays, we could show that HSANIE associated mutations perturb DNMT1 heterochromatin association and catalytic complex formation at methylation sites and decrease protein stability in late S and G2 phase. To investigate the neuronal phenotype of HSANIE mutations, we performed DNMT1 rescue assays and could show that cells expressing mutated DNMT1 were prone to apoptosis and failed to differentiate into neuronal lineage. Our results provide insights into the molecular basis of DNMT1 dysfunction in HSANIE patients and emphasize the importance of the TS domain in the regulation of DNA methylation in pluripotent and differentiating cells.
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http://dx.doi.org/10.1093/hmg/ddx057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5393148PMC
April 2017

DNA methylation requires a DNMT1 ubiquitin interacting motif (UIM) and histone ubiquitination.

Cell Res 2015 Aug 12;25(8):911-29. Epub 2015 Jun 12.

1] Department of Biology II, Ludwig Maximilians University Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany [2] Center for Integrated Protein Science Munich (CIPSM), Via Manara 7, 21052 Busto Arsizio (VA), Italy [3] Nanosystems Initiative Munich (NIM), Via Manara 7, 21052 Busto Arsizio (VA), Italy.

DNMT1 is recruited by PCNA and UHRF1 to maintain DNA methylation after replication. UHRF1 recognizes hemimethylated DNA substrates via the SRA domain, but also repressive H3K9me3 histone marks with its TTD. With systematic mutagenesis and functional assays, we could show that chromatin binding further involved UHRF1 PHD binding to unmodified H3R2. These complementation assays clearly demonstrated that the ubiquitin ligase activity of the UHRF1 RING domain is required for maintenance DNA methylation. Mass spectrometry of UHRF1-deficient cells revealed H3K18 as a novel ubiquitination target of UHRF1 in mammalian cells. With bioinformatics and mutational analyses, we identified a ubiquitin interacting motif (UIM) in the N-terminal regulatory domain of DNMT1 that binds to ubiquitinated H3 tails and is essential for DNA methylation in vivo. H3 ubiquitination and subsequent DNA methylation required UHRF1 PHD binding to H3R2. These results show the manifold regulatory mechanisms controlling DNMT1 activity that require the reading and writing of epigenetic marks by UHRF1 and illustrate the multifaceted interplay between DNA and histone modifications. The identification and functional characterization of the DNMT1 UIM suggests a novel regulatory principle and we speculate that histone H2AK119 ubiquitination might also lead to UIM-dependent recruitment of DNMT1 and DNA methylation beyond classic maintenance.
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http://dx.doi.org/10.1038/cr.2015.72DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528052PMC
August 2015

Gallic acid induces apoptosis in human cervical epithelial cells containing human papillomavirus type 16 episomes.

J Med Virol 2016 Jan 25;88(1):127-34. Epub 2015 Jun 25.

Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA.

The high-risk human papillomaviruses (HPV) that infect the anogenital tract are strongly associated with the development of cervical carcinoma, which is the second most common cancer in women worldwide. Therapeutic drugs specifically targeting HPV are not available. Polyphenolic compounds have gained considerable attention because of their cytotoxic effects against a variety of cancers and certain viruses. In this study, we examined the effects of several polyphenols on cellular proliferation and death of the human cervical cancer cells and human cervical epithelial cells containing stable HPV type 16 episomes (HPVep). Our results show that three polyphenols inhibited proliferation of HeLa cells dose-dependently. Furthermore, one of the examined polyphenols, gallic acid (GA), also inhibited the proliferation of HPVep cells and exhibited significant specificity towards HPV-positive cells. The anti-proliferative effect of GA on HPVep and HeLa cells was associated with apoptosis and upregulation of p53. These results suggest that GA can be a potential candidate for the development of anti-HPV agents.
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http://dx.doi.org/10.1002/jmv.24291DOI Listing
January 2016

A modular open platform for systematic functional studies under physiological conditions.

Nucleic Acids Res 2015 Sep 24;43(17):e112. Epub 2015 May 24.

Ludwig Maximilians University Munich, Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany

Any profound comprehension of gene function requires detailed information about the subcellular localization, molecular interactions and spatio-temporal dynamics of gene products. We developed a multifunctional integrase (MIN) tag for rapid and versatile genome engineering that serves not only as a genetic entry site for the Bxb1 integrase but also as a novel epitope tag for standardized detection and precipitation. For the systematic study of epigenetic factors, including Dnmt1, Dnmt3a, Dnmt3b, Tet1, Tet2, Tet3 and Uhrf1, we generated MIN-tagged embryonic stem cell lines and created a toolbox of prefabricated modules that can be integrated via Bxb1-mediated recombination. We used these functional modules to study protein interactions and their spatio-temporal dynamics as well as gene expression and specific mutations during cellular differentiation and in response to external stimuli. Our genome engineering strategy provides a versatile open platform for efficient generation of multiple isogenic cell lines to study gene function under physiological conditions.
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http://dx.doi.org/10.1093/nar/gkv550DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4787826PMC
September 2015

Intrinsic and extrinsic connections of Tet3 dioxygenase with CXXC zinc finger modules.

PLoS One 2013 14;8(5):e62755. Epub 2013 May 14.

Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Ludwig Maximilians University Munich, Planegg-Martinsried, Germany.

Tet proteins are emerging as major epigenetic modulators of cell fate and plasticity. However, little is known about how Tet proteins are targeted to selected genomic loci in distinct biological contexts. Previously, a CXXC-type zinc finger domain in Tet1 was shown to bind CpG-rich DNA sequences. Interestingly, in human and mouse the Tet2 and Tet3 genes are adjacent to Cxxc4 and Cxxc10-1, respectively. The CXXC domains encoded by these loci, together with those in Tet1 and Cxxc5, identify a distinct homology group within the CXXC domain family. Here we provide evidence for alternative mouse Tet3 transcripts including the Cxxc10-1 sequence (Tet3(CXXC)) and for an interaction between Tet3 and Cxxc4. In vitro Cxxc4 and the isolated CXXC domains of Tet1 and Tet3(CXXC) bind DNA substrates with similar preference towards the modification state of cytosine at a single CpG site. In vivo Tet1 and Tet3 isoforms with and without CXXC domain hydroxylate genomic 5-methylcytosine with similar activity. Relative transcript levels suggest that distinct ratios of Tet3(CXXC) isoforms and Tet3-Cxxc4 complex may be present in adult tissues. Our data suggest that variable association with CXXC modules may contribute to context specific functions of Tet proteins.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062755PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3653909PMC
December 2013

Dissection of cell cycle-dependent dynamics of Dnmt1 by FRAP and diffusion-coupled modeling.

Nucleic Acids Res 2013 May 27;41(9):4860-76. Epub 2013 Mar 27.

Department of Biology and Center for Integrated Protein Science, Ludwig Maximilians University Munich (LMU), 82152 Planegg-Martinsried, Germany.

DNA methyltransferase 1 (Dnmt1) reestablishes methylation of hemimethylated CpG sites generated during DNA replication in mammalian cells. Two subdomains, the proliferating cell nuclear antigen (PCNA)-binding domain (PBD) and the targeting sequence (TS) domain, target Dnmt1 to the replication sites in S phase. We aimed to dissect the details of the cell cycle-dependent coordinated activity of both domains. To that end, we combined super-resolution 3D-structured illumination microscopy and fluorescence recovery after photobleaching (FRAP) experiments of GFP-Dnmt1 wild type and mutant constructs in somatic mouse cells. To interpret the differences in FRAP kinetics, we refined existing data analysis and modeling approaches to (i) account for the heterogeneous and variable distribution of Dnmt1-binding sites in different cell cycle stages; (ii) allow diffusion-coupled dynamics; (iii) accommodate multiple binding classes. We find that transient PBD-dependent interaction directly at replication sites is the predominant specific interaction in early S phase (residence time Tres ≤ 10 s). In late S phase, this binding class is taken over by a substantially stronger (Tres ∼22 s) TS domain-dependent interaction at PCNA-enriched replication sites and at nearby pericentromeric heterochromatin subregions. We propose a two-loading-platform-model of additional PCNA-independent loading at postreplicative, heterochromatic Dnmt1 target sites to ensure faithful maintenance of densely methylated genomic regions.
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http://dx.doi.org/10.1093/nar/gkt191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3643600PMC
May 2013

Regulation of DNA methyltransferase 1 by interactions and modifications.

Nucleus 2011 Sep-Oct;2(5):392-402. Epub 2011 Sep 1.

Center for Integrated Protein Science, Department of Biology II, Ludwig Maximilians University, 82152 Munich, Germany.

DNA methylation plays a central role in the epigenetic regulation of gene expression during development and disease. Remarkably, the complex and changing patterns of genomic DNA methylation are established and maintained by only three DNA methyltransferases. Here we focus on DNMT1, the major and ubiquitously expressed DNA methyltransferase in vertebrates, to outline possible regulatory mechanisms. A list of all protein interactions and post-translational modifications reported for DNMT1 clearly shows that DNMT1, and by extension also DNA methylation in general, are functionally linked with several other epigenetic pathways and cellular processes. General themes of these interactions and modifications include the activation, stabilization and recruitment of DNMT1 at specific sites and heterochromatin regions. For a comprehensive understanding of the regulation of DNA methylation it is now necessary to systematically quantify the interactions and modifications of DNMT1, to elucidate their function at the molecular level and to integrate these data at the cellular level.
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http://dx.doi.org/10.4161/nucl.2.5.17928DOI Listing
March 2012

Different binding properties and function of CXXC zinc finger domains in Dnmt1 and Tet1.

PLoS One 2011 Feb 2;6(2):e16627. Epub 2011 Feb 2.

Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Ludwig Maximilians University Munich, Planegg, Germany.

Several mammalian proteins involved in chromatin and DNA modification contain CXXC zinc finger domains. We compared the structure and function of the CXXC domains in the DNA methyltransferase Dnmt1 and the methylcytosine dioxygenase Tet1. Sequence alignment showed that both CXXC domains have a very similar framework but differ in the central tip region. Based on the known structure of a similar MLL1 domain we developed homology models and designed expression constructs for the isolated CXXC domains of Dnmt1 and Tet1 accordingly. We show that the CXXC domain of Tet1 has no DNA binding activity and is dispensable for catalytic activity in vivo. In contrast, the CXXC domain of Dnmt1 selectively binds DNA substrates containing unmethylated CpG sites. Surprisingly, a Dnmt1 mutant construct lacking the CXXC domain formed covalent complexes with cytosine bases both in vitro and in vivo and rescued DNA methylation patterns in dnmt1⁻/⁻ embryonic stem cells (ESCs) just as efficiently as wild type Dnmt1. Interestingly, neither wild type nor ΔCXXC Dnmt1 re-methylated imprinted CpG sites of the H19a promoter in dnmt1⁻/⁻ ESCs, arguing against a role of the CXXC domain in restraining Dnmt1 methyltransferase activity on unmethylated CpG sites.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0016627PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3032784PMC
February 2011

Usp7 and Uhrf1 control ubiquitination and stability of the maintenance DNA methyltransferase Dnmt1.

J Cell Biochem 2011 Feb;112(2):439-44

Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany.

In mammals Dnmt1 is the DNA methyltransferase chiefly responsible for maintaining genomic methylation patterns through DNA replication cycles, but how its maintenance activity is controlled is still not well understood. Interestingly, Uhrf1, a crucial cofactor for maintenance of DNA methylation by Dnmt1, is endowed with E3 ubiquitin ligase activity. Here, we show that both Dnmt1 and Uhrf1 coprecipitate with ubiquitin specific peptidase 7 (Usp7), a de-ubiquitinating enzyme. Overexpression of Uhrf1 and Usp7 resulted in opposite changes in the ubiquitination status and stability of Dnmt1. Our findings suggest that, by balancing Dnmt1 ubiquitination, Usp7 and Uhrf1 fine tune Dnmt1 stability.
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http://dx.doi.org/10.1002/jcb.22998DOI Listing
February 2011

[Vegetation diversity of wild Chinese alligator (Alligator sinensis) habitats].

Ying Yong Sheng Tai Xue Bao 2004 Jul;15(7):1157-60

College of Life Science, Anhui Normal University, Wuhu 241000, China.

In June and July of 2003, a field survey on the vegetation of 22 Chinese alligator habitats distributed in Nanling county, Jingxian county, Guangde county, Langxi county and Xuancheng city of Anhui province was conducted, and the plant species of the habitats were recorded and analyzed. The results showed that the vegetation of the whole habitats was secondary, and there were 294 species vascular plants, belonging to 92 families. Pteioblastus amarus shrubbery could be found in all sites, and part differences of the vegetation consisted in different habitats. The relationship between Chinese alligator and habitat vegetation was also analyzed. All of these could offer some basic botanical data for the further protection of the Chinese alligator.
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July 2004