The hallmark of a stem cell is its ability to self-renew and to produce numerous differentiated cells. This unique property is controlled by dynamic interplays between extrinsic signalling, epigenetic, transcriptional and post-transcriptional regulations. Recent research indicates that microRNAs (miRNAs) have an important role in regulating stem cell self-renewal and differentiation by repressing the translation of selected mRNAs in stem cells and differentiating daughter cells. Such a role has been shown in embryonic stem cells, germline stem cells and various somatic tissue stem cells. These findings reveal a new dimension of gene regulation in controlling stem cell fate and behaviour.

The contribution of lncRNAs to tumor progression and regulatory mechanisms driving their expression are areas of intense investigation. Here, we characterize the binding of heterogeneous nuclear ribonucleoprotein E1 (hnRNP E1) to a nucleic acid structural element located in exon 12 of PNUTS (also known as PPP1R10) pre-RNA that regulates its alternative splicing. HnRNP E1 release from this structural element, following its silencing, nucleo-cytoplasmic translocation or in response to TGFβ, allows alternative splicing and generates a non-coding isoform of PNUTS. Functionally the lncRNA-PNUTS serves as a competitive sponge for miR-205 during epithelial-mesenchymal transition. In mesenchymal breast tumor cells and in breast tumor samples, the expression of lncRNA-PNUTS is elevated and correlates with levels of ZEB mRNAs. Thus, PNUTS is a bifunctional RNA encoding both PNUTS-mRNA and lncRNA-PNUTS each eliciting distinct biological functions. While PNUTS-mRNA is ubiquitously expressed, lncRNA-PNUTS appears to be tightly regulated dependent on hnRNP E1’s status and tumor context.

There are several classes of ATP-dependent chromatin remodeling complexes, which modulate the structure of chromatin to regulate a variety of cellular processes. The budding yeast, Saccharomyces cerevisiae, encodes two ATPases of the ISWI class, Isw1p and Isw2p. Previously Isw1p was shown to copurify with three other proteins. Here we identify these associated proteins and show that Isw1p forms two separable complexes in vivo (designated Isw1a and Isw1b). Biochemical assays revealed that while both have equivalent nucleosomestimulated ATPase activities, Isw1a and Isw1b differ in their abilities to bind to DNA and nucleosomal substrates, which possibly accounts for differences in specific activities in nucleosomal spacing and sliding. In vivo, the two Isw1 complexes have overlapping functions in transcriptional regulation of some genes yet distinct functions at others. In addition, these complexes show different contributions to cell growth at elevated temperatures.As eukaryotes have evolved larger and more complex genomes, they have required the coevolution of enzymatic and structural mechanisms to physically organize large amounts of genetic material. For example, nearly every human cell packages approximately 2 m of DNA into a nucleus with a diameter 5 to 6 orders of magnitude smaller. This extraordinary level of compaction must, however, be flexible and organized for such processes as replication, repair, mitotic and meiotic chromosome segregation, and transcription to occur throughout the genome. The nucleosome, the primary unit of this chromatin organization, was described over 30 years ago (34). However, the higher-order structure of chromatin and its regulation are still largely undefined (32, 51).Two groups of factors remodel chromatin to regulate a variety of cellular processes. One such group, the histone-modifying enzymes, covalently modifies histone proteins. In contrast, the ATP-dependent nucleosome-remodeling factors utilize the energy of ATP hydrolysis to reposition or alter the structure of nucleosomes along a DNA template. The first, and best characterized, of this group is the SWI/SNF complex from Saccharomyces cerevisiae, a large (ϳ2 MDa) complex consisting of at least 10 subunits, including the ATPase Swi2/Snf2p. Homologs of the SWI/SNF complex have been found in nearly all eukaryotes studied, with several members often present in the same organism (16,20,40,45). Three other classes of ATP-dependent chromatin remodeling complexes have also been identified and are classified by the sequences of their Swi2/Snf2p-like ATPase subunits: the imitation-switch (ISWI) class, the chromodomain helicase DNA-binding (CHD)/Mi-2 class, and the most recently identified INO80 class. Like members of the SWI/SNF class, ISWI, CHD/Mi-2, and INO80 homologs have also been found in a wide variety of eukaryotes from yeasts to humans, suggesting that each class has important cellular functions that may have been evolutionarily conserved (for a review, see reference 18).The founding member of the ISWI class, Drosophila...

The inter-relationship between DNA repair and ATP dependent chromatin remodeling has begun to become very apparent with recent discoveries. ATP dependent remodeling complexes mobilize nucleosomes along DNA, promote the exchange of histones, or completely displace nucleosomes from DNA. These remodeling complexes are often categorized based on the domain organization of their catalytic subunit. The biochemical properties and structural information of several of these remodeling complexes are reviewed. The different models for how these complexes are able to mobilize nucleosomes and alter nucleosome structure are presented incorporating several recent findings. Finally the role of histone tails and their respective modifications in ATP-dependent remodeling are discussed.

Canalization, also known as developmental robustness, describes an organism's ability to produce the same phenotype despite genotypic variations and environmental influences 1,2. In Drosophila, Hsp90, the Trithorax group proteins, and transposon silencing have been implicated in canalization 3,4. Despite this, molecular mechanism underlying canalization remains elusive. Here, using an Drosophila eye-outgrowth assay sensitized by the dominant Kr Irregular facets-1 (Kr If-1), allele 3 , we show that the piRNA pathway, but not siRNA or miRNA pathways, is involved in canalization. Furthermore, we isolated a protein complex composed of Hsp90, Piwi, and the Hsp70/Hsp90 Organizing Protein Homolog (Hop), and demonstrated the function of this complex in canalization. Our data indicate that Hsp90 and Hop regulate the piRNA pathway via Piwi to mediate canalization. Moreover, they point to epigenetic silencing of the expression of existing genetic variants and the suppression of transposon-induced new genetic variation as two major mechanisms underlying piRNA pathway-mediated canalization. In both plants and animals, Hsp90 buffers against morphological changes induced either by genetic or non-genetic mechanisms, thereby promoting the robustness of the developmental programs that have been subjected to natural selection 5-8. However, under certain conditions, such as environmental stress, Hsp90 becomes overwhelmed, loosens its grip on canalization, and fails to repress the expression of genotype variants that have accumulated during evolution. The expressed phenotypes quickly become independent of Hsp90 deficiency, can be inherited in later generations, and could be subject to natural selection 3,5. In addition to Hsp90, maternally inherited epigenetic machineries also prevent expression of Users may view, print, copy, download and text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:

The nucleosome remodeling activity of ISW1a was dependent on whether ISW1a was bound to one or both extranucleosomal DNAs. ISW1a preferentially bound nucleosomes with an optimal length of ϳ33 to 35 bp of extranucleosomal DNA at both the entry and exit sites over nucleosomes with extranucleosomal DNA at only one entry or exit site. Nucleosomes with extranucleosomal DNA at one of the entry/exit sites were readily remodeled by ISW1a and stimulated the ATPase activity of ISW1a, while conversely, nucleosomes with extranucleosomal DNA at both entry/exit sites were unable either to stimulate the ATPase activity of ISW1a or to be mobilized. DNA footprinting revealed that a major conformational difference between the nucleosomes was the lack of ISW1a binding to nucleosomal DNA two helical turns from the dyad axis in nucleosomes with extranucleosomal DNA at both entry/exit sites. The Ioc3 subunit of ISW1a was found to be the predominant subunit associated with extranucleosomal DNA when ISW1a is bound either to one or to both extranucleosomal DNAs. These two conformations of the ISW1a-nucleosome complex are suggested to be the molecular basis for the nucleosome spacing activity of ISW1a on nucleosomal arrays. ISW1b, the other isoform of ISW1, does not have the same dependency for extranucleosomal DNA as ISW1a and, likewise, is not able to space nucleosomes.Chromatin remodeling complexes make chromatin more accessible for various cellular processes inside the cell by either covalently modifying histones (34) or mobilizing the histone octamer along DNA in cis or trans (7). A link between these two distinct chromatin remodeling activities has been shown, and in some instances, they even reside together in the same complex (20, 44). ATP-dependent chromatin remodeling causes changes in the nucleosome translational position (12,18,21,42), the exchange of histone variants (3,9,15,19,26,29), and even the removal of nucleosomes (31).ISWI, a class of ATP-dependent chromatin remodeling complexes (24), forms a number of distinct complexes in Saccharomyces cerevisiae (36), Drosophila melanogaster (37), and vertebrates (22). These remodeling complexes have an ATPase subunit that belongs to the SWI2/SNF2 subfamily of DEAD/H helicases (8). The ISWI family of ATPases is characterized by SANT and SANT-like domains in the catalytic subunit (11) that have been proposed to interact with histone tails (1, 2). ISWI requires histone H4 tail for stimulation of the ATPase activity, and several of the ISWI class remodelers generate regularly spaced nucleosomal arrays (13,36,39) and facilitate the deposition of histones onto DNA (14). In S. cerevisiae, there are two distinct ISWI genes, ISW1 and ISW2 (36). Isw1 is in two different complexes, ISW1a (Isw1 and Ioc3) and ISW1b (Isw1, Ioc2, and Ioc4), in addition to being present as a monomer (41). While no known protein motifs are evident in Ioc3, Ioc2 has a PHD finger, and Ioc4 has a PWWP motif, a putative DNA-binding (30) and chromatin-targeting domain (10). ISW2 is a four-subunit complex composed of I...

Summary Distinct stages in ATP-dependent chromatin remodeling are found as ISW2, an ISWI type complex, forms a stable and processive complex with nucleosomes upon hydrolysis of ATP. There are two conformational changes of the ISW2-nucleosome complex associated with binding and hydrolysis of ATP. The initial binding of ISW2 to extranucleosomal DNA, the entry site and near the dyad axis of the nucleosome is enhanced by ATP binding; while subsequent ATP hydrolysis is required for template-commitment and causes ISW2 to expand its interactions with nucleosomal DNA to an entire gyre of the nucleosome and a short ~3–4 bp site on the other gyre. The histone-fold like subunit Dpb4 associates with nucleosomal DNA ~15 bp from the ATPase domain as part of this change and may help disrupt histone-DNA interactions. These additional contacts are independent of the ATPase domain tracking along nucleosomal DNA and are maintained as ISW2 moves nucleosomes on DNA.

RNA-binding proteins (RBP) and noncoding RNAs (ncRNA), such as long noncoding RNAs (lncRNA) and microRNAs (miRNA), control co- and posttranscriptional gene regulation (PTR). At the PTR level, RBPs and ncRNAs contribute to pre-mRNA processing, mRNA maturation, transport, localization, turnover, and translation. Deregulation of RBPs and ncRNAs promotes the onset of cancer progression and metastasis. Both RBPs and ncRNAs are altered by signaling cascades to cooperate or compete with each other to bind their nucleic acid targets. Most importantly, transforming growth factor-beta (TGFβ) signaling plays a significant role in controlling gene expression patterns by targeting RBPs and ncRNAs. Because of TGFβ signaling in cancer, RBP-RNA or RNA-RNA interactions are altered and cause enhanced cell growth and tumor cell dissemination. This review focuses on the emerging concepts of TGFβ signaling on posttranscriptional gene regulation and highlights the implications of RBPs and ncRNAs in cancer progression and metastasis. .