Characterization of the human RFX transcription factor family by regulatory and target gene analysis

Debora Sugiaman-Trapman,Peter Swoboda,Morana Vitezic,Eeva-Mari Jouhilahti,Sougat Misra,Juha Kere,Carsten O Daub,Anthony Mathelier,Gilbert Lauter

doi:10.1186/s12864-018-4564-6

Abstract

BackgroundEvolutionarily conserved RFX transcription factors (TFs) regulate their target genes through a DNA sequence motif called the X-box. Thereby they regulate cellular specialization and terminal differentiation. Here, we provide a comprehensive analysis of all the eight human RFX genes (RFX1–8), their spatial and temporal expression profiles, potential upstream regulators and target genes.ResultsWe extracted all known human RFX1–8 gene expression profiles from the FANTOM5 database derived from transcription start site (TSS) activity as captured by Cap Analysis of Gene Expression (CAGE) technology. RFX genes are broadly (RFX1–3, RFX5, RFX7) and specifically (RFX4, RFX6) expressed in different cell types, with high expression in four organ systems: immune system, gastrointestinal tract, reproductive system and nervous system. Tissue type specific expression profiles link defined RFX family members with the target gene batteries they regulate. We experimentally confirmed novel TSS locations and characterized the previously undescribed RFX8 to be lowly expressed. RFX tissue and cell type specificity arises mainly from differences in TSS architecture. RFX transcript isoforms lacking a DNA binding domain (DBD) open up new possibilities for combinatorial target gene regulation. Our results favor a new grouping of the RFX family based on protein domain composition. We uncovered and experimentally confirmed the TFs SP2 and ESR1 as upstream regulators of specific RFX genes. Using TF binding profiles from the JASPAR database, we determined relevant patterns of X-box motif positioning with respect to gene TSS locations of human RFX target genes.ConclusionsThe wealth of data we provide will serve as the basis for precisely determining the roles RFX TFs play in human development and disease.

Highlights

Conserved Regulatory Factor binding to the X-box (RFX) transcription factors (TFs) regulate their target genes through a DNA sequence motif called the X-box
In this study – using extensive analysis of data from the Functional Annotation of Mammalian Genome 5 (FANTOM5) database followed by experimental validations – we present an in-depth characterization of the entire human RFX gene family (RFX1–8), including the previously undescribed RFX8 and RFX transcript isoforms that encode TFs without DNA binding domain (DBD)
We found most transcription start site (TSS) locations of RFX1–3, 5 and 7 to be expressed broadly in many tissue types whereas the TSS locations of RFX4 and RFX6 are all expressed in specific tissue types. promoter A (pA)@RFX4 is highly specific in brain and spinal cord tissues, while pB and pC@RFX4 are highly specific in testis

Summary

Introduction

Conserved RFX transcription factors (TFs) regulate their target genes through a DNA sequence motif called the X-box. Thereby they regulate cellular specialization and terminal differentiation. RFX TFs have been shown to regulate genes involved in various and seemingly disparate cellular and developmental processes [7] like the cell cycle and DNA repair [11, 12], or aspects of cellular differentiation, like the functional maturation of cells of the immune response [13] and the development of cilia on the surface of polarized cells [14,15,16].

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