MicroRNAs and the regulation of cell death

Programmed cell death, or apoptosis, is ubiquitous, both during development and in the adult. Many components of the evolutionarily conserved machinery that brings about and regulates cell death have been identified, and all of these are proteins. However, in the past three years it has become clear that roughly 1% of predicted genes in animals encode small noncoding RNAs known as microRNAs, which regulate gene function. Here we review the recent identification of microRNA cell death regulators in Drosophila, hints that such regulators are also likely to exist in mammals, and more generally the approaches and tools that are now available to probe roles for noncoding RNAs in the control of cell death.     

MicroRNAs in the miR-106b family regulate p21/CDKN1A and promote cell cycle progression

microRNAs in the miR-106b family are overexpressed in multiple tumor types and are correlated with the expression of genes that regulate the cell cycle. Consistent with these observations, miR-106b family gain of function promotes cell cycle progression, whereas loss of function reverses this phenotype. Microarray profiling uncovers multiple targets of the family, including the cyclin-dependent kinase inhibitor p21/CDKN1A. We show that p21 is a direct target of miR-106b and that its silencing plays a key role in miR-106b-induced cell cycle phenotypes. We also show that miR-106b overrides a doxorubicin-induced DNA damage checkpoint. Thus, miR-106b family members contribute to tumor cell proliferation in part by regulating cell cycle progression and by modulating checkpoint functions.     

MicroRNAs and cell differentiation in mammalian development

MicroRNAs (miRNAs) are a group of recently discovered small RNAs produced by the cell using a unique process, involving RNA polymerase II, Microprocessor protein complex, and the RNAase III/Dicer endonuclease complex, and subsequently sequestered in an miRNA ribonucleoprotein complex. The biological functions of miRNAs depend on their ability to silence gene expression, primarily via degradation of the target mRNA and/or translational suppression, mediated by the RNA-induced silencing complex (RISC). First discovered in Caenorhabditis elegans (lin-4), miRNAs have now been identified in a wide array of organisms, including plants, zebrafish, Drosophila, and mammals. The expression of miRNAs in multicellular organisms exhibits spatiotemporal, and tissue- and cell-specificity, suggesting their involvement in tissue morphogenesis and cell differentiation. More than 200 miRNAs have been identified or predicted in mammalian cells. Recent studies have demonstrated the importance of miRNAs in embryonic stem cell differentiation, limb development, adipogenesis, myogenesis, angiogenesis and hematopoiesis, neurogenesis, and epithelial morphogenesis. Overexpression (gain-of-function) and inactivation (loss-of-function) are currently the primary approaches to studying miRNA functions. Another family of small RNAs related to miRNAs is the small interfering RNAs (siRNAs), generated by Dicer from long double-stranded RNAs (dsRNAs), and produced from an induced transgene, a viral intruder, or a rogue genetic element. siRNAs silence genes via either mRNA degradation, using the RISC, or DNA methylation. siRNAs are actively being applied in basic, functional genetic studies, particularly in the generation of gene knockdown animals, as well as in gene knockdown studies of cultured cells. These studies have provided invaluable information on the specific function(s) of individual genes. siRNA technology also presents exciting potential as a therapeutic approach in disease prevention and treatment, as suggested by a recent study targeting apolipoprotein B (ApoB) in primates. Further elucidation of how miRNAs and other small RNAs interact with known and yet-to-be identified gene regulatory pathways in the cell should provide us with a more in-depth understanding of the mechanisms regulating cellular function and differentiation, and facilitate the application of small RNA technology in disease control and treatment.     

MicroRNAs regulate dendritic cell differentiation and function

MicroRNAs (miRNAs) are an important class of cellular regulators that modulate gene expression and thereby influence cell fate and function. In the immune system, miRNAs act at checkpoints during hematopoietic development and cell subset differentiation, they modulate effector cell function, and they are implicated in the maintenance of homeostasis. Dendritic cells (DCs), the professional APCs involved in the coordination of adaptive immune responses, are also regulated by miRNAs. Some DC-relevant miRNAs, including miR-155 and miR-146a, are shared with other immune cells, whereas others have been newly identified. In this review, we summarize the current understanding of where miRNAs are active during DC development from myeloid precursors and differentiation into specialized subsets, and which miRNAs play roles in DC function.     

Neurogenesis and the cell cycle

For a long time, it has been understood that neurogenesis is linked to proliferation and thus to the cell cycle. Recently, the gears that mediate this linkage have become accessible to molecular investigation. This review describes some of the progress that has been made in understanding how the molecular machinery of the cell cycle is used in the processes of size regulation in the brain, histogenesis, neuronal differentiation, and the maintenance of stem cells.     

Proteolysis and the cell cycle

Without doubt, one of the more dramatic breakthroughs in recent cell cycle history has been the discovery that growth regulators are controlled by proteolysis. This concept blossomed within the last six or seven years, but the story really began when cyclins were discovered, soon followed by the suggestion that proteolysis events might control cell cycle transitions. Proteolytic targets that are now known include most of the cyclins, cyclin dependent kinase inhibitors, DNA replication factors, the securin class of proteins that inhibit loss of sister chromatid cohesion following DNA replication and, of course, the cohesion factor itself. Protein degradation is controlled in various ways including ubiquitin-dependent targeting to proteasomes, activation of ubiquitin ligases by ubiquitin-like molecule conjugation, phosphorylation of proteolytic targets, and activation of the separin class of proteases.     

Archaea and the cell cycle

Sequence similarity data suggest that archaeal chromosome replication is eukaryotic in character. Putative nucleoid-processing proteins display similarities to both eukaryotic and bacterial counterparts, whereas cell division may occur through a predominantly bacterial mechanism. Insights into the organization of the archaeal cell cycle are therefore of interest, not only for understanding archaeal biology, but also for investigating how components from the other two domains interact and work in concert within the same cell; in addition, archaea may have the potential to provide insights into eukaryotic initiation of chromosome replication.     

Malaria and the cell cycle

The current model of cell cycle control features a succession of active cyclin-CDK (cyclin-dependent kinase) complexes, where accumulation of each successive cyclin leads to activation of its associated kinase. Cell fusion experiments have shown that nuclei sharing common cytoplasm progress through the cell cycle in synchrony. During schizogony of Plasmodium falciparum, nuclear division occurs asynchronously, and thus cannot be regulated by synthesis and accumulation of cyclins in the cytoplasm. We suggest that schizonts must have a ready pool of cyclins for activating all stages of the cycle, and that the cell cycle is regulated independently in each nucleus.     

Apoptosis and the cell cycle

Apoptosis is an evolutionarily conserved ‘suicide’ programme present in all metazoan cells. Despite its highly conserved nature, it is only recently that any of the molecular mechanisms underlying apoptosis have been identified. Several lines of reasoning indicate that apoptosis and cell proliferation coincide to some degree: many oncogenes that promote cell cycle progression also induce apoptosis; damage to the cell cycle or to DNA integrity is a potent trigger of apoptosis; and the key tumour suppressor proteins, p105^rb and p53, exert direct effects both on cell viability and on cell cycle progression. There is less evidence, however, to indicate that apoptosis and the cell cycle share common molecular mechanisms. Moreover, the interleukin-1β converting enzyme (ICE) family of cysteine proteases is now known to play a key role in apoptosis but has no discernible role in the cell cycle, arguing that the two processes are discrete.     

Apoptosis and the cell cycle

In this review, we consider apoptosis as a process intimately linked to the cell cycle. There are several reasons for thinking of apoptosis as a cell cycle phenomenon. First, within the organism, apoptosis is almost exclusively found in proliferating tissues. Second, artificial manipulation of the cell cycle can either prevent or potentiate apoptosis, depending on the point of arrest. Data from such studies have suggested that molecules acting late in G1 are required for apoptosis. Since passage through late G1 into S phase in mammalian cells is known to be regulated by p53 and by activation of cyclin-dependent kinases, we also examine recent studies linking these molecules to the apoptotic pathway.     

Morphogenesis and the cell cycle

Studies of the processes leading to the construction of a bud and its separation from the mother cell in Saccharomyces cerevisiae have provided foundational paradigms for the mechanisms of polarity establishment, cytoskeletal organization, and cytokinesis. Here we review our current understanding of how these morphogenetic events occur and how they are controlled by the cell-cycle-regulatory cyclin-CDK system. In addition, defects in morphogenesis provide signals that feed back on the cyclin-CDK system, and we review what is known regarding regulation of cell-cycle progression in response to such defects, primarily acting through the kinase Swe1p. The bidirectional communication between morphogenesis and the cell cycle is crucial for successful proliferation, and its study has illuminated many elegant and often unexpected regulatory mechanisms. Despite considerable progress, however, many of the most puzzling mysteries in this field remain to be resolved.