MeTRN 1.0: An integrative database for reconstructing transcriptional regulatory network in cassava (Manihot esculenta Crantz)

Transcriptional regulation is a crucial biological process for controlling gene expression in a living cell.  To comprehend it, several genome-wide experiments and computational approaches have been applied to unravel the complex system. Comparing to other eukaryotes, a multi-cell organism like plant obtains a specific transcriptional regulation by distinctive transcription factors (TFs) containing plant-specific DNA binding domain such as TCP, NAM, EIN3, DUF573. The unique transcriptional regulation in plants is vital to explore specially in cash crops like cassava. Cassava (Manihot esculenta Crantz) is an important starchy tuberous crop serving millions of people worldwide. In this work, a genome-scale transcriptional regulatory network of cassava, called Manihot esculenta Transcriptional Regulatory Network (MeTRN), was reconstructed using three systems biology approaches including template-based, reverse engineering-based, and cis-regulatory element analysis-based methods. The constructed MeTRN contains 4,812,519 interactions of 33,006 genes (99.92% of annotated protein-coding genes in the genome) and 2,116 TF genes from 64 TF families in cassava genome version 6.1 in Phytozome database. MeTRN has combined transcriptional regulations from PlantRegMap and extended the landscape of regulatory region to distal promoter up to 2 kb from translational start site resulting in 11 times higher numbers of interactions than PlantRegMap. Additionally, a user-friendly search for finding a set of regulatory proteins controlling all target genes functioning in a particular metabolic pathway is provided. The MeTRN is available for public access at https://bml.kmutt.ac.th/MeTRN.