The Prevalence and Regulation of Antisense Transcripts in Schizosaccharomyces pombe

A strand-specific transcriptome sequencing strategy, directional ligation sequencing or DeLi-seq, was employed to profile antisense transcriptome of Schizosaccharomyces pombe. Under both normal and heat shock conditions, we found that polyadenylated antisense transcripts are broadly expressed while distinct expression patterns were observed for protein-coding and non-coding loci. Dominant antisense expression is enriched in protein-coding genes involved in meiosis or stress response pathways. Detailed analyses further suggest that antisense transcripts are independently regulated with respect to their sense transcripts, and diverse mechanisms might be potentially involved in the biogenesis and degradation of antisense RNAs. Taken together, antisense transcription may have profound impacts on global gene regulation in S. pombe

Repression of Meiotic Genes by Antisense Transcription and by Fkh2 Transcription Factor in Schizosaccharomyces pombe

In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. Disruption of the antisense transcription of three of these mid-meiotic genes allowed vegetative sense transcription. These results suggest that antisense transcription represses sense transcription of meiotic genes in vegetative cells. Although the mechanism(s) of antisense mediated transcription repression need to be further explored, our data indicates that RNAi machinery is not required for repression. Previously, we and others used non-strand specific methods to study splicing regulation of meiotic genes and concluded that 28 mid-meiotic genes are spliced only in meiosis. We now demonstrate that the “unspliced” signal in vegetative cells comes from the antisense RNA, not from unspliced sense RNA, and we argue against the idea that splicing regulates these mid-meiotic genes. Most of these mid-meiotic genes are induced in mid-meiosis by the forkhead transcription factor Mei4. Interestingly, deletion of a different forkhead transcription factor, Fkh2, allows low levels of sense expression of some mid-meiotic genes in vegetative cells. We propose that vegetative expression of mid-meiotic genes is repressed at least two independent ways: antisense transcription and Fkh2 repression

The Impact of Local Genome Sequence on Defining Heterochromatin Domains

Characterizing how genomic sequence interacts with trans-acting regulatory factors to implement a program of gene expression in eukaryotic organisms is critical to understanding genome function. One means by which patterns of gene expression are achieved is through the differential packaging of DNA into distinct types of chromatin. While chromatin state exerts a major influence on gene expression, the extent to which cis-acting DNA sequences contribute to the specification of chromatin state remains incompletely understood. To address this, we have used a fission yeast sequence element (L5), known to be sufficient to nucleate heterochromatin, to establish de novo heterochromatin domains in the Schizosaccharomyces pombe genome. The resulting heterochromatin domains were queried for the presence of H3K9 di-methylation and Swi6p, both hallmarks of heterochromatin, and for levels of gene expression. We describe a major effect of genomic sequences in determining the size and extent of such de novo heterochromatin domains. Heterochromatin spreading is antagonized by the presence of genes, in a manner that can occur independent of strength of transcription. Increasing the dosage of Swi6p results in increased heterochromatin proximal to the L5 element, but does not result in an expansion of the heterochromatin domain, suggesting that in this context genomic effects are dominant over trans effects. Finally, we show that the ratio of Swi6p to H3K9 di-methylation is sequence-dependent and correlates with the extent of gene repression. Taken together, these data demonstrate that the sequence content of a genomic region plays a significant role in shaping its response to encroaching heterochromatin and suggest a role of DNA sequence in specifying chromatin state

Structures Related to the Emplacement of Shallow-Level Intrusions

A systematic view of the vast nomenclature used to describe the structures of shallow-level intrusions is presented here. Structures are organised in four main groups, according to logical breaks in the timing of magma emplacement, independent of the scales of features: (1) Intrusion-related structures, formed as the magma is making space and then develops into its intrusion shape; (2) Magmatic flow-related structures, developed as magma moves with suspended crystals that are free to rotate; (3) Solid-state, flow-related structures that formed in portions of the intrusions affected by continuing flow of nearby magma, therefore considered to have a syn-magmatic, non-tectonic origin; (4) Thermal and fragmental structures, related to creation of space and impact on host materials. This scheme appears as a rational organisation, helpful in describing and interpreting the large variety of structures observed in shallow-level intrusions

The effects of Al and vacancies on Li substitution in iron staurolite: a synthesis approach

Synthesis of a variety of single phase iron lithium staurolite samples (at 720°C, 30 kbar, fO2 = IW) demonstrates that a saturation level of Li is attained in iron staurolite at ~ 1.5 Li ions per 48 O via substitution [4]Li+ + 0.33[6]Al3- = [4]Fe2+ + 0.33[6]□. -from Autho

Tourmaline at diagenetic to low-grade metamorphic conditions: Its petrologic applicability

Tourmaline developed under low-temperature conditions (\u3c~300. °C) typically has distinctive morphological and chemical characteristics that reveal significant information about the environments in which they crystallize. Under diagenetic conditions, tourmaline can develop as overgrowths on detrital tourmaline cores or as new, authigenic crystals. Tourmaline, as monopolar crystal overgrowths, is found in sandstones, shales, conglomerates, dolostones and limestones nucleating exclusively at the positive end of the c axis (. +c pole) on the detrital grain, a feature related to the mineral\u27s polar nature. These overgrowths tend to have compositions dominated by X-site vacant tourmaline species (e.g. foitite) and can be linked to growth in aqueous environments low in Na, with other chemical characteristics related to the host rocks. As temperature increases, tourmaline overgrowths develop at both the +c pole and -. c pole, but continue to exhibit a significant degree of morphological and chemical asymmetries. These differences at either pole diminish as a function of increasing temperature such that it can be used as an intramineral geothermometer.Authigenic tourmalines without detrital tourmaline nuclei are found in many sedimentary or weakly metamorphosed metasedimentary rocks as well as fluid-dominated geothermal systems. Here, tourmalines are commonly foititic, but have Mg-Fe contents influenced by the host rock composition. Low-temperature tourmalines developed in hypersaline environments (e.g. salt domes) have distinct chemical characteristics - high Na, Fe 3+ and WO, and follow a trend between oxy-dravite and povondraite (O-P trend). This compositional trend can be used as a guide to indicate tourmaline development within low-temperature hypersaline environments and appears to be diagnostic of an oxidizing environment with high Na in the fluid and high salinity with the resulting reduction of the activity of H 2O. The O-P trend is retained in some meta-evaporite deposits that are relatively high grade and is found in tourmaline from some types of economically important metal deposits. Although tourmalines in low temperature environments are largely overlooked, they have potential to be a useful indicator of the chemical and thermal environments in a regime largely absent of such indicators. © 2012 Elsevier B.V

Compositional zoning and element partitioning in nickeloan tourmaline from a metamorphosed karstbauxite from Samos, Greece

Blue-green nickeloan tourmaline from a micaceous enclave of a marble from Samos, Greece, contains unusually high concentrations of Ni (up to 3.5 wt% NiO). Co (up to 1.3 wt% CoO), and Zn (up to 0.8 wt% ZnO). The polymetamorphic karstbauxite sample has an uncommon assemblage of nickeloan tourmaline, calcite, zincian staurolite, gahnite, zincohögbomite, diaspore, muscovite, paragonite, and rutile. The complex geologic history is reflected in multi-staged tourmaline growth, with cores that represent detrital fragments surrounded by two-staged metamorphic overgrowths. Zone-1 metamorphic overgrowths, which nucleated next to detrital cores, are highly asymmetric and exhibit compositional polarity such that narrow overgrowths of brown schorl developed at the (-)c-pole are enriched in Mg, Ti, and F, and depleted in Al, Fe, and X-site vacancies (x) relative to wider, gray-blue schorl-to-foitite overgrowths developed at the (+) c-pole. Volumetrically dominant Zone-2 overgrowths are strongly zoned nickeloan dravites with a continuous increase in Mg, Co, Ca, and F at the expense of Fe, Zn, Cr, and V from the Zone-1 interface to the outermost rim. Within Zone 2, Ni reaches a maximum of 0.5 apfu before decreasing in the outer 20-40 μm. Zone-2 overgrowths also exhibit compositional polarity such that, at the (-) c-pole, overgrowths are enriched in Mg, F, Na, Ca, and Cr relative to overgrowths at the (+) c-pole that are, in turn, enriched in Al, Fe, Ni, Co, and x. Element partitioning involving tourmaline rims and coexisting minerals indicates that relative partitioning of Ni is tourmaline ≫ staurolite \u3e gahnite; Co is tourmaline \u3e staurolite \u3e gahnite; and Zn is gahnite \u3e staurolite ≫ tourmaline