Looking for organization patterns of highly expressed genes: purine-pyrimidine composition of precursor mRNAs

Nuclear retention of unspliced pre-mRNAs by mutant DHX16/hPRP2, a spliceosomal DEAH-box protein

Defective or imbalanced expression of spliceosomal factors has been linked to human disease; however, how a defective spliceosome affects intron-containing gene transcripts in human cells is largely unknown. DEAH-box protein DHX16 is a human orthologue of Saccharomyces cerevisiae spliceosomal protein Prp2, an RNA-dependent ATPase that activates the spliceosome before the first catalytic step of splicing. Yeast prp2 mutants accumulate unspliced RNAs from the vast majority of intron-containing genes. Here we used a genomic tiling microarray to screen transcripts from four chromosomes in human cells expressing a dominant negative DHX16 mutant and identified a number of gene transcripts that retained their introns. The mutant protein also affected gene transcripts that are sensitive to pladienolide, an SF3b inhibitor. The unspliced RNAs were retained in the nucleus, and block of nonsense-mediated decay did not affect their accumulation. Thus, a perturbation of human PRP2/DHX16 results in accumulation of unspliced transcripts, similar to the outcome in yeast prp2 mutants. The results further suggest that mutant DHX16/hPRP2 causes a defective spliceosome to retain unspliced gene transcripts in the nuclei of human cells.

Ecological nitrogen limitation shapes the DNA composition of plant genomes

Phenotypes and behaviors respond to resource constraints via adaptation, but the influence of ecological limitations on the composition of eukaryotic genomes is still unclear. We trace connections between plant ecology and genomes through their elemental composition. Inorganic sources of nitrogen (N) are severely limiting to plants in natural ecosystems. This constraint would favor the use of N-poor nucleotides in plant genomes. We show that the transcribed segments of undomesticated plant genomes are the most N poor, with genomes and proteomes bearing signatures of N limitation. Consistent with the predictions of natural selection for N conservation, the precursors of transcriptome show the greatest deviations from Chargaff's second parity rule. Furthermore, crops show higher N contents than undomesticated plants, likely due to the relaxation of natural selection owing to the use of N-rich fertilizers. These findings indicate a fundamental role of N limitation in the evolution of plant genomes, and they link the genomes with the ecosystem context within which biota evolve.

Conflicting selection pressures on synonymous codon use in yeast suggest selection on mRNA secondary structures

BACKGROUND

Eukaryotic mRNAs often contain secondary structures in their untranslated regions that are involved in expression regulation. Whether secondary structures in the protein coding regions are of functional importance remains unclear: laboratory studies suggest stable secondary structures within the protein coding sequence interfere with translation, while several bioinformatic studies indicate stable mRNA structures are more frequent than expected.

RESULTS

In contrast to several studies testing for unexpected structural stabilities, I directly compare the selective constraint of sites that differ in their structural importance. I.e. for each nucleotide, I identify whether it is paired with another nucleotide, or unpaired, in the predicted secondary structure. I assume paired sites are more important for the predicted secondary structure than unpaired sites. I look at protein coding yeast sequences and use optimal codons and synonymous substitutions to test for structural constraints. As expected under selection for secondary structures, paired sites experience higher constraint than unpaired sites, i.e. significantly lower numbers of conserved optimal codons and consistently lower numbers of synonymous substitutions. This is true for structures predicted by different algorithms.

CONCLUSION

The results of this study are consistent with purifying selection on mRNA secondary structures in yeast protein coding sequences and suggest their biological importance. One should be aware, however, that accuracy of structure prediction is unknown for mRNAs and interrelated selective forces may contribute as well. Note that if selection pressures alternative to translational selection affect synonymous (and optimal) codon use, this may lead to under- or over-estimates of selective strength on optimal codon use depending on strength and direction of translational selection.