Characterization Of Transcription Factor Binding In Promoter And Enhancer Element Of Human And Mouse Imprinted Genes

In mammals,imprinted genes are expressed from one of the two alleles of the diploid genome in a parental specific expression pattern.To date,approximately more than 100 genes for imprinting effects have been identified in human or mouse.Although the fact that imprinted genes have been confirmed in a small proportion of all genes(< 1% in human or mouse),those genes have been demonstrated to play important roles in the regulation of embryonic growth,placentation,development of lineages and postnatal processes.In humans,the disruption in expression of imprinted genes can lead to human diseases,which affects the normal growth and development of individuals.The importance of genomic imprinting has prompted investigators to focus on the mechanisms underlying parent-of-origin-specific expression of imprinted genes,previous studies have focused on the epigenetic modification of two parental alleles of imprinted genes during gametogenesis,which mainly includes DNA methylation,histone modifications,non-coding RNAs and chromatin spatial structure.Although the epigenetic regulatory mechanism of several imprinted genes has been analyzed by experimental methods in detail,little is known about DNA sequence preference of imprinted genes compared with non-imprinted genes,and no studies have attempted to explain parental specific expression of imprinted genes from this perspective.There are many binding sites of transcription factors in the cis-regulatory elements(CREs)of imprinted and non-imprinted genes.In this study,we speculated that there might be some transcription factors(TFs)preferentially binding in the CREs of imprinted genes compared with non-imprinted genes,and these TFs may be involved in the regulation of parent-specific expression of imprinted genes.In the present work,we studied 92 human imprinted genes and 110 mouse imprinted genes that are located on chromosomes and encoding protein.We first performed a computational analysis of human and mouse protein-coding imprinted genes in their CREs using a set of DNA binding motifs of known TFs to investigate whether sequence-specific transcription factor binding sites(TFBSs)are more enriched in CREs of imprinted genes than non-imprinted genes.The results suggest that:(1)The binding sites of 35 TFs were significantly more enriched in the promoter region of human imprinted genes when compared with non-imprinted genes,and the binding sites of 48 TFs were significantly more enriched in the enhancers region of imprinted genes than non-imprinted genes expressed in the human placenta tissue.(2)Similarly,the binding sites of 30 TFs were significantly more enriched in the promoter region of mouse imprinted genes when compared with non-imprinted genes,and the binding sites of 55 TFs were significantly more enriched in the enhancers region of imprinted genes than non-imprinted genes expressed in the mouse placenta tissue.(3)13transcription factors of those TFBSs significantly enriched in CREs of human and mouse imprinted genes are conserved among species.(4)For promoter region of human and mouse imprinted genes,we also analyzed the enrichment of TFs between the imprinted genes and the equal number of non-imprinted genes and found that the binding sites of 56 TFs were significantly more enriched in the promoter region of imprinted genes when compared with non-imprinted genes between human and mouse,and 9 important TFs of those TFBSs are conserved among species,such as EPAS1 and NRF1.The above results suggest that these candidate TFs may be involved in the expression regulation of imprinted genes.Secondly,the expression patterns of imprinted genes and candidate TFs were compared through the analysis of RNA-seq data from 20 human tissues and 19 mouse tissues.The results suggest that:(1)These candidate TFs were transcribed in the placental tissues,and the Ch IP-seq data of a few TFs supported that candidate TFs did bind in the CREs of imprinted genes.(2)The tissue specificity of imprinted gene expression was verified,mainly in the placenta and brain tissues.Thirdly,in order to further analysis of TFs preferentially binding in the CREs of imprinted genes during the process of dynamic expression,we analyzed the tissue/cell-type-specific DNase? hypersensitive sites(DHSs)regions to their target imprinted gene.We analyzed 12 groups DHSs data of human placental tissues and 3 groups parent-specific DHSs data of mouse embryonic development,and found that TFBSs of EPAS1 and SP were enriched in CREs of imprinted genes between human and mouse.In addition,we found that 17 transcription factors of those TFBSs significantly enriched in DHSs of human and mouse imprinted genes were conserved among species.Finally,we tried to distinguish these two classes of genes by a classifier based on machine learning using DNA sequence features.In conclusion,our research provides new insights into the relationship of promoters,enhancers and TFBSs of imprinted genes.Our results provide more understanding about regulation of the mammalian imprinted gene expression from DNA sequence-level analysis.In addition,the candidate TFs,which might regulate the expression of imprinted gene,could provide some targeted guidance for molecular biology experiments in the future.