Oct 24, 2017

dreamBase: DNA modification, RNA regulation and protein binding of expressed pseudogenes in human health and disease

Nucleic Acids Research
Ling-Ling ZhengLiang-Hu Qu

Abstract

Although thousands of pseudogenes have been annotated in the human genome, their transcriptional regulation, expression profiles and functional mechanisms are largely unknown. In this study, we developed dreamBase (http://rna.sysu.edu.cn/dreamBase) to facilitate the investigation of DNA modification, RNA regulation and protein binding of potential expressed pseudogenes from multidimensional high-throughput sequencing data. Based on ∼5500 ChIP-seq and DNase-seq datasets, we identified genome-wide binding profiles of various transcription-associated factors around pseudogene loci. By integrating ∼18 000 RNA-seq data, we analysed the expression profiles of pseudogenes and explored their co-expression patterns with their parent genes in 32 cancers and 31 normal tissues. By combining microRNA binding sites, we demonstrated complex post-transcriptional regulation networks involving 275 microRNAs and 1201 pseudogenes. We generated ceRNA networks to illustrate the crosstalk between pseudogenes and their parent genes through competitive binding of microRNAs. In addition, we studied transcriptome-wide interactions between RNA binding proteins (RBPs) and pseudogenes based on 458 CLIP-seq datasets. In conjunction with epitranscriptome sequ...Continue Reading

Mentioned in this Paper

Study
Transcriptional Regulation
Protein Binding
Deoxyribonuclease I
DNA Modification Process
Post-Transcriptional Regulation
Genome
Genes
Regulation of Biological Process
Sequence Determinations, RNA

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