# Mining of Root-Specific Expression Genes and Their Core Cis-Regulatory Elements in Plants

## TL;DR

This paper identifies root-specific genes and their regulatory elements in plants using RNA-seq data from Arabidopsis, rice, and maize.

## Contribution

The study discovers conserved root-specific genes and novel cis-regulatory elements across three plant species.

## Key findings

- 489, 276, and 728 root-specific genes were identified in Arabidopsis, rice, and maize, respectively.
- 34 root-specific genes in rice are conserved across all three species, with 29 being previously unreported.
- 16 new cis-acting elements (REM1-16) were predicted to regulate root-specific gene expression.

## Abstract

Mining tissue-specific genes is important for studying the processes of life activities within tissues, and it is a way of finding genes that regulate relevant traits. In recent years, the massive growth of expression data from various tissues has provided important opportunities for the large-scale analysis of tissue-specific genes. We found 489, 276, and 728 RTEGs (root tissue-specific expression genes) using 35 RNA-seq databases in 13 different tissues from three species of plants, e.g., Arabidopsis, rice, and maize, respectively, by bioinformatics methods. A total of 34 RTEGs in rice were found to be conserved in all three species, and 29 genes of them were unreported. Furthermore, 16 newly core cis-acting elements, named REM1-16 (root expression motif), were predicted by four well-known bioinformatics tools, which might determine the root tissue expression pattern. In particular, REM2 is conserved in not only Arabidopsis, but also rice. These cis-acting elements may be an important genetic resource that can be introduced into synthetic memory circuits to precisely regulate the spatiotemporal expression of genes in a user-defined manner.