Mutational biases and selective forces shaping the structure of Arabidopsis genes

Abstract

Recently features of gene expression profiles have been associated with structural parameters of gene sequences in organisms representing a diverse set of taxa. The emerging picture indicates that natural selection, mediated by gene expression profiles, has a significant role in determining genic structures. However the current situation is less clear in plants as the available data indicates that the effect of natural selection mediated by gene expression is very weak. Moreover, the direction of the patterns in plants appears to contradict those observed in animal genomes. In the present work we analized expression data for >18000 Arabidopsis genes retrieved from public datasets obtained with different technologies (MPSS and high density chip arrays) and compared them with gene parameters. Our results show that the impact of natural selection mediated by expression on genes sequences is significant and distinguishable from the effects of regional mutational biases. In addition, we provide evidence that the level and the breadth of gene expression are related in opposite ways to many structural parameters of gene sequences. Higher levels of expression abundance are associated with smaller transcripts, consistent with the need to reduce costs of both transcription and translation. Expression breadth, however, shows a contrasting pattern, i.e. longer genes have higher breadth of expression, possibly to ensure those structural features associated with gene plasticity. Based on these results, we propose that the specific balance between these two selective forces play a significant role in shaping the structure of Arabidopsis genes.

Figure 1. Cluster on the correlations (Pearson's r) among the different measures of expression considered both for (A) oligo-array and (B) MPSS.

The experimental unit is represented by the developemental stage in the DS method and by the Organ in the O method. Expression profiles were reduced to discrete measures considering all (A-methods) or only informative (I-methods) experimental units.

Figure 2. Relationship between the expression profile and (a) the CDS length, (b) the Total Intron Length and (c) 5utr Length.

The points indicated by the symbol • and interpolated by the continuous line refer to the expression level, whereas the points indicated by the symbol ○ and interpolated by a dashed line refer to the expression breadth. In both cases 14236 genes were considered which have been grouped in bins, each representing the 5% of the whole dataset.

Figure 3. Results of multiple regression analyses between intron length and espression level (EL) and breadth (EB) by intron position.

The analysis was conducted considering both microarray (ma) and MPSS (mp) data and all genes. Full circles: significant at P<0.05; empty circles: not significant at P>0.05.

Figure 4. Relation between the expression level (oligoarray DS-I) and the Total Domain Length and Non-domain protein length.

Variables on the Y axis have been normalized