And now introducing mammalian mirtrons

Mirtrons are short hairpin introns recently found in flies and nematodes that provide an alternative source for animal microRNA biogenesis and use the splicing machinery to bypass Drosha cleavage in initial maturation. The presence of mirtrons outside of invertebrates was not previously known. In the October 26 issue of Molecular Cell, Berezikov et al. expose a number of short mammalian introns as mirtrons.     

Identification of mirtrons in rice using MirtronPred: a tool for predicting plant mirtrons

Studies from flies and insects have reported the existence of a special class of miRNA, called mirtrons that are produced from spliced-out introns in a DROSHA-independent manner. The spliced-out lariat is debranched and refolded into a stem-loop structure resembling the pre-miRNA, which can then be processed by DICER into mature ~21 nt species. The mirtrons have not been reported from plants. In this study, we present MirtronPred, a web based server to predict mirtrons from intronic sequences. We have used the server to predict 70 mirtrons in rice introns that were put through a stringent selection filter to shortlist 16 best sequences. The prediction accuracy was subsequently validated by northern analysis and RT-PCR of a predicted Os-mirtron-109. The target sequences for this mirtron were also found in the rice degradome database. The possible role of the mirtron in rice regulon is discussed. The MirtronPred web server is available at http://bioinfo.icgeb.res.in/mirtronPred.     

Functional VEGFA knockdown with artificial 3′-tailed mirtrons defined by 5′ splice site and branch point

Mirtrons are introns that form pre-miRNA hairpins after splicing to produce RNA interference (RNAi) effectors distinct from Drosha-dependent intronic miRNAs, and will be especially useful for co-delivery of coding genes and RNAi. A specific family of mirtrons – 3′-tailed mirtrons – has hairpins precisely defined on the 5′ end by the 5′ splice site and 3′ end by the branch point. Here, we present design principles for artificial 3′-tailed mirtrons and demonstrate, for the first time, efficient gene knockdown with tailed mirtrons within eGFP coding region. These artificial tailed mirtrons, unlike canonical mirtrons, have very few sequence design restrictions. Tailed mirtrons targeted against VEGFA mRNA, the misregulation of which is causative of several disorders including cancer, achieved significant levels of gene knockdown. Tailed mirtron-mediated knockdown was further shown to be splicing-dependent, and at least as effective as equivalent artificial intronic miRNAs, with the added advantage of very defined cleavage sites for generation of mature miRNA guide strands. Further development and exploitation of this unique mirtron biogenesis pathway for therapeutic RNAi coupled into protein-expressing genes can potentially enable the development of precisely controlled combinatorial gene therapy.     

Conservation of mammals on a tobacco farm on the Highlands of Malawi

The natural vegetation of the Shire Highlands of Malawi has become fragmented because of human activities. As a consequence, some species of mammals have become locally extinct and the population numbers and geographical ranges of other species have declined. This study investigated the species richness of mammals on a commercial tobacco farm, and the importance of remnants of natural vegetation on farms for the conservation of mammals. The farm covered 180 ha and supported 44 species of mammals (equivalent to 66% of the species known to occur in the Shire Highlands at a similar altitude, and 24% of the total mammalian fauna of Malawi). Most of the species were bats (22 species) and rodents (13 species). The largest remnants of natural 'miombo' woodland supported more species and more individuals than smaller remnants. The high species richness was due, in part, to the variety of different habitats on the farm ('miombo' woodland, riverine forest, grassland, swamp, streams and dams), as well as to good conservation practices. The farm is especially important for the conservation of 13 species which are rare and/or have limited geographical ranges in Malawi. It is suggested that well-managed farms which contain remnants of natural vegetation can play a significant role in the conservation of mammals, and other vertebrates, in Central Africa.     

Marsupial genetics and genomics

Marsupials, the 'other' mammals, are found only in Australasia and the Americas. They are quite different from eutherian ('placental') mammals, as well they might be after 130 million years of separate evolution. They display a unique pattern of mammalian organization and development that is reflected by differences in their genomes. Here, we introduce marsupials as alternative (but not inferior!) mammals and summarize the state of knowledge of marsupial relationships, marsupial chromosomes, maps, genes and genetic regulatory systems. We shamelessly present the case for a Kangaroo Genome Project.     

The tempo and mode of evolution: body sizes of island mammals

The tempo and mode of body size evolution on islands are believed to be well known. It is thought that body size evolves relatively quickly on islands toward the mammalian modal value, thus generating extreme cases of size evolution and the island rule. Here, we tested both theories in a phylogenetically explicit context, by using two different species-level mammalian phylogenetic hypotheses limited to sister clades dichotomizing into an exclusively insular and an exclusively mainland daughter nodes. Taken as a whole, mammals were found to show a largely punctuational mode of size evolution. We found that, accounting for this, and regardless of the phylogeny used, size evolution on islands is no faster than on the continents. We compared different selection regimes using a set of Ornstein-Uhlenbeck models to examine the effects of insularity of the mode of evolution. The models strongly supported clade-specific selection regimes. Under this regime, however, an evolutionary model allowing insular species to evolve differently from their mainland relatives performs worse than a model that ignores insularity as a factor. Thus, insular taxa do not experience statistically different selection from their mainland relatives.     

Defining structural homology between the mammalian and avian hippocampus through conserved gene expression patterns observed in the chick embryo

The mammalian hippocampus, a center of neurogenesis in the adult brain, is involved in critical functions such as learning and memory processing. Although there is an overall functional conservation between birds and mammals in the hippocampal region of the brain, there are several morphological differences. A few different models have been proposed for identifying regional and structural homology between the avian and mammalian hippocampus however a consensus is yet to be reached. In this study we have systematically and comprehensively characterized the developing chicken hippocampus at the molecular level. We have identified the time window of neurogenesis and apoptosis during hippocampal development as well as the likely origin and migration path of neurons of the ventral v-shaped region of chick hippocampus. In addition to this we have identified several genes with expression patterns that are conserved between the hippocampus of chicken and mice. Our study provides molecular data that partially supports one of the models reported in literature for structural homology between the avian and mammalian hippocampus. Functional characterization of the genes found in this study to be specifically expressed in the developing chicken hippocampus is likely to provide valuable information on the mechanisms regulating hippocampus development of birds and perhaps could be extrapolated to mammalian hippocampus development as well.     

The Decline of Isochores in Mammals: An Assessment of the GC ContentVariation Along the Mammalian Phylogeny

Whether isochores, the large-scale variation of the GC content in mammalian genomes, are being maintained has recently been questioned. It has been suggested that GC-rich isochores originated in the ancestral amniote genome but that whatever force gave rise to them is no longer effective and that isochores are now disappearing from mammalian genomes. Here we investigated the evolution of the GC content of 41 coding genes in 6 to 66 species of mammals by estimating the ancestral GC content using a method which allows for different rates of substitution between sites. We found a highly significant decrease in the GC content during early mammalian evolution, as well as a weaker but still significant decrease in the GC content of GC-rich genes later in at least three groups of mammals: primates, rodents, and carnivores. These results are of interest because they confirm the recently suggested disappearance of GC-rich isochores in some mammalian genomes, and more importantly, they suggest that this disappearance started very early in mammalian evolution.This article contains online supplementary material.     

Ecomorphology reveals Euler spiral of mammalian whiskers

Whiskers are present in many species of mammals. They are specialised vibrotactile sensors that sit within strongly innervated follicles. Whisker size and shape will affect the mechanical signals that reach the follicle, and hence the information that reaches the brain. However, whisker size and shape have not been quantified across mammals before. Using a novel method for describing whisker curvature, this study quantifies whisker size and shape across 19 mammalian species. We find that gross two-dimensional whisker shape is relatively conserved across mammals. Indeed, whiskers are all curved, tapered rods that can be summarised by Euler spiral models of curvature and linear models of taper, which has implications for whisker growth and function. We also observe that aquatic and semi-aquatic mammals have relatively thicker, stiffer, and more highly tapered whiskers than arboreal and terrestrial species. In addition, smaller mammals tend to have relatively long, slender, flexible whiskers compared to larger species. Therefore, we propose that whisker morphology varies between larger aquatic species, and smaller scansorial species. These two whisker morphotypes are likely to induce quite different mechanical signals in the follicle, which has implications for follicle anatomy as well as whisker function.     

Synthesis of a new Cre recombinase gene based on optimal codon usage for mammalian systems

The origin of the Cre recombinase gene is bacteriophage P1, and thus the codon usages are different from in mammals. In order to adapt this codon usage for mammals, we synthesized a "mammalian Cre recombinase gene" and examined its expression in Chinese hamster ovarian tumor (CHO) cells. Significant increases in protein production as well as mRNA levels were observed. When the recombination efficiency was compared using CHO cell transfectants having a cDNA containing loxP sites, the "mammalian Cre recombinase gene" recombined the loxP sites much more efficiently than the wild-type Cre recombinase gene.     

Differential effect of 1,10-phenanthroline on mammalian, yeast, and parasite glycosylphosphatidylinositol anchor synthesis.

Glycosylphosphatidylinositol (GPI) anchoring of proteins to the plasma membrane is a common mechanism utilized by all eukaryotes including mammals, yeast, and the Trypanosoma brucei parasite. We have previously shown that in mammals phenanthroline (PNT) blocks the attachment of phosphoethanolamine (P-EthN) groups to mannose residues in GPI anchor intermediates, thus preventing the synthesis of mammalian GPI anchors. Therefore, PNT is likely to inhibit GPI-phosphoethanolamine transferases (GPI-PETs). Here we report that in yeast, PNT also inhibits the synthesis of the GPI anchor as well as GPI-anchored proteins. Interestingly, the mechanism of PNT inhibition of GPI synthesis is different from that of YW3548, another putative GPI-PET inhibitor. In contrast to mammals and yeast, the synthesis of GPIs in T. brucei is not affected by PNT. Our results indicate that the T. brucei GPI-PET could be a potential target for antiparasitic drugs.     

Xist and the order of silencing

X inactivation is the mechanism by which mammals adjust the genetic imbalance that arises from the different numbers of gene-rich X-chromosomes between the sexes. The dosage difference between XX females and XY males is functionally equalized by silencing one of the two X chromosomes in females. This dosage-compensation mechanism seems to have arisen concurrently with early mammalian evolution and is based on the long functional Xist RNA, which is unique to placental mammals. It is likely that previously existing mechanisms for other cellular functions have been recruited and adapted for the evolution of X inactivation. Here, we critically review our understanding of dosage compensation in placental mammals and place these findings in the context of other cellular processes that intersect with mammalian dosage compensation.     

Retinal Attachment Instability Is Diversified among Mammalian Melanopsins

Melanopsins play a key role in non-visual photoreception in mammals. Their close phylogenetic relationship to the photopigments in invertebrate visual cells suggests they have evolved to acquire molecular characteristics that are more suited for their non-visual functions. Here we set out to identify such characteristics by comparing the molecular properties of mammalian melanopsin to those of invertebrate melanopsin and visual pigment. Our data show that the Schiff base linking the chromophore retinal to the protein is more susceptive to spontaneous cleavage in mammalian melanopsins. We also find this stability is highly diversified between mammalian species, being particularly unstable for human melanopsin. Through mutagenesis analyses, we find that this diversified stability is mainly due to parallel amino acid substitutions in extracellular regions. We propose that the different stability of the retinal attachment in melanopsins may contribute to functional tuning of non-visual photoreception in mammals.