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Frost, Jennifer M.; Lee, Jaehoon; Hsieh, Ping-Hung; Lin, Samuel J. H.; Min, Yunsook; Bauer, Matthew; Runkel, Anne M.; Cho, Hyung-Taeg; Hsieh, Tzung-Fu; Fischer, Robert L.; et al(
, BMC Plant Biology)
AbstractBackground
H2A.X is an H2A variant histone in eukaryotes, unique for its ability to respond to DNA damage, initiating the DNA repair pathway. H2A.X replacement within the histone octamer is mediated by the FAcilitates Chromatin Transactions (FACT) complex, a key chromatin remodeler. FACT is required for DEMETER (DME)-mediated DNA demethylation at certain loci inArabidopsis thalianafemale gametophytes during reproduction. Here, we sought to investigate whether H2A.X is involved in DME- and FACT-mediated DNA demethylation during reproduction.
Results
H2A.X is encoded by two genes in Arabidopsis genome,HTA3andHTA5. We generatedh2a.xdouble mutants, which displayed a normal growth profile, whereby flowering time, seed development, and root tip organization, S-phase progression and proliferation were all normal. However,h2a.xmutants were more sensitive to genotoxic stress, consistent with previous reports. H2A.X fused to Green Fluorescent Protein (GFP) under theH2A.Xpromoter was highly expressed especially in newly developing Arabidopsis tissues, including in male and female gametophytes, where DME is also expressed. We examined DNA methylation inh2a.xdeveloping seeds and seedlings using whole genome bisulfite sequencing, and found that CG DNA methylation is decreased genome-wide inh2a.xmutant endosperm. Hypomethylation was most striking in transposon bodies, and occurred on both parental alleles in the developing endosperm, but not the embryo or seedling.h2a.x-mediated hypomethylated sites overlapped DME targets, but also included other loci, predominately located in heterochromatic transposons and intergenic DNA.
Conclusions
Our genome-wide methylation analyses suggest that H2A.X could function in preventing access of the DME demethylase to non-canonical sites. Overall, our data suggest that H2A.X is required to maintain DNA methylation homeostasis in the unique chromatin environment of the Arabidopsis endosperm.
Han, Qiang; Hung, Yu-Hung; Zhang, Changqing; Bartels, Arthur; Rea, Matthew; Yang, Hanwen; Park, Christine; Zhang, Xiang-Qian; Fischer, Robert L.; Xiao, Wenyan; et al(
, Frontiers in Plant Science)
The Arabidopsis DEMETER (DME) DNA glycosylase demethylates the central cell genome prior to fertilization. This epigenetic reconfiguration of the female gamete companion cell establishes gene imprinting in the endosperm and is essential for seed viability. DME demethylates small and genic-flanking transposons as well as intergenic and heterochromatin sequences, but how DME is recruited to these loci remains unknown. H1.2 was identified as a DME-interacting protein in a yeast two-hybrid screen, and maternal genome H1 loss affects DNA methylation and expression of selected imprinted genes in the endosperm. Yet, the extent to which H1 influences DME demethylation and gene imprinting in the Arabidopsis endosperm has not been investigated. Here, we showed that without the maternal linker histones, DME-mediated demethylation is facilitated, particularly in the heterochromatin regions, indicating that H1-bound heterochromatins are barriers for DME demethylation. Loss of H1 in the maternal genome has a very limited effect on gene transcription or gene imprinting regulation in the endosperm; however, it variably influences euchromatin TE methylation and causes a slight hypermethylation and a reduced expression in selected imprinted genes. We conclude that loss of maternal H1 indirectly influences DME-mediated demethylation and endosperm DNA methylation landscape but does not appear to affect endosperm gene transcription and overall imprinting regulation.
Fischer, Robert S.; Sun, Xiaoyu; Baird, Michelle A.; Hourwitz, Matt J.; Seo, Bo Ri; Pasapera, Ana M.; Mehta, Shalin B.; Losert, Wolfgang; Fischbach, Claudia; Fourkas, John T.; et al(
, Proceedings of the National Academy of Sciences)
Contact guidance is a powerful topographical cue that induces persistent directional cell migration. Healthy tissue stroma is characterized by a meshwork of wavy extracellular matrix (ECM) fiber bundles, whereas metastasis-prone stroma exhibit less wavy, more linear fibers. The latter topography correlates with poor prognosis, whereas more wavy bundles correlate with benign tumors. We designed nanotopographic ECM-coated substrates that mimic collagen fibril waveforms seen in tumors and healthy tissues to determine how these nanotopographies may regulate cancer cell polarization and migration machineries. Cell polarization and directional migration were inhibited by fibril-like wave substrates above a threshold amplitude. Although polarity signals and actin nucleation factors were required for polarization and migration on low-amplitude wave substrates, they did not localize to cell leading edges. Instead, these factors localized to wave peaks, creating multiple “cryptic leading edges” within cells. On high-amplitude wave substrates, retrograde flow from large cryptic leading edges depolarized stress fibers and focal adhesions and inhibited cell migration. On low-amplitude wave substrates, actomyosin contractility overrode the small cryptic leading edges and drove stress fiber and focal adhesion orientation along the wave axis to mediate directional migration. Cancer cells of different intrinsic contractility depolarized at different wave amplitudes, and cell polarization response to wavy substrates could be tuned by manipulating contractility. We propose that ECM fibril waveforms with sufficiently high amplitude around tumors may serve as “cell polarization barriers,” decreasing directional migration of tumor cells, which could be overcome by up-regulation of tumor cell contractility.
Morris, Dylan H; Yinda, Kwe Claude; Gamble, Amandine; Rossine, Fernando W; Huang, Qishen; Bushmaker, Trenton; Fischer, Robert J; Matson, M Jeremiah; Van Doremalen, Neeltje; Vikesland, Peter J; et al(
, eLife)
null
(Ed.)
Ambient temperature and humidity strongly affect inactivation rates of enveloped viruses, but a mechanistic, quantitative theory of these effects has been elusive. We measure the stability of SARS-CoV-2 on an inert surface at nine temperature and humidity conditions and develop a mechanistic model to explain and predict how temperature and humidity alter virus inactivation. We find SARS-CoV-2 survives longest at low temperatures and extreme relative humidities (RH); median estimated virus half-life is >24 hours at 10C and 40% RH, but ~1.5 hours at 27C and 65% RH. Our mechanistic model uses fundamental chemistry to explain why inactivation rate increases with increased temperature and shows a U-shaped dependence on RH. The model accurately predicts existing measurements of five different human coronaviruses, suggesting that shared mechanisms may affect stability for many viruses. The results indicate scenarios of high transmission risk, point to mitigation strategies, and advance the mechanistic study of virus transmission.
Göhler, Fabian; Hamann, Danielle M.; Rösch, Niels; Wolff, Susanne; Logan, Jacob T.; Fischer, Robert; Speck, Florian; Johnson, David C.; Seyller, Thomas(
, Journal of Materials Research)
A series of ${\left\hbox[ {{{\left\hbox( {{\rm{SnSe}}} \right\hbox)}_{1 \hbox+ \delta }}} \right\hbox]_m}{\left\hbox[ {{\rm{TiS}}{{\rm{e}}_2}} \right\hbox]_2}$ heterostructure thin films built up from repeating units of m bilayers of SnSe and two layers of TiSe 2 were synthesized from designed precursors. The electronic structure of the films was investigated using X-ray photoelectron spectroscopy for samples with m = 1, 2, 3, and 7 and compared to binary samples of TiSe 2 and SnSe. The observed binding energies of core levels and valence bands of the heterostructures are largely independent of m . For the SnSe layers, we can observe a rigid band shift in the heterostructures compared to the binary, which can be explained by electron transfer from SnSe to TiSe 2 . The electronic structure of the TiSe 2 layers shows a more complicated behavior, as a small shift can be observed in the valence band and Se3 d spectra, but the Ti2 p core level remains at a constant energy. Complementary UV photoemission spectroscopy measurements confirm a charge transfer mechanism where the SnSe layers donate electrons into empty Ti3 d states at the Fermi energy.
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