We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor–binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor–binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.

Increased expression of the transcription/translation regulatory protein Y-box binding protein-1 (YB-1) is associated with cancer aggressiveness, particularly in breast carcinoma. Here we establish that YB-1 levels are elevated in invasive breast cancer cells and correlate with reduced expression of E-cadherin and poor patient survival. Enforced expression of YB-1 in noninvasive breast epithelial cells induced an epithelial-mesenchymal transition (EMT) accompanied by enhanced metastatic potential and reduced proliferation rates. YB-1 directly activates cap-independent translation of messenger RNAs encoding Snail1 and other transcription factors implicated in downregulation of epithelial and growth-related genes and activation of mesenchymal genes. Hence, translational regulation by YB-1 is a restriction point enabling coordinated expression of a network of EMT-inducing transcription factors, likely acting together to promote metastatic spread.

YB-1 is a broad-specificity RNA-binding protein that is involved in regulation of mRNA transcription, splicing, translation, and stability. In both germinal and somatic cells, YB-1 and related proteins are major components of translationally inactive messenger ribonucleoprotein particles (mRNPs) and are mainly responsible for storage of mRNAs in a silent state. However, mechanisms regulating the repressor activity of YB-1 are not well understood. Here we demonstrate that association of YB-1 with the capped 5 terminus of the mRNA is regulated via phosphorylation by the serine/threonine protein kinase Akt. In contrast to its nonphosphorylated form, phosphorylated YB-1 fails to inhibit cap-dependent but not internal ribosome entry site-dependent translation of a reporter mRNA in vitro. We also show that similar to YB-1, Akt is associated with inactive mRNPs and that activated Akt may relieve translational repression of the YB-1-bound mRNAs. Using Affymetrix microarrays, we found that many of the YB-1-associated messages encode stress-and growth-related proteins, raising the intriguing possibility that Akt-mediated YB-1 phosphorylation could, in part, increase production of proteins regulating cell proliferation, oncogenic transformation, and stress response.More than two decades ago, several abundant proteins within the size range of ϳ50 to 60 kDa were identified in complexes with maternal mRNA in Xenopus laevis oocytes and reported to be involved in translational "masking" of mRNA during early metazoan development (9, 34). Subsequently, these proteins initially cloned as FRGY1 and FRGY2 (frog Y-box proteins 1 and 2) (42) turned out to be common for male and female germ cells in all organisms studied, including mammals (27, 37). In somatic mammalian cells, the closely related 50-kDa protein (Ͼ96% amino acid identity), first designated p50 and most recently YB-1 (Y-box-binding protein 1), was shown to be a predominant component of translationally inactive messenger ribonucleoprotein particles (mRNPs) (14, 28). Interestingly, YB-1 was independently cloned as a transcription factor that specifically binds to the Y-box promoter element of major histocompatibility complex class II genes (11). It is now well established that YB-1 and related proteins are involved in regulation of both transcription and translation by virtue of sequence-specific and nonspecific binding to nucleic acids (45). The DNA and RNA sequence specificity of YB-1 is mediated through an evolutionarily conserved cold shock domain (CSD), which contains the RNA-binding motifs RNP1 and RNP2. The C terminus of YB-1 possesses alternating basic and acidic clusters and is implicated in both nonspecific DNA or RNA binding and protein-protein interactions (12,24). YB-1 functions as a structural protein involved in spatial organization of mRNPs (36). It is also known to bind in close proximity to the mRNA cap structure and to displace the initiation factors eukaryotic translation initiation factor 4E (eIF4E) and eIF4G, thereby causing mRNA translational silenci...

mRNA silencing and storage play an important role in gene expression under diverse circumstances, such as throughout early metazoan development and in response to many types of environmental stress. Here we demonstrate that the major mRNA-associated protein YB-1, also termed p50, is a potent cap-dependent mRNA stabilizer. YB-1 addition or overexpression dramatically increases mRNA stability in vitro and in vivo, whereas YB-1 depletion results in accelerated mRNA decay. The cold shock domain of YB-1 is responsible for the mRNA stabilizing activity, and a blocked mRNA 5¢ end is required for YB-1-mediated stabilization. Signi®cantly, exogenously added YB-1 destabilizes the interaction of the cap binding protein, eIF4E, with the mRNA cap structure. Conversely, sequestration of eIF4E from the cap increases the association of endogenous YB-1 with mRNA at or near the cap, and signi®cantly enhances mRNA stability. These data support a model whereby down-regulation of eIF4E activity or increasing the YB-1 mRNA binding activity or concentration in cells activates a general default pathway for mRNA stabilization.