In this work we have described the translatome of two mammalian cell lines, NIH3T3 and Jurkat, by scoring the family member polysome association of 10,000 mRNA under normal and ER stress conditions. is usually characterized by high translation rates in both control and stress conditions. Translation inducible class includes mRNA whose translation was relieved after stress, showing a high enrichment in early response transcription factors of bZIP and zinc finger C2H2 classes. Unlike yeast, a general coordination between changes in translation and transcription upon stress (potentiation) was not observed 61371-55-9 IC50 in mammalian cells. Among the different features of mRNA analyzed, we found a relevant association of translation efficiency with the presence of upstream ATG in the 5UTR and with the length of coding sequence of mRNA, and a looser association with other parameters such as the length and the G+C content of 5UTR. A model for translatome remodeling during the acute phase of stress response in mammalian cells is usually proposed. Introduction Gene manifestation is usually regulated at multiple levels to adjust the concentration of macromolecular components to the physiological demands of the cell and organism. The amount of a given protein in the 61371-55-9 IC50 cell depends not only on the 61371-55-9 IC50 transcriptional activity of its gene, but also on the sense of balance between post-transcriptional and post-translational processes that impact the synthesis and stability of the protein [1], [2], [3], [4]. For years, the relevance of translation in the control of gene manifestation outputs has been underestimated and restricted to a few examples of mRNA that undergo extreme cases of translation control [5], [6], [7], [8]. However, the finding that the activities of important translation initiation factors such as eIF2 and eIF4F are tightly regulated by environmental stress and by mitogenic or developmental signals, definitely changed our view of translation control in mammalian cells [9], [10], [11], [12], [13], [14], [15], [16]. More recently, the finding of common changes in protein synthesis induced by microRNAs further supported the key role of post-transcriptional actions of mRNA in gene manifestation control [17], [18], [19]. Initiation is usually the limiting step of protein synthesis and the most important control point in eukaryotic translation. Collectively, the activity of eIF4F complex promotes the recruitment of mRNA to ribosomes via cap acknowledgement and scanning services to reach the initiation codon [14], [20], [21]. At this last step, the activity of eIF2 is usually essential for delivering the Met-tRNAi 61371-55-9 IC50 to the 40 S ribosome that promotes codon-anticodon base pairing on AUG triplet during initiation. The activity of eIF2 is usually blocked by phosphorylation at the S51 of the alpha subunit (eIF2) that prevents the normal recycling of this factor necessary for ongoing translation of most mRNA in the cell [7], [22]. Four stress-activated kinases phosphorylate eIF2 in response to a wide variety of stresses producing in an almost instantaneous halt of general translation necessary for a effective response to stress [7], [23], [24]. Apart from this general rules, specific features in mRNA such as the presence of cis-acting sequences and structures in the 5- and 3-UTRs, together with the context of initiation codon (AUG) can influence the rate of translation initiation of particular mRNA [25], [26], [27], [28], [29]. Considerable secondary structure in the 5UTR can prevent ribosome recruitment or scanning in some mRNA, but not in others that initiate by binding of the ribosomes to internal structures within 5UTR (at the.g viral IRES) [14], [21], [30], [31], [32]. The acknowledgement of initiator AUG by the 40 S ribosome also requires an optimal sequence context (A/GnnAUGG) that has been found in most of murine and human mRNA [25], [26]. However, under suboptimal context a portion of 40 S can skip initiation codon and continues scanning services in 3 direction to initiate at downstream AUG (leaky scanning services). The presence of AUG triplets upstream the initiation codon can also influence the rate of translation initiation when eIF2 is usually available in the cell. The paradigmatic example of this control operates on ATF4 mRNA that encodes a grasp regulator of stress response in both vertebrate and yeast cells (called GCN4) [5], [13], [33], [34]. Under optimal conditions, upstream short ORFs in IL2R 5UTR are busy by 40 S ribosomes that after translating short peptides do not resume scanning to reach the downstream, authentic initiation codon of ATF4. Stress-induced phosphorylation of eIF2 relieves translation repression of ATF4 mRNA by promoting reinitiation at the authentic mRNA [5], [33]. A comparable mechanism of translation activation during stress has been.