Research On The Association Of Hypotocyte Genomic DNA Exposure With Gene Transcription And Its Fuctions In The Rat Liver Regeneration

It is reported that DNA always deplete of proteins before its corresponding gene transcribe to mRNA. Many genes are activated and transcribe during the rat liver regeneration, meanwhile, it is necessary to identify the sites of DNA exposure and their relationship with gene transcription. To achive this goal, we carried out the pre-research on the correlation between the sites of DNA exposure and gene transcription during the rat liver regeneration.In this paper, we adopt a new meathod to extract the protein-crosslinked fragments based on ChIP-seq which is widely used in the study of the regulatory sequences, that follows these technical routes: separating the hepatocytes of the regenerating liver, fixing the hepatocyte chromatin with formalin, sonicating the hepotocyte genomic DNA into fragments a few hundred nucleotides long, separating the protein-crosslinked fragments with protein-free fragments by phenol-chloroform extraction, precipitating the protein-free fragments dissolving in the aqueous phase, sequencing the protein-free fragments. Meanwhile, we detected the mRNA of more than20thousand gene in the hepotocyte with the rat genome2302.0microarray during the rat liver regeneration. Finally, we analysed part of the protein-free fragments that encodes the proteins, and the corresponding gene’s transcription.The protein-free fragments:The abundance of the protein-free fragments of a cell changes significantly during the rat liver regeneration, and the protein-free fragments contain the encoding ones and the untranslated ones. Among that, the encoding ones belong to16,912different genes of the rat genome. Under the principle of "When Ratio≥3or Ratio≤1/3, the gene is selected", we get a total of1701genes among them. And they are mainly involved in9different physiological activities such as response to stimulus, signaling, cell communication, developmental process, nucleic acid metabolic process, organ development, protein metabolic process, cell differentiation and cell proliferation during the rat liver regeneration.The cDNA microarray test:A total of13,920genes’s transcriptions were detected during the rat liver regeneration. Under the principle of "When Ratio≥3or Ratio≤1/3, the gene is selected", we get a total of4654genes. Despite The physiological activities that the genes selected in different stages of the rat liver regeneration are mainly involved in have great comparability, they change in some respect.Comparing the protein-free fragments with the cDNA microarray: The protein-free fragments abundance of single gene has less relativity with its cDNA abundance; However, at the same time of the liver’s recovery time, the genes selected in different experiments are are mainly involved in the same physiological activities.Conclusion: It indicates that gene expression may be affected by the protein-free DNA fragments.