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Background  Theauxin efflux carrier PIN1 is a key mediator of polar auxin transport in developing plant tissues. This is why factors that are supposed to be involved in auxin distribution are frequently tested in the regulation of  PIN1  expression. As a result, diverse aspects of  PIN1  expression are dispersed across dozens of papers entirely devoted to other specific topics related to the auxin pathway. Integration of these puzzle pieces about  PIN1  expression revealed that, along with a recurring pattern, some features of  PIN1  expression varied from article to article. To determine if this uncertainty is related to the specific foci of articles or has a basis in the variability of  PIN1  gene activity, we performed a comprehensive 3D analysis of  PIN1  expression patterns in  Arabidopsis thaliana  roots.    Results  We provide here a detailed map of  PIN1  expression in the primary root, in the lateral root primordia and at the root-shoot junction. The variability in  PIN1  expression pattern observed in individual roots may occur due to differences in auxin distribution between plants. To simulate this effect, we analysed  PIN1  expression in the roots from wild type seedlings treated with different IAA concentrations and  pin  mutants. Most changes in  PIN1  expression after exogenous IAA treatment and in  pin  mutants were also recorded in wild type but with lower frequency and intensity. Comparative studies of exogenous auxin effects on  PIN1pro : GUS  and  PIN1pro : PIN1 - GFP  plants indicated that a positive auxin effect is explicit at the level of  PIN1  promoter activity, whereas the inhibitory effect relates to post-transcriptional regulation.    Conclusions  Our results suggest that the PIN1 expression pattern in the root meristem accurately reflects changes in auxin content. This explains the variability of PIN1 expression in the individual roots and makes PIN1 a good marker for studying root meristem activity.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-015-0685-0) contains supplementary material, which is available to authorized users.

A detailed expression map of the PIN1 auxin transporter in Arabidopsis thaliana root