Genome-wide identification of target genes repressed by the zinc finger transcription factor REST/NRSF in the HEK 293 cell line

Transcriptional repression is as important as transcriptional activation in establishing cell-type specific patterns of gene expression. RE1-silencing transcription factor (REST), also known as neuronal restrictive silencing factor (NRSF), is a transcriptional regulator that represses a battery of neuronal differentiation genes in non-neuronal cells or in neural progenitor cells by binding to a specific DNA sequence (repressor element-1/neuron-restrictive silencer element, RE1/NRSE). REST/NRSF functions in the neuronal development are widely studied, however, little is known about target genes in various non-neuronal lineages that may result in cell differentiation. Here, we use RNA interference (RNAi) technology combined with the microarray strategy to identify potential REST/NRSF targets and RE1/NRSEs in human non-neuronal cell line HEK 293. Expression of 54 genes was up-regulated by inhibition of REST/NRSF in the HEK 293 cells according to the microarray experiment and 13 of those were further confirmed by quantitative RT-PCR. Our results confirmed the good confidence and reliability of current research data based on in silico, chromatin immunoprecipitation in combination with microarrays (ChIP-chip), and high-throughput sequencing (ChIP-seq). However, in view of the fact that thousands of genes have been testified or predicted to be recognized by REST/NRSF, our data show that only a few genes among those are directly up-regulated by the interaction of REST/NRSF with RE1/NRSEs sites in gene sequences.