Effect of interactions of chromatin regulatory elements with different promoters on the regulation of gene expression / 生物工程学报

The effect of altering the promoter region of ubiquitous chromatin-opening element (UCOE) and matrix attachment region (MAR) on stable and efficient expression of genes was investigated. Four different promoters were tested, namely, oct4 containing an enhancer region, sox2 having a CpG island, nanog having no regulatory elements, and CMV containing a CpG island and an enhancer region. Eight reporter plasmids were constructed: pOCT4-UCOE, pOCT4-MAR, pSOX2-UCOE, pSOX2-MAR, pNANOG-UCOE, pNANOG-MAR, pCMV-UCOE, and pCMV-MAR. Stable and efficient expression was observed when UCOE combined with the oct4 promoter, whereas the sox2 was the best promoter suited for MAR. Comparison of the stable clones of oct4-UCOE and sox2-MAR showed that UCOE-regulated expression is more stable and efficient than MAR-regulated expression. When CpG island-containing promoter is linked with UCOE, stable and efficient expression could be observed. These data suggest that an enhancer region in the promoter leads to high, yet unstable expression when combined with UCOE, whereas CpG islands stabilize expression. In conclusion, UCOE and MAR interact with regulatory elements on the promoter by altering the chromatin open state and chromatin loop to regulate gene expression.

Role of nuclear receptor in the development and progression of primary biliary cholangitis / 临床肝胆病杂志

Primary biliary cholangitis (PBC) is an chronic progressive intrahepatic cholestasis autoimmune liver disease with unknown causes, and at present, the etiology and pathogenesis of PBC remain unclear. Nuclear receptor is a ligand-dependent transcription factor superfamily that regulates cell growth and differentiation by establishing a relationship between signal molecules and transcriptional responses. The human nuclear receptor family consists of 48 members, including peroxisome proliferator-activated receptors, pregnane X receptor, constitutive androstane receptor, liver X receptors, farnesoid X receptor, vitamin D receptor, and glucocorticoid receptor, which have attracted wide attention. These nuclear receptors regulate the key enzymes and transporter genes of bile acid metabolism at the transcriptional level and thus regulate the level of bile acid in the body and participate in inflammatory response. Bile acid metabolism disorder and persistent inflammation may be the key factors for the development and progression of PBC. This article reviews the research advances in nuclear receptors in the development and progression of PBC, in order to provide a theoretical basis for exploring the pathogenesis of PBC and new therapeutic targets.

Regulatory elements in gene circuits:research progress / 军事医学

Promoters, terminators, riboswitches and ribosome-related sequences are involved in gene expression regulation at transcription and translation levels to achieve precise expression of the target gene .As regulatory elements of genes, they are widely used in the construction of gene circuits and play important roles in genome engineering and metabolic engineering.This paper not only summarized the structural characteristics of the common gene regulatory elements, the mechanism of action and modification , but expounded the function of natural and artificial gene regulatory elements in the optimization of metabolic pathways , and the future construction of gene circuits and applications .

Regulatory elements in gene circuits:research progress / 军事医学

Promoters, terminators, riboswitches and ribosome-related sequences are involved in gene expression regulation at transcription and translation levels to achieve precise expression of the target gene .As regulatory elements of genes, they are widely used in the construction of gene circuits and play important roles in genome engineering and metabolic engineering.This paper not only summarized the structural characteristics of the common gene regulatory elements, the mechanism of action and modification , but expounded the function of natural and artificial gene regulatory elements in the optimization of metabolic pathways , and the future construction of gene circuits and applications .

ENCODE: A Sourcebook of Epigenomes and Chromatin Language

Until recently, since the Human Genome Project, the general view has been that the majority of the human genome is composed of junk DNA and has little or no selective advantage to the organism. Now we know that this conclusion is an oversimplification. In April 2003, the National Human Genome Research Institute (NHGRI) launched an international research consortium called Encyclopedia of DNA Elements (ENCODE) to uncover non-coding functional elements in the human genome. The result of this project has identified a set of new DNA regulatory elements, based on novel relationships among chromatin accessibility, histone modifications, nucleosome positioning, DNA methylation, transcription, and the occupancy of sequence-specific factors. The project gives us new insights into the organization and regulation of the human genome and epigenome. Here, we sought to summarize particular aspects of the ENCODE project and highlight the features and data that have recently been released. At the end of this review, we have summarized a case study we conducted using the ENCODE epigenome data.

Characterization of Chromatin Structure-associated Histone Modifications in Breast Cancer Cells

Chromatin structure and dynamics that are influenced by epigenetic marks, such as histone modification and DNA methylation, play a crucial role in modulating gene transcription. To understand the relationship between histone modifications and regulatory elements in breast cancer cells, we compared our chromatin immunoprecipitation sequencing (ChIP-Seq) histone modification patterns for histone H3K4me1, H3K4me3, H3K9/16ac, and H3K27me3 in MCF-7 cells with publicly available formaldehyde-assisted isolation of regulatory elements (FAIRE)-chip signals in human chromosomes 8, 11, and 12, identified by a method called FAIRE. Active regulatory elements defined by FAIRE were highly associated with active histone modifications, like H3K4me3 and H3K9/16ac, especially near transcription start sites. The H3K9/16ac-enriched genes that overlapped with FAIRE signals (FAIRE-H3K9/14ac) were moderately correlated with gene expression levels. We also identified functional sequence motifs at H3K4me1-enriched FAIRE sites upstream of putative promoters, suggesting that regulatory elements could be associated with H3K4me1 to be regarded as distal regulatory elements. Our results might provide an insight into epigenetic regulatory mechanisms explaining the association of histone modifications with open chromatin structure in breast cancer cells.

Site-directed analysis of key transcriptional regulatory regions of ezrin gene in HeLa cells / 肿瘤

Objective: To identify key transcriptional regulatory regions of ezrin gene in HeLa cells, thus this work maked a preliminary study for revealing its transcriptional regulatory mechanism. Methods: The recombinant pGLB plasmids containing different lengths of DNA fragments upstream of translation initiation site of ezrin gene as reporter promoters were constructed using nested-deletion method, and the promoter activities were detected using dual-luciferase reporter assay system. The potential transcription factor binding sites at key transcriptional regulatory region of ezrin gene were predicted using on-line analyzing programme. Results: The recombinant pGLB plasmids containing different lengths of 5′-flanking region of ezrin gene were obtained. When the lengths of ezrin 5′-flanking region were reduced from - 1 324 to - 890, the transcriptional activity decreased by about 80%. If the length of 5′-flanking region were deleted from - 146 to - 32, the transcriptional activities were nearly abolished. Sp 1 transcriptional factor binding sites were ubiquitous at the - 1 324/ - 890 and - 146/ - 32 regions. Conclusion: The - 1 324/ - 890 and - 146/ - 32 regions were two key transcriptional regulatory regions of ezrin gene in HeLa cells. Sp 1 may be an important factor for regulating the transcription of ezrin gene.

Cloning of Human PRL-3 Gene Promoter and Preliminary Identification of Its Snail Binding Site / 生物化学与生物物理进展

PRL-3 is a key gene related to metastasis of colorectal carcinoma. However, it is known little about the possible regulatory mechanisms of PRL-3 gene expression. There were three possible promoter regions predicted by TRED, a promoter prediction software,which were all located in the upstream regions of PRL-3 gene. One of PRL-3 gene candidate promoters was located in the region of about -1kb upstream proximal to 5′ UTR of PRL-3 gene. Many possible transcription factor binding sites such as Snail, n-MYC, ARNT, E74A, NF-kappaB, NRF-2 and AML-1 were predicted in the region by Consite, a promoter analysis web system. Interestingly, a 5′ CACCTG 3′ core sequence and other related sequences of snail binding sites were found in promoter region of PRL-3 genes. Two PRL-3 gene promoters between -699 to 299 nt and between -642 to -383 nt were cloned into pGL3 vector with luciferase report gene. Both of them had promoter activities in four different cell lines including colorectal carcinoma cell lines SW480 and SW620, nasopharyngeal carcinoma cell line CNE2 and human embryo kidney cell line 293A. Interestingly, the luciferase activities of the short DNA fragmentations with Snail binding site′s core sequence 5′ CACCTG 3′ were higher than that of the longer one. PRL-3 promoter obtaining the 5′ CACCTG 3′ core sequence of Snail binding sites, was validated to bind to snail by chromatin immunoprecipitation (CHIP) analysis and electrophoretic mobility shift assay (EMSA) in SW480 cells. The data suggested that Snail was involved in regulation of PRL-3.