Polymorphic core promoter GA-repeats alter gene expression of the early embryonic developmental genes

Protein complexes that bind to ‘GAGA’ DNA elements are necessary to replace nucleosomes to create a local chromatin environment that facilitates a variety of site-specific regulatory responses. Three to four elements are required for the disruption of a preassembled nucleosome. We have previously identified human protein-coding gene core promoters that are composed of exceptionally long GA-repeats. The functional implication of those GA-repeats is beginning to emerge in the core promoter of the human SOX5 gene, which is involved in multiple developmental processes. In the current study, we analyze the functional implication of GA-repeats in the core promoter of two additional genes, MECOM and GABRA3, whose expression is largely limited to embryogenesis. We report a significant difference in gene expression as a result of different alleles across those core promoters in the HEK-293 cell line. Across-species homology check for the GABRA3 GA-repeats revealed that those repeats are evolutionary conserved in mouse and primates (p < 1 × 10^− 8). The MECOM core promoter GA-repeats are also conserved in numerous species, of which human has the longest repeat and complexity. We propose a novel role for GA-repeat core promoters to regulate gene expression in the genes involved in development and evolution.     

Synthetic promoter libraries--tuning of gene expression

The study of gene function often requires changing the expression of a gene and evaluating the consequences. In principle, the expression of any given gene can be modulated in a quasi-continuum of discrete expression levels but the traditional approaches are usually limited to two extremes: gene knockout and strong overexpression. However, applications such as metabolic optimization and control analysis necessitate a continuous set of expression levels with only slight increments in strength to cover a specific window around the wild-type expression level of the studied gene; this requirement can be met by using promoter libraries. This approach generally consists of inserting a library of promoters in front of the gene to be studied, whereby the individual promoters might deviate either in their spacer sequences or bear slight deviations from the consensus sequence of a vegetative promoter. Here, we describe the two different methods for obtaining promoter libraries and compare their applicability.     

HBV基因型、基本核心启动子区双突变和肝细胞癌发生及临床病理特征的关系

目的探讨乙型肝炎病毒(HBV)基因型、基本核心启动子(BCP)区双突变(简称BCP双突变)和肝硬化(LC)、肝细胞癌(HCC)发生的关联,分析BCP双突变和HCC临床病理特征的关系。方法随机收集233例慢性HBV感染者的血清,其中80例为慢性乙型肝炎(CHB)患者、75例为LC患者、78例为HCC患者,并系统整理患者的常规检查和病理等资料。采用实时荧光定量聚合酶链反应(FQ-PCR)检测BCP双突,用特异性引物多重PCR扩增确定HBV基因型。用SPSS 11.0分析结果。结果 HBV基因型结果均为B和C型,分别在CHB和LC组,CHB和HCC组间分布差异有统计学意义(P<0.05),在LC和HCC组间分布差异无统计学意义(P>0.05),感染C基因型与LC和HCC发生相关(分别OR=2.73,95%CI=1.29～5.82;OR=2.00,95%CI=0.98～4.09)。BCP双突变也分别在CHB和LC组,CHB和HCC组间分布差异有统计学意义(P<0.05),在LC和HCC组间分布差异无统计学意义(P>0.05),双突变与LC和HCC发生相关(分别OR=1.91,95%CI=0.96～3.82;OR=2.05,95%CI=1.04～4.06)。BCP双突变和伴肝硬化的HCC相关(P<0.05)。结论感染HBV C基因型、BCP双突变可能均是LC和HCC发生的危险因素,BCP双突变可作为LC和HCC早期预警生物标记物。     

The initiator element of the Drosophila beta2 tubulin gene core promoter contributes to gene expression in vivo but is not required for male germ-cell specific expression

The tissue-specific expression of the Drosophila β2 tubulin gene (B2t) is accomplished by the action of a 14-bp activator element (β2UE1) in combination with certain regulatory elements of the TATA-less, Inr-containing B2t core promoter. We performed an in vivo analysis of the Inr element function in the B2t core promoter using a transgenic approach. Our experiments demonstrate that the Inr element acts as a functional cis-regulatory element in vivo and quantitatively regulates tissue-specific reporter expression in transgenic animals. However, our mutational analysis of the Inr element demonstrates no essential role of the Inr in mediating tissue specificity of the B2t promoter. In addition, a downstream element seems to affect promoter activity in combination with the Inr. In summary, our data show for the first time the functionality of the Inr element in an in vivo background situation in Drosophila.     

Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures

This work assesses relationships for 30 complete prokaryotic genomes between the presence of the Shine-Dalgarno (SD) sequence and other gene features, including expression levels, type of start codon, and distance between successive genes. A significant positive correlation of the presence of an SD sequence and the predicted expression level of a gene based on codon usage biases was ascertained, such that predicted highly expressed genes are more likely to possess a strong SD sequence than average genes. Genes with AUG start codons are more likely than genes with other start codons, GUG or UUG, to possess an SD sequence. Genes in close proximity to upstream genes on the same coding strand in most genomes are significantly higher in SD presence. In light of these results, we discuss the role of the SD sequence in translation initiation and its relationship with predicted gene expression levels and with operon structure in both bacterial and archaeal genomes.     

Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors

Background

Although numerous mouse models of breast carcinomas have been developed, we do not know the extent to which any faithfully represent clinically significant human phenotypes. To address this need, we characterized mammary tumor gene expression profiles from 13 different murine models using DNA microarrays and compared the resulting data to those from human breast tumors.

Results

Unsupervised hierarchical clustering analysis showed that six models (TgWAP-Myc, TgMMTV-Neu, TgMMTV-PyMT, TgWAP-Int3, TgWAP-Tag, and TgC3(1)-Tag) yielded tumors with distinctive and homogeneous expression patterns within each strain. However, in each of four other models (TgWAP-T ₁₂₁ , TgMMTV-Wnt1, Brca1 ^Co/Co ;TgMMTV-Cre;p53 ^+/- and DMBA-induced), tumors with a variety of histologies and expression profiles developed. In many models, similarities to human breast tumors were recognized, including proliferation and human breast tumor subtype signatures. Significantly, tumors of several models displayed characteristics of human basal-like breast tumors, including two models with induced Brca1 deficiencies. Tumors of other murine models shared features and trended towards significance of gene enrichment with human luminal tumors; however, these murine tumors lacked expression of estrogen receptor (ER) and ER-regulated genes. TgMMTV-Neu tumors did not have a significant gene overlap with the human HER2+/ER- subtype and were more similar to human luminal tumors.

Conclusion

Many of the defining characteristics of human subtypes were conserved among the mouse models. Although no single mouse model recapitulated all the expression features of a given human subtype, these shared expression features provide a common framework for an improved integration of murine mammary tumor models with human breast tumors.