Volume 3, Issue 5

Dynamic DNA methylation is a prerequisite for many developmental processes and maintenance of cellular integrity. In mammals however, mechanisms of active DNA demethylation have for long been elusive. The discovery of the ten-eleven translocation (Tet) family of enzymes that oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) or 5-carboxylcytosine (5caC) provided new means by which DNA methylation could actively be reversed. This review focuses on the possible mechanisms of DNA demethylation via Tet proteins and their metabolites 5hmC, 5fC and 5caC. Additionally, it discusses the roles of the three Tet protein family members Tet1, Tet2 and Tet3 as developmental regulators, probably in part independent of their enzymatic activity. By contrast, recent evidence suggests a function of 5hmC as an epigenetic mark on its own, going beyond the expectation of only acting as an intermediate in an active DNA demethylation pathway.

The development of genome-wide analysis tools has prompted global investigation of the gene expression program, revealing highly coordinated control mechanisms that ensure proper spatiotemporal activity of a cell’s macromolecular components. With respect to the regulation of RNA transcripts, the concept of RNA regulons, which – by analogy with DNA regulons in bacteria – refers to the coordinated control of functionally related RNA molecules, has emerged as a unifying theory that describes the logic of regulatory RNA-protein interactions in eukaryotes. Hundreds of RNA-binding proteins and small non-coding RNAs, such as microRNAs, bind to distinct elements in target RNAs, thereby exerting specific and concerted control over posttranscriptional events. In this review, we discuss recent reports committed to systematically explore the RNA-protein interaction network and outline some of the principles and recurring features of RNA regulons: the coordination of functionally related mRNAs through RNA-binding proteins or non-coding RNAs, the modular structure of its components, and the dynamic rewiring of RNA-protein interactions upon exposure to internal or external stimuli. We also summarize evidence for robust combinatorial control of mRNAs, which could determine the ultimate fate of each mRNA molecule in a cell. Finally, the compilation and integration of global protein-RNA interaction data has yielded first insights into network structures and provided the hypothesis that RNA regulons may, in part, constitute noise ‘buffers’ to handle stochasticity in cellular transcription.

The mammalian cell nucleus is a highly compartmentalized system in which multiple subnuclear structures, called nuclear bodies, exist in the nucleoplasmic spaces. Some of the nuclear bodies contain specific long non-coding RNAs (ncRNAs) as their components, and may serve as sites for long ncRNA functions that remain largely enigmatic. A paraspeckle is a nuclear body that is almost ubiquitously observed in mammalian cultured cells but is cell population-specific in adult mouse tissue. The paraspeckle structure is RNase-sensitive. Long ncRNAs, termed MENε/β ncRNAs (also referred to as NEAT1 ncRNAs), have been identified as the RNA components of the paraspeckles. Specific elimination has revealed that MENε/β ncRNAs are essential components for the formation of the intact paraspeckle structure. Paraspeckle formation requires the continual MENε/β ncRNA biogenesis process, including ongoing transcription, alternative 3′-end processing, and stabilization. Some paraspeckle-localized RNA-binding proteins (p54/nrb and PSF) direct paraspeckle formation through the selective stabilization of MENβ ncRNA. Both MENε/β ncRNA expression and their subsequent interactions with paraspeckle proteins can be regulated under environmental and developmental conditions, which are reflected in the size and number of the paraspeckles. However, how paraspeckles function remains largely unsolved. Paraspeckles appear to serve as the site of nuclear retention of specific mRNAs that are selectively transported to the cytoplasm upon certain signals. Alternatively, MENε/β ncRNAs may sequester paraspeckle proteins that function outside the paraspeckles. This review focuses on known aspects of paraspeckles and provides a model of their structure and function.

Transforming growth factor-β (TGF-β) family members, including TGF-βs and bone morphogenetic proteins (BMPs), play important roles in directing the fate of stem cells. In embryonic stem cells, the TGF-β superfamily participates in almost all stages of cell development, such as cell maintenance, lineage selection, and progression of differentiation. In adult mesenchymal stem cells (MSCs), TGF-βs can provide competence for early stages of chondroblastic and osteoblastic differentiation, but they inhibit myogenesis, adipogenesis, and late-stage osteoblast differentiation. BMPs also inhibit adipogenesis and myogenesis, but they strongly promote osteoblast differentiation. The TGF-β superfamily members signal via specific serine/threonine kinase receptors and their nuclear effectors termed Smad proteins as well as through non-Smad pathways, which explain their pleiotropic effects in self-renewal and differentiation of stem cells. This review summarizes the current knowledge on the pleiotropic effects of the TGF-β superfamily of growth factors on the fate of stem cells and also discusses the mechanisms by which the TGF-β superfamily members control embryonic and MSCs differentiation.

Orexin peptides and their cognate receptors were discovered 14 years ago. They soon took a very central position in the regulation of sleep and wakefulness. Active studies have further elucidated these functions as well as the role of orexins in, for instance, appetite, metabolism, analgesia, addiction, and stress response. This review summarizes all the important fields but especially aims at focusing on novel findings and future directions.

Telomere composition and structure have been studied in several arthropods allowing us to better understand the evolution of such an important portion of the eukaryotic chromosomes. Genes coding for telomerase reverse transcriptase (TERT) have been sequenced and studied in few arthropod species only, where they resulted highly transcribed also in somatic tissues suggesting a different TERT regulation in respect to vertebrates. Contrary to the strict conservation of telomeres, subtelomeric regions were more polymorphic and heterogeneous in composition and frequently contained retrotransposable elements that strongly influenced subtelomere evolution.

Phospholipase A 1 is an enzyme that hydrolyzes phospholipids, producing 2-acyl-lysophospholipids and fatty acids. The intracellular phospholipase A 1 (iPLA 1 ) protein family is a relatively recently discovered lipid-metabolizing enzyme family. Lower eukaryotes, such as yeasts and nematodes, and plants have only one iPLA 1 protein, whereas mammals have three iPLA 1 family proteins (PA-PLA 1 /DDHD1/iPLA 1 α, p125/Sec23IP/iPLA 1 β and KIAA0725p/DDHD2/iPLA 1 γ). Mammalian iPLA 1 proteins are localized in different cellular compartments, and two of them, p125 and KIAA0725p, have been implicated in membrane trafficking events. Recent gene targeting studies on several organisms showed that iPLA 1 family proteins are involved in various physiological functions, including plant shoot gravitropism, epithelial stem cell differentiation and spermiogenesis. In this review, we describe the features of iPLA 1 family proteins and recent progress regarding our understanding of their physiological functions.

A crucial challenge for vaccine development is to design vaccines that induce a long-lasting protective immune response, i.e., immune memory. The persistence of antigen-specific antibody titers over a protective threshold, and the ability to exibit a ‘recall response’ to a subsequent encounter with an antigen have long been the only measurable correlates of vaccine take and immune memory development, suffering from the disadvantage of relying on long-term monitoring of the immune response. In the last few years, advances in the technologies for the identification and characterization of the cell subsets and molecular pathways involved in the immune response to vaccination have allowed innovative approaches to the identification of early correlates of immune memory. In this review, we discuss recent data and hypotheses on early correlates of the development of immune memory, with special emphasis on the gene expression signatures that underlie the self-renewal ability of some lymphocyte subsets, and their similarities with gene expression signatures in stem cells.