DNA Methylation and Histone Modifications Regulate De Novo Shoot Regeneration in Arabidopsis by Modulating WUSCHEL Expression and Auxin Signaling

Plants have a profound capacity to regenerate organs from differentiated somatic tissues, based on which propagating plants in vitro was made possible. Beside its use in biotechnology, in vitro shoot regeneration is also an important system to study de novo organogenesis. Phytohormones and transcription factor WUSCHEL (WUS) play critical roles in this process but whether and how epigenetic modifications are involved is unknown. Here, we report that epigenetic marks of DNA methylation and histone modifications regulate de novo shoot regeneration of Arabidopsis through modulating WUS expression and auxin signaling. First, functional loss of key epigenetic genes—including METHYLTRANSFERASE1 (MET1) encoding for DNA methyltransferase, KRYPTONITE (KYP) for the histone 3 lysine 9 (H3K9) methyltransferase, JMJ14 for the histone 3 lysine 4 (H3K4) demethylase, and HAC1 for the histone acetyltransferase—resulted in altered WUS expression and developmental rates of regenerated shoots in vitro. Second, we showed that regulatory regions of WUS were developmentally regulated by both DNA methylation and histone modifications through bisulfite sequencing and chromatin immunoprecipitation. Third, DNA methylation in the regulatory regions of WUS was lost in the met1 mutant, thus leading to increased WUS expression and its localization. Fourth, we did a genome-wide transcriptional analysis and found out that some of differentially expressed genes between wild type and met1 were involved in signal transduction of the phytohormone auxin. We verified that the increased expression of AUXIN RESPONSE FACTOR3 (ARF3) in met1 indeed was due to DNA demethylation, suggesting DNA methylation regulates de novo shoot regeneration by modulating auxin signaling. We propose that DNA methylation and histone modifications regulate de novo shoot regeneration by modulating WUS expression and auxin signaling. The study demonstrates that, although molecular components involved in organogenesis are divergently evolved in plants and animals, epigenetic modifications play an evolutionarily convergent role in this process

Base-Pair Resolution DNA Methylation Sequencing Reveals Profoundly Divergent Epigenetic Landscapes in Acute Myeloid Leukemia

We have developed an enhanced form of reduced representation bisulfite sequencing with extended genomic coverage, which resulted in greater capture of DNA methylation information of regions lying outside of traditional CpG islands. Applying this method to primary human bone marrow specimens from patients with Acute Myelogeneous Leukemia (AML), we demonstrated that genetically distinct AML subtypes display diametrically opposed DNA methylation patterns. As compared to normal controls, we observed widespread hypermethylation in IDH mutant AMLs, preferentially targeting promoter regions and CpG islands neighboring the transcription start sites of genes. In contrast, AMLs harboring translocations affecting the MLL gene displayed extensive loss of methylation of an almost mutually exclusive set of CpGs, which instead affected introns and distal intergenic CpG islands and shores. When analyzed in conjunction with gene expression profiles, it became apparent that these specific patterns of DNA methylation result in differing roles in gene expression regulation. However, despite this subtype-specific DNA methylation patterning, a much smaller set of CpG sites are consistently affected in both AML subtypes. Most CpG sites in this common core of aberrantly methylated CpGs were hypermethylated in both AML subtypes. Therefore, aberrant DNA methylation patterns in AML do not occur in a stereotypical manner but rather are highly specific and associated with specific driving genetic lesions

Heterogeneous conversion of NO₂ on secondary organic aerosol surfaces: A possible source of nitrous acid (HONO) in the atmosphere?

The heterogeneous conversion of NO₂ on different secondary organic aerosols (SOA) was investigated with the focus on a possible formation of nitrous acid (HONO). In one set of experiments different organic aerosols were produced in the reactions of O₃ with alpha-pinene, limonene or catechol and OH radicals with toluene or limonene, respectively. The aerosols were sampled on filters and exposed to humidified NO₂&nbsp; mixtures under atmospheric conditions. The estimated upper limits for the uptake coefficients of NO₂&nbsp; and the reactive uptake coefficients NO_2&nbsp; -> HONO are in the range of 10^-6and 10^-7, respectively. The integrated HONO formation for 1 h reaction time was <10¹³ cm^-2 geometrical surface and <10¹⁷ g^-1 particle mass. In a second set of experiments the conversion of NO₂ into HONO in the presence of organic particles was carried out in an aerosol flow tube under atmospheric conditions. In this case the aerosols were produced in the reaction of O₃ with beta-pinene, limonene or catechol, respectively. The upper limits for the reactive uptake coefficients NO₂-> HONO were in the range of 7 x 10^-7- 9 x 10^-6. The results from the present study show that heterogeneous formation of nitrous acid on secondary organic aerosols (SOA) is unimportant for the atmosphere

DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction. Nat Genet. 2009; 41(11):1207–1215. [PubMed: 19801979

2 0 7 A r t i c l e s The crucial molecular mechanisms that control stem cell fate have received widespread attention because these mechanisms could potentially be manipulated to engineer stem cell biology for therapeutic interventions or tissue repair. Moreover, increasing evidence indicates that many tumors are sustained by cancer stem cells (CSCs) whose self-renewal may be controlled by mechanisms similar to those that control normal stem cells 1,2 . The hematopoietic system provides a paradigm for studying molecular mechanisms controlling stem cell function 3,4 . Lifelong replenishment of all hematopoietic cells is maintained by HSCs, which in a tightly controlled process give rise to a hierarchy of multipotent and lineage-committed progenitors 5 . Regulation of the diverse functional repertoire of HSCs requires the coordinated action of transcription factors 6 . The activity of most transcription factors relies on the recruitment of cofactors, many of which control gene expression by catalyzing epigenetic modifications of chromatin 7 . However, the functional impact of epigenetic modification mechanisms on coordination of stem cell fate programs is still poorly understood. Methylation of CpG dinucleotides within the DNA is a major epigenetic modification, which in mammals is controlled by at least three different DNA methyltransferases (DNMTs): DNMT3a and DNMT3b for de novo methylation, and DNMT1 for methylation maintenance 8 . The impact of methylation on stem cell features has been studied in embryonic stem cells, but little is known about its function in somatic stem cells in vivo Here we address this issue using mice with gradually diminished Dnmt1 expression. We show that distinct methylation threshold levels are required for alternative fate decisions of both HSCs and CSCs. The data suggest that competing stem cell programs require different methylation dosage-dependent control mechanisms and identify CpG methylation as a shared epigenetic program in the control of normal and neoplastic stem cells. RESULTS DNMT1 is indispensable for cell-autonomous survival of HSCs HSCs express high levels of Dnmt1, the major methyltransferase of postnatal mammalian cells 10 . To investigate the role of DNA methylation in HSCs, we bred mice in which exons 4 and 5 of Dnmt1 were flanked by loxP sites 12 with mice expressing Cre recombinase under the control of the type I interferon-inducible Mx1 promoter 13 (transgene officially named Tg(Mx1-cre); referred to here as MxCre). This strategy allowed inducible deletion of the catalytic Dnmt1 domain DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction DNA methylation is a dynamic epigenetic mark that undergoes extensive changes during differentiation of self-renewing stem cells. However, whether these changes are the cause or consequence of stem cell fate remains unknown. Here, we show that alternative functional programs of hematopoietic stem cells (HSCs) are governed by gradual differences in methylation levels. Constitutive methylation is essential for HSC self-renewal but dispensable for homing, cell cycle control and suppression of apoptosis. Notably, HSCs from mice with reduced DNA methyltransferase 1 activity cannot suppress key myeloerythroid regulators and thus can differentiate into myeloerythroid, but not lymphoid, progeny. A similar methylation dosage effect controls stem cell function in leukemia. These data identify DNA methylation as an essential epigenetic mechanism to protect stem cells from premature activation of predominant differentiation programs and suggest that methylation dynamics determine stem cell functions in tissue homeostasis and cancer

Polar stratospheric chlorine kinetics from a self-match flight during SOLVE-II/EUPLEX

In-situ measurements of ClO made onboard the Geophysica aircraft on 30 January 2003 in the Arctic afford a novel approach to constrain the kinetic parameters governing polar stratospheric chlorine chemistry using atmospheric observations. The self-match flight pattern, i.e.sampling individual air masses twice at different zenith angles, was utilized by simulating the evolution of ClO mixing ratios between two 'matching' points using a photochemical model and optimizing the model parameters to fit the observations within a retrieval framework. Our results suggest a ClO/ClOOCl thermal equilibrium constant K-eq a factor of 5 smaller and a ratio J/k(f) a factor of 2 larger than the values based on the JPL recommendations. This concurs with other studies based on observed ClOx partitioning and corroborates that our understanding of stratospheric chlorine chemistry is incomplete, particularly in the light of the most recent laboratory experiments pointing to a J/k(f) ratio almost an order of magnitude below the JPL recommendation