Plant Science: Eucarya

Enhancers control the correct temporal and cell-type-specific activation of gene expression in multicellular eukaryotes. Knowing their properties, regulatory activity and targets is crucial to understand the regulation of differentiation and homeostasis. Here we use the FANTOM5 panel of samples, covering the majority of human tissues and cell types, to produce an atlas of active, in vivo-transcribed enhancers. We show that enhancers share properties with CpG-poor messenger RNA promoters but produce bidirectional, exosome-sensitive, relatively short unspliced RNAs, the generation of which is strongly related to enhancer activity. The atlas is used to compare regulatory programs between different cells at unprecedented depth, to identify disease-associated regulatory single nucleotide polymorphisms, and to classify cell-type-specific and ubiquitous enhancers. We further explore the utility of enhancer redundancy, which explains gene expression strength rather than expression patterns. The online FANTOM5 enhancer atlas represents a unique resource for studies on cell-type-specific enhancers and gene regulation. [ABSTRACT FROM AUTHOR]

The Golgi complex is part of the endomembrane system and is responsible for receiving transport cargos from the endoplasmic reticulum and for sorting and targeting them to their final destination. To perform its function in higher eukaryotic cells, the Golgi needs to be correctly assembled as a flattened membrane sandwich kept together by a protein matrix. The precise mechanism controlling the Golgi cisternae assembly is not yet known, but it is widely accepted that the Golgi Reassembly and Stacking Protein (GRASP) is a main component of the Golgi protein matrix. Unlike mammalian cells, which have two GRASP genes, lower eukaryotes present only one gene and distinct Golgi cisternae assembly. In this study, we performed a set of biophysical studies to get insights on the structural properties of the GRASP domains (DGRASPs) from both human GRASP55 and GRASP65 and compare them with GRASP domains from lower eukaryotes (Saccharomyces cerevisiae and Cryptococcus neoformans). Our data suggest that both human DGRASPs are essentially different from each other and that DGRASP65 is more similar to the subgroup of DGRASPs from lower eukaryotes in terms of its biophysical properties. GRASP55 is present mainly in the Golgi medial and trans faces, which are absent in both fungi, while GRASP65 is located in the cis‐Golgi. We suggest that the GRASP65 gene is more ancient and that its paralogue GRASP55 might have appeared later in evolution, together with the medial and trans Golgi faces in mammalians. [ABSTRACT FROM AUTHOR]

As an important regulator of gene expression in eukaryotes, microRNAs (miRNAs) have been subject to extensive research to understand their pleiotropic roles in development and pathological processes. Here, we review strategies that have been developed to map microRNA‐target interactions and the most effective methods to attribute post‐transcriptional gene regulation through miRNA‐mediated silencing. We further discuss the importance of the biological context for silencing. The tiny ribonucleic acid (RNA) molecules called microRNAs play an essential role in the maintenance of cells as demonstrated by several studies focusing on a plethora of human diseases. In this review, we discuss about strategies used to identify the molecular targets of those RNA molecules as well as describe the importance of studying their roles in their natural biological context. [ABSTRACT FROM AUTHOR]

There can be little doubt that mitochondria do not need much of an introduction. It is widely known that they are the "powerhouses" of the cell and that they produce all of the ATP (adenosine triphosphate) needed to sustain life. In addition, all eukaryotes (organisms with a cell nucleus) contain these important organelles—or so it was thought. Here lies an interesting paradox: Although it was generally believed that all eukaryotes did have mitochondria, it was also generally believed that the serial endosymbiosis theory was correct; the endosymbiosis theory required the existence of eukaryotes without mitochondria. This assumption was formalized with the now-disproven Archezoa hypothesis, which stated that several groups of "primitive" eukaryotes were of premitochondrial descent. This paradoxically defined group of amitochondriate eukaryotes has resulted in a spate of publications that have significantly changed the perception of the role of mitochondria in overall cellular metabolism and that have important ramifications for our understanding of the origin of eukaryotic life. [ABSTRACT FROM AUTHOR]