Abstract
SummaryGene expression is controlled at multiple layers, and cells may integrate different regulatory steps for coherent production of proper protein levels. We applied various microarray-based approaches to determine key gene-expression intermediates in exponentially growing fission yeast, providing genome-wide data for translational profiles, mRNA steady-state levels, polyadenylation profiles, start-codon sequence context, mRNA half-lives, and RNA polymerase II occupancy. We uncovered widespread and unexpected relationships between distinct aspects of gene expression. Translation and polyadenylation are aligned on a global scale with both the lengths and levels of mRNAs: efficiently translated mRNAs have longer poly(A) tails and are shorter, more stable, and more efficiently transcribed on average. Transcription and translation may be independently but congruently optimized to streamline protein production. These rich data sets, all acquired under a standardized condition, reveal a substantial coordination between regulatory layers and provide a basis for a systems-level understanding of multilayered gene-expression programs.
Highlights
The characteristics of organisms result largely from the complex interplay between DNA or RNA and the regulatory apparatus
The 78 nucleotide rpl4101 is the shortest mRNA in S. pombe and is not expected to be associated with many ribosomes; it peaked around fraction 6, which corresponds to the binding of a single ribosome
Polysome profiles were obtained for almost all mRNAs, we focused on a conservative, high-confidence ciated with the Gene Ontology (GO) terms ‘‘translational intiation,’’ ‘‘translational elongation,’’ or ‘‘translational termination.’’
Summary
The characteristics of organisms result largely from the complex interplay between DNA or RNA and the regulatory apparatus. Proper control of gene expression is fundamental to implement the information in the genome and pervades most of biology, from cell proliferation and differentiation to development. Gene expression is controlled at multiple levels, and cells need to coordinate different regulatory processes to function properly and prevent disease. There is increasing appreciation that the different processes involved in gene expression are integrated with each other (Maniatis and Reed, 2002; Moore, 2005; Orphanides and Reinberg, 2002; Proudfoot et al, 2002). The sophistication of geneexpression control has been recognized through numerous in-depth studies on the regulation of specific genes at several levels (Lal et al [2006] and references therein)
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