Studying the functional relationship between transcription factors and non-coding RNAs

Transcription factors (TFs) as well as chromatin associated protein complexes, activate and repress transcription by binding to regulatory regions of the DNA and recruiting the transcriptional machinery. To-date there are increasing evidence that in addition to the TFs, long intergenic non-coding RNAs (lincRNAs) play an important role in gene regulation. To study the functional relationship between TFs and lincRNAs we have analyzed large sets of high-throughput data derived from RNA sequencing, proteomics, and high-throughput DNA binding experiments from human tissues and during human embryonic stem cell (hESC) differentiation. Our results propose novel regulatory interactions between TFs and lincRNA, involved in gene regulation in human cells.

A) A correlation heatmap demonstrating the correlated RNA expression between Transcription Factors (TFs) and Long intergenic noncoding RNAs (lincRNA) in six time points during differentiation of human Emryonic Stem Cells (hESCs) to Embryoid Bodies (EBs). Shown are only differentially expressed genes (>log2(1.5)) fold change), all the replicates of the days of experiments were averaged. Clustering method = Euclidian, not scaled. B) The TF, HNF4G showing positive correlation with the lincRNA LINC01970. C) The TFs IRF5 and ONECUT1 showing negative correlation with the lincRNA CASC18.

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