DOI: 10.5061/dryad.fttdz08sg
title: Data from: Length variation in short tandem repeats affects gene expression in natural populations of Arabidopsis thaliana

description: The genetic basis for the fine-tuned regulation of gene expression is
 complex and ultimately influences the phenotype and thus the local
 adaptation of natural populations. Short tandem repeats (STRs) consisting
 of repetitive DNA motifs have been shown to regulate gene expression. STRs
 are variable in length within a population and serve as a heritable, but
 semi-reversible, reservoir of standing genetic variation. For sessile
 organisms such as plants, STRs could be of major importance in fine-tuning
 gene expression as a response to a shifting local environment. Here, we
 used a transcriptome dataset from natural accessions of Arabidopsis
 thaliana to investigate population-wide gene expression patterns in light
 of genome-wide STR variation. We empirically modeled gene expression as a
 response to the STR length within and around the gene and demonstrated
 that an association between gene expression and STR length variation is
 unequivocally present in the sampled population. To support our model, we
 explored the promoter activity in a transcriptional regulator involved in
 root hair formation and provided experimentally determined causality
 between coding sequence length variation and promoter activity. Our
 results support a general link between gene expression variation and STR
 length variation in A. thaliana.
description: Please see the manuscript for details.
description: This depository contains the Supplemental Data Sets of
 "Length variation in short tandem repeats affects gene expression in
 natural populations of <em>Arabidopsis thaliana</em>"
 (Reinar et al. 2021). <strong>Supplemental Data
 Set S1</strong>: Gene Ontology enrichment of genes with STRs in
 close proximity (excel sheet)
 <strong>Supplemental Data Set S2</strong>: Diploid
 STR unit number counts in the sampled population (tab separated
 values) <strong>Supplemental Data Set
 S3</strong>: Genetic relatedness of samples (covariance matrix) (tab
 separated values) <strong>Supplemental Data Set
 S4</strong>: Comparison of scored STR lengths to an independent
 study (comma separated values)
 <strong>Supplemental Data Set S5</strong>: Modelling
 results, mock STR genotypes (665,330 tests) (tab separated
 values) <strong>Supplemental Data Set
 S6</strong>: Modelling results, true STR genotypes (665,364
 tests) (tab separated values)
 <strong>Supplemental Data Set S7</strong>: Modelling
 results, SNPs (893,372 tests) (tab separated values)
 <strong>Supplemental Data Set S8</strong>: Modelling
 results, SNPs close to eSTRs (2,306 tests) (tab separated
 values) <strong>Supplemental Data Set
 S9</strong>: Counts used in Fisher Exact tests (excel
 sheet) <strong>Supplemental Data Set
 S10</strong>: Named genes affected by eSTRs (excel sheet)
 <strong>Supplemental Data Set S11</strong>: Sequenced
 <em>AL6</em> cDNA from Col-0 and natural sample CS77246 (FASTA
 file) <strong>Supplemental Data Set
 S12</strong>: GUS and FRET experimental data and statistical
 analysis (excel sheet) In order to reproduce the
 Figures and to run the modelling, we have included Python scripts as
 Jupyter Notebooks: 
 <strong>GeneExp.Figures.ipynb</strong>
 <strong>GeneExp.Modelling.ipynb</strong>
 Note that Python dependencies has to be installed prior to
 running code in the Jupyter Notebooks. To run these Notebooks, some
 additional materials are required, which are also included in this
 depository. <strong>Extra Material:
 Log-transformed gene expression values</strong>
 <strong>Extra Material: STRs within 100kb of
 genes</strong> <strong>Extra Material: Gene
 regions in the Araport11 annotation of TAIR10 </strong>(python
 pickle format) Note that the .html versions of the
 Notebooks can be viewed in a web-browser:
 <strong>GeneExp.Figures.html</strong>
 <strong>GeneExp.Modelling.html</strong>