https://www.cell.com/cell/pdf/S0092-8674(09)00083-X.pdf

Origins and Mechanisms of miRNAs and siRNAs

Cytosine DNA methylation is a stable epigenetic mark that is crucial for diverse biological processes, including gene and transposon silencing, imprinting and X chromosome inactivation. Recent findings in plants and animals have greatly increased our understanding of the pathways used to accurately target, maintain and modify patterns of DNA methylation and have revealed unanticipated mechanistic similarities between these organisms. Key roles have emerged for small RNAs, proteins with domains that bind methylated DNA and DNA glycosylases in these processes. Drawing on insights from both plants and animals should deepen our understanding of the regulation and biological significance of DNA methylation.

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

MicroRNAs (miRNAs) are small, endogenous RNAs that regulate gene expression in plants and animals. In plants, these approximately 21-nucleotide RNAs are processed from stem-loop regions of long primary transcripts by a Dicer-like enzyme and are loaded into silencing complexes, where they generally direct cleavage of complementary mRNAs. Although plant miRNAs have some conserved functions extending beyond development, the importance of miRNA-directed gene regulation during plant development is now particularly clear. Identified in plants less than four years ago, miRNAs are already known to play numerous crucial roles at each major stage of development-typically at the cores of gene regulatory networks, targeting genes that are themselves regulators, such as those encoding transcription factors and F-box proteins.

/pdf/micrornas-and-their-regulatory-roles-in-plants-11zqu0d6p0.pdf

MicroRNAs AND THEIR REGULATORY ROLES IN PLANTS

Since the discovery in 1993 of the first small silencing RNA, a dizzying number of small RNA classes have been identified, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). These classes differ in their biogenesis, their modes of target regulation and in the biological pathways they regulate. There is a growing realization that, despite their differences, these distinct small RNA pathways are interconnected, and that small RNA pathways compete and collaborate as they regulate genes and protect the genome from external and internal threats.

/pdf/small-silencing-rnas-an-expanding-universe-4g07glsh6g.pdf

Small silencing RNAs: an expanding universe

Overlapping epigenetic mechanisms have evolved in eukaryotic cells to silence the expression and mobility of transposable elements (TEs). Owing to their ability to recruit the silencing machinery, TEs have served as building blocks for epigenetic phenomena, both at the level of single genes and across larger chromosomal regions. Important progress has been made recently in understanding these silencing mechanisms. In addition, new insights have been gained into how this silencing has been co-opted to serve essential functions in 'host' cells, highlighting the importance of TEs in the epigenetic regulation of the genome.

http://depa.fquim.unam.mx/amyd//archivero/Tarea3_23133.pdf

Transposable elements and the epigenetic regulation of the genome.

Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation.

The Arabidopsis Chromatin-Modifying Nuclear siRNA Pathway Involves a Nucleolar RNA Processing Center

Cities, due to the presence of ports and airports and the high diversity of trees in streets, parks, and gardens, may play an important role for the introduction of invasive forest pests. We hypothesize that areas of urban forest facilitate the establishment of non-native forest pests. Based on scientific literature and a pan-European database on non-native species feeding on woody plants, we analysed where the first detections occurred in European countries. We collected site data for 137 first detections in Europe and 508 first European country-specific records. We also estimated the percentage of tree cover and suitable habitat (green areas with trees) in buffers around detection points. The large majority of first records (89% for first record in Europe and 88% for first records in a European country) were found in cities or suburban areas. Only 7% of the cases were in forests far from cities. The probability of occurrence decreased sharply with distance from the city. The probability to be detected in urban areas was higher for sap feeders, gall makers, and seed or fruit feeders (>90%) than for bark and wood borers (81%). Detection sites in cities were highly diverse, including public parks, street trees, university campus, arboreta, zoos, and botanical gardens. The average proportion of suitable habitat was less than 10% in urban areas where the species were detected. Further, more than 72% of the cases occurred in sites with less than 20% of tree cover. Hotspots of first detection were identified along the coastal regions of the Mediterranean and Atlantic, and near industrial areas of central Europe. We conclude that urban trees are main facilitators for the establishment of non-native forest pests, and that cities should thus be intensely surveyed. Moreover, as urban areas are highly populated, the involvement of citizens is highly recommended.

Urban trees facilitate the establishment of non-native forest insects

The pine wood nematode (PWN) is an invasive species which was introduced into Europe in 1999. It represents a major economic and ecological threat to European forests. In Europe, the maritime pine is the main host and Monochamus galloprovinciallis is its only vector. Our goal was to analyze the effect of landscape heterogeneity on the vector’s dispersal. We further aimed at developing a new method to locate the origin of insects captured in a systematic network of pheromone traps. A mark-release-recapture experiment was carried out in a heterogeneous landscape combining maritime pine plantations, clear-cuts and isolated patches of broadleaved and mixed forests in the southwest of France. Least-cost path analysis was used to model dispersal trajectories and assign friction values to each land-use type in the landscape. We used the trap’s geographical coordinates, capture levels and mean friction values of neighbouring patches to calculate a weighed barycentre and the position of the release of marked beetles. Least Cost Path modelling revealed the vector’s tendency to avoid habitat patches such as mixed or deciduous forests and not avoid clear-cuts. The weighted barycentre method was greatly improved when the friction values of the trap’s surrounding land-uses were used. Our study demonstrates the value of applying landscape ecology concepts and methods to improve our understanding and prediction of pest invasion processes. A practical application is the design of systematic grids of pheromone traps to locate the infection focus from which PWN vectors originate in a newly colonized area.

Pedro Costa Nunes

Papers

Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation.

The Arabidopsis Chromatin-Modifying Nuclear siRNA Pathway Involves a Nucleolar RNA Processing Center

Urban trees facilitate the establishment of non-native forest insects

Modelling Monochamus galloprovincialis dispersal trajectories across a heterogeneous landscape to optimize monitoring by trapping networks