Establishment and functions of DNA methylation in the germline.

Epigenetic modifications established during gametogenesis regulate transcription and other nuclear processes in gametes, but also have influences in the zygote, embryo and postnatal life. This is best understood for DNA methylation which, established at discrete regions of the oocyte and sperm genomes, governs genomic imprinting. In this review, we describe how imprinting has informed our understanding of de novo DNA methylation mechanisms, highlight how recent genome-wide profiling studies have provided unprecedented insights into establishment of the sperm and oocyte methylomes and consider the fate and function of gametic methylation and other epigenetic modifications after fertilization

Early Acidification of Mars and the Potential Implications for Biology

A leading paleoclimate theory for Mars, based on the identification of phyllosilicate minerals in ancient terrains, posits that the first several million years of the planet’s history were dominated by neutral to alkaline pH. However, evidence is mounting for the consideration of an alternate hypothesis: that some smectites on Mars formed under acidic conditions, and that the early surface of Mars may not have been subject to circum-neutral pH conditions, at least not uniformly. Work on shergottitic liquids suggests that up to 2400 ppm of sulfur could have degassed from martian magma, supplying more than enough sulfur for the planet’s sulfate-rich sediments and sedimentary rocks, and isotopic evidence of mass independent fractionation reveals that sulfur in martian meteorites underwent atmospheric reactions. Radiative modeling of sulfur volatiles in the martian atmosphere indicates that SO2 and H2S would have acted as powerful greenhouse gases trapping heat in different wavelength-dependent atmospheric windows than CO2 and H2O, supplying the necessary heat for surface temperatures to rise above freezing. Photochemistry suggests that sulfur would have been removed from the atmosphere through the deposition of sulfur dioxide, oxidized to sulfate at the surfaceatmosphere interface. This, in turn, could have led to the early acidification of the surface, thereby explaining the paucity of carbonates on Mars. This idea is supported by 1) the recent laboratory synthesis of Fe/Mg smectite from an Adirondack basalt simulant in an acidic hydrothermal system, and 2) studies of the mineral composition of terrestrial analogs, particularly at acid salt lakes

Biosignatures in Mars Analog Acid Salt Lakes

Paleolake sites on Mars, particularly buried deposits that have been shielded from surface radiation, serve as intriguing targets for the search for life. Mars-like ephemeral playa lakes here on Earth can offer insights and perspectives on the possibilities for physical, metabolic, and biomolecular biosignature recovery from similar environments on Mars

A multi-modal approach to measuring particulate iron speciation in buoyant hydrothermal plumes

Processes active within buoyant hydrothermal plumes are expected to modulate the flux of elements, such as Fe, to the deep ocean; however, they are yet to be described in a comprehensive manner through observations or models. In this study, we compare observed particulate Fe (pFe) speciation with thermodynamic (equilibrium) reaction path modeling for three vent fields in the Eastern Lau Spreading Center (ELSC). At each site, particles were collected from the buoyant rising portion of hydrothermal plumes using in situ filtration with a Remotely Operated Vehicle. Filter bound particles were analyzed by synchrotron micro-probe X-ray fluorescence mapping (XRF), X-ray diffraction (XRD), XRF spectroscopy, and X-ray absorption near edge structure (XANES) spectroscopy at the Fe 1 s edge, as well as XRF-based chemical speciation mapping for Fe. For buoyant plumes of the ELSC, diversity in solid-state chemistry was high, and poorly crystalline, meta-stable phases were common. We demonstrate that to fully describe the crystalline-to-noncrystalline character of plume pFe, a multi-modal XRD-XANES analytical approach is needed. We found that an equilibrium modeling approach worked well for pyrite but performed poorly for important families of meta-stable pFe, namely Fe (oxyhydr)oxides and monosulfides. Based on our findings, we recommend future field expeditions strategically explore sites representing a diversity of site-specific conditions to better capture the full range of processes active in plumes. We also recommend development of kinetic models, as well as expansion of thermodynamic databases to better reflect the solid-state composition of plumes. These steps should allow oceanographers to understand the processes controlling Fe speciation in plumes well enough to create realistic models of hydrothermal fluxes to the ocean

Transcription and chromatin determinants of de novo DNA methylation timing in oocytes.

BACKGROUND: Gametogenesis in mammals entails profound re-patterning of the epigenome. In the female germline, DNA methylation is acquired late in oogenesis from an essentially unmethylated baseline and is established largely as a consequence of transcription events. Molecular and functional studies have shown that imprinted genes become methylated at different times during oocyte growth; however, little is known about the kinetics of methylation gain genome wide and the reasons for asynchrony in methylation at imprinted loci. RESULTS: Given the predominant role of transcription, we sought to investigate whether transcription timing is rate limiting for de novo methylation and determines the asynchrony of methylation events. Therefore, we generated genome-wide methylation and transcriptome maps of size-selected, growing oocytes to capture the onset and progression of methylation. We find that most sequence elements, including most classes of transposable elements, acquire methylation at similar rates overall. However, methylation of CpG islands (CGIs) is delayed compared with the genome average and there are reproducible differences amongst CGIs in onset of methylation. Although more highly transcribed genes acquire methylation earlier, the major transitions in the oocyte transcriptome occur well before the de novo methylation phase, indicating that transcription is generally not rate limiting in conferring permissiveness to DNA methylation. Instead, CGI methylation timing negatively correlates with enrichment for histone 3 lysine 4 (H3K4) methylation and dependence on the H3K4 demethylases KDM1A and KDM1B, implicating chromatin remodelling as a major determinant of methylation timing. We also identified differential enrichment of transcription factor binding motifs in CGIs acquiring methylation early or late in oocyte growth. By combining these parameters into multiple regression models, we were able to account for about a fifth of the variation in methylation timing of CGIs. Finally, we show that establishment of non-CpG methylation, which is prevalent in fully grown oocytes, and methylation over non-transcribed regions, are later events in oogenesis. CONCLUSIONS: These results do not support a major role for transcriptional transitions in the time of onset of DNA methylation in the oocyte, but suggest a model in which sequences least dependent on chromatin remodelling are the earliest to become permissive for methylation

Stromal senescence establishes an immunosuppressive microenvironment that drives tumorigenesis

Age is a significant risk factor for the development of cancer. However, the mechanisms that drive age-related increases in cancer remain poorly understood. To determine if senescent stromal cells influence tumorigenesis, we develop a mouse model that mimics the aged skin microenvironment. Using this model, here we find that senescent stromal cells are sufficient to drive localized increases in suppressive myeloid cells that contributed to tumour promotion. Further, we find that the stromal-derived senescence-associated secretory phenotype factor interleukin-6 orchestrates both increases in suppressive myeloid cells and their ability to inhibit anti-tumour T-cell responses. Significantly, in aged, cancer-free individuals, we find similar increases in immune cells that also localize near senescent stromal cells. This work provides evidence that the accumulation of senescent stromal cells is sufficient to establish a tumour-permissive, chronic inflammatory microenvironment that can shelter incipient tumour cells, thus allowing them to proliferate and progress unabated by the immune system

Dynamic changes in histone modifications precede de novo DNA methylation in oocytes.

Erasure and subsequent reinstatement of DNA methylation in the germline, especially at imprinted CpG islands (CGIs), is crucial to embryogenesis in mammals. The mechanisms underlying DNA methylation establishment remain poorly understood, but a number of post-translational modifications of histones are implicated in antagonizing or recruiting the de novo DNA methylation complex. In mouse oogenesis, DNA methylation establishment occurs on a largely unmethylated genome and in nondividing cells, making it a highly informative model for examining how histone modifications can shape the DNA methylome. Using a chromatin immunoprecipitation (ChIP) and genome-wide sequencing (ChIP-seq) protocol optimized for low cell numbers and novel techniques for isolating primary and growing oocytes, profiles were generated for histone modifications implicated in promoting or inhibiting DNA methylation. CGIs destined for DNA methylation show reduced protective H3K4 dimethylation (H3K4me2) and trimethylation (H3K4me3) in both primary and growing oocytes, while permissive H3K36me3 increases specifically at these CGIs in growing oocytes. Methylome profiling of oocytes deficient in H3K4 demethylase KDM1A or KDM1B indicated that removal of H3K4 methylation is necessary for proper methylation establishment at CGIs. This work represents the first systematic study performing ChIP-seq in oocytes and shows that histone remodeling in the mammalian oocyte helps direct de novo DNA methylation events