The c-Myc oncoprotein regulates transcription of genes that are associated with cell growth, proliferation and apoptosis. c-Myc levels are modulated by ubiquitin/proteasome-mediated degradation. Proteasome inhibition leads to c-Myc accumulation within nucleoli, indicating that c-Myc might have a nucleolar function. Here we show that the proteins c-Myc and Max interact in nucleoli and are associated with ribosomal DNA. This association is increased upon activation of quiescent cells and is followed by recruitment of the Myc cofactor TRRAP, enhanced histone acetylation, recruitment of RNA polymerase I (Pol I), and activation of rDNA transcription. Using small interfering RNAs (siRNAs) against c-Myc and an inhibitor of Myc-Max interactions, we demonstrate that c-Myc is required for activating rDNA transcription in response to mitogenic signals. Furthermore, using the ligand-activated MycER (ER, oestrogen receptor) system, we show that c-Myc can activate Pol I transcription in the absence of Pol II transcription. These results suggest that c-Myc coordinates the activity of all three nuclear RNA polymerases, and thereby plays a key role in regulating ribosome biogenesis and cell growth.

The yeast SWI/SNF complex is required for the transcription of several yeast genes and has been shown to alter nucleosome structure in an ATP-dependent reaction. In this study, we show that the complex stimulated in vitro transcription from nucleosome templates in an activation domain-dependent manner. Transcription stimulation by SWI/SNF required an activation domain with which it directly interacts. The acidic activation domains of VP16, Gcn4, Swi5, and Hap4 interacted directly with the purified SWI/SNF complex and with the SWI/SNF complex in whole-cell extracts. The similarity of activation domain interactions and transcriptional stimulation between SWI/SNF and the SAGA histone acetyltransferase complex may account for their apparent overlapping functions in vivo.

Nuclear receptors (NRs) comprise a family of ligand inducible transcription factors. To achieve transcriptional activation of target genes, DNA-bound NRs directly recruit general transcription factors (GTFs) to the preinitiation complex or bind intermediary factors, so-called coactivators. These coactivators often constitute subunits of larger multiprotein complexes that act at several functional levels, such as chromatin remodeling, enzymatic modification of histone tails, or modulation of the preinitiation complex via interactions with RNA polymerase II and GTFs. The binding of NR to coactivators is often mediated through one of its activation domains. Many NRs have at least two activation domains, the ligand-independent activation function (AF)-1, which resides in the N-terminal domain, and the ligand-dependent AF-2, which is localized in the C-terminal domain. In this review, we summarize and discuss current knowledge regarding the molecular mechanisms of AF-1- and AF-2-mediated gene activation, focusing on AF-1 and AF-2 conformation and coactivator binding.

The so-called thioredoxin system, thioredoxin (Trx), thioredoxin reductase (Trr), and NADPH, acts as a disulfide reductase system and can protect cells against oxidative stress. In Saccharomyces cerevisiae, two thioredoxins (Trx1 and Trx2) and one thioredoxin reductase (Trr1) have been characterized, all of them located in the cytoplasm. We have identified and characterized a novel thioredoxin system in S. cerevisiae. The TRX3 gene codes for a 14-kDa protein containing the characteristic thioredoxin active site (WCGPC). The TRR2 gene codes for a protein of 37 kDa with the active-site motif (CAVC) present in prokaryotic thioredoxin reductases and binding sites for NADPH and FAD. We cloned and expressed both proteins in Escherichia coli, and the recombinant Trx3 and Trr2 proteins were active in the insulin reduction assay. Trx3 and Trr2 proteins have N-terminal domain extensions with characteristics of signals for import into mitochondria. By immunoblotting analysis of Saccharomyces subcellular fractions, we provide evidence that these proteins are located in mitochondria. We have also constructed S. cerevisiae strains null in Trx3 and Trr2 proteins and tested them for sensitivity to hydrogen peroxide. The ⌬trr2 mutant was more sensitive to H 2 O 2 , whereas the ⌬trx3 mutant was as sensitive as the wild type. These results suggest an important role of the mitochondrial thioredoxin reductase in protection against oxidative stress in S. cerevisiae. Thioredoxin (Trx)1 is a small protein (M r 12,000) with a conserved sequence (Trp-Cys-Gly-Pro-Cys) in its active site. When thioredoxin is in a reduced state, Trx-(SH) 2 , the two active-site cysteines form a dithiol group that is able to catalyze the reduction of disulfides in a number of proteins. Oxidized thioredoxin (Trx-S 2 ) can be reduced by NADPH through the catalytic action of the flavoenzyme thioredoxin reductase (Trr). Thus, Trx, Trr, and NADPH form a system (the thioredoxin system) that operates as a general disulfide reductase system by the following sequence of reactions (Reactions 1 and 2).

The N-terminal regions of the estrogen receptor ␣ (ER␣-N) and ␤ (ER␤-N) were expressed and purified to homogeneity. Using NMR and circular dichroism spectroscopy, we conclude that both ER␣-N and ER␤-N are unstructured in solution. The TATA box-binding protein (TBP) has been shown previously to interact with ER␣-N in vitro and to potentiate ER-activated transcription. We used surface plasmon resonance and circular dichroism spectroscopy to confirm and further characterize The estrogen receptors (ERs)1 are ligand-inducible transcription factors that mediate the biological effects of estrogens. Two isoforms of human ER, encoded by two different genes, have been cloned and characterized, ER␣ and ER␤ (1-3). The ERs belong to a superfamily of nuclear receptors (NRs) that includes receptors for steroid hormones, thyroid hormones, and other hormones, as well as orphan receptors for which no ligand is known (4). All nuclear receptors share a similar modular structure; a variable N-terminal region, followed by a DNA binding domain (DBD), a hinge region, and a C-terminal ligand binding domain (LBD) (5). Transactivation regions have been localized to the LBD and in many cases also to the N-terminal region of the nuclear receptors (6, 7). The ligand-bound ERs bind as homodimers to specific DNA sequences termed estrogen response elements and regulate transcription through interaction with transcription modulators and recruitment of the general transcription machinery (8). ER␣ and ER␤ have also been shown to heterodimerize on estrogen response elements (9 -11).ER␣ contains two major transcription activation functions (AFs): one located in the N-terminal region (AF-1) and one in the C-terminal region of the LBD (AF-2) (12). A third activation function has been reported (AF-2a) residing in the boundary between the hinge and the LBD domains of ER␣ (13). The AF-1 function is hormone-independent, whereas the AF-2 function requires the presence of hormone (12). Full transcription activity of the ER␣ is thought to be achieved by synergism between the AFs. Further, the activities of the AFs are dependent on promoter and cellular context (14 -16). The ER␤ has a high homology to ER␣ in the DBD (96% amino acid identity) and in the LBD (58% amino acid identity) (2). In contrast, the Nterminal region of ER␤ is ϳ80 amino acids shorter than that of ER␣ and has also very poor sequence homology to that of ER␣. The N-terminal region in ER␤ is well conserved between different species such as rat, mouse, and human, which would imply functional importance.To date relatively little information has been available on the structure of the N-terminal regions of the NRs. The glucocorticoid receptor (GR) N-terminal transactivation region 1 (AF-1) and a shorter core fragment of 1, the 1core, have been shown by NMR and circular dichroism (CD) spectroscopy to be unstructured in aqueous solution (17). Furthermore, the isolated N-terminal transactivation region of the progesterone receptor A (PR A) has been shown to be sensitive to rapid degradation in limit...

The glucocorticoid receptor belongs to an important class of transcription factors that alter the expression of target genes in response to a specific hormone signal. The glucocorticoid receptor can function at least at three levels: (1) recruitment of the general transcription machinery; (2) modulation of transcription factor action, independent of DNA binding, through direct proteinprotein interactions; and (3) modulation of chromatin structure to allow the assembly of other gene regulatory proteins and/or the general transcription machinery on the DNA. This review will focus on the multifaceted nature of protein-protein interactions involving the glucocorticoid receptor and basal transcription factors, coactivators and other transcription factors, occurring at Accepted these different levels of regulation.

It is well established that differences in migratory behavior between populations of songbirds have a genetic basis but the actual genes underlying these traits remains largely unknown. In an attempt to identify such candidate genes we de novo assembled the genome of the willow warbler Phylloscopus trochilus, and used whole-genome resequencing and a SNP array to associate genomic variation with migratory phenotypes across two migratory divides around the Baltic Sea that separate SW migrating P. t. trochilus wintering in western Africa and SSE migrating P. t. acredula wintering in eastern and southern Africa. We found that the genomes of the two migratory phenotypes lack clear differences except for three highly differentiated regions located on chromosomes 1, 3, and 5 (containing 146, 135, and 53 genes, respectively). Within each migratory phenotype we found virtually no differences in allele frequencies for thousands of SNPs, even when comparing geographically distant populations breeding in Scandinavia and Far East Russia (>6000 km). In each of the three differentiated regions, multidimensional scaling-based clustering of SNP genotypes from more than 1100 individuals demonstrates the presence of distinct haplotype clusters that are associated with each migratory phenotype. In turn, this suggests that recombination is absent or rare between haplotypes, which could be explained by inversion polymorphisms. Whereas SNP alleles on chromosome 3 correlate with breeding altitude and latitude, the allele distribution within the regions on chromosomes 1 and 5 perfectly matches the geographical distribution of the migratory phenotypes. The most differentiated 10 kb windows and missense mutations within these differentiated regions are associated with genes involved in fatty acid synthesis, possibly representing physiological adaptations to the different migratory strategies.The ß200 genes in these regions, of which several lack described function, will direct future experimental and comparative studies in the search for genes that underlie important migratory traits. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Evolution Letters 1-3: 155-168MAX LUNDBERG ET AL. Impact SummaryHow animals find their way when migrating between continents is one of the most fascinating phenomena in nature. It is well established that migratory behavior has a strong genetic basis in many bird species, and different routes and wintering areas are also likely to select for adaptations related to optimal migratory performance, such as changes in physiology. However, virtually nothing is known about the specific genes underlying these traits. Here we aim to detect migration genes by contrasting the genomes of two recently diverged populations of a small migratory songbird, the willow warbler, which are very similar in appearance but that differ markedly in migration routes and wintering areas ...

RNA interference is a form of gene silencing in which the nuclease Dicer cleaves double-stranded RNA into small interfering RNAs. Here we report a role for Dicer in chromosome segregation of fission yeast. Deletion of the Dicer (dcr1 ؉ ) gene caused slow growth, sensitivity to thiabendazole, lagging chromosomes during anaphase, and abrogated silencing of centromeric repeats. As Dicer in other species, Dcr1p degraded double-stranded RNA into Ϸ23 nucleotide fragments in vitro, and dcr1⌬ cells were partially rescued by expression of human Dicer, indicating evolutionarily conserved functions. Expression profiling demonstrated that dcr1 ؉ was required for silencing of two genes containing a conserved motif.