Localization of the human H3F3A histone gene to 1q41, outside of the normal histone gene clusters

Gene expression analysis in LLC-PK1 renal tubular cells by atrial natriuretic peptide (ANP): correlation of homologous human genes with renal response

We used human DNA microarray to explore the differential gene expression profiling of atrial natriuretic peptide (ANP)-stimulated renal tubular epithelial kidney cells (LLC-PK1) in order to understand the biological effect of ANP on renal kidney cell's response. Gene expression profiling revealed 807 differentially expressed genes, consisting of 483 up-regulated and 324 down-regulated genes. The bioinformatics tool was used to gain a better understanding of differentially expressed genes in porcine genome homologous with human genome and to search the gene ontology and category classification, such as cellular component, molecular function and biological process. Four up-regulated genes of ATP1B1, H3F3A, ITGB1 and RHO that were typically validated by real-time quantitative PCR (RT-qPCR) analysis serve important roles in the alleviation of renal hypertrophy as well as other related effects. Therefore, the human array can be used for gene expression analysis in pig kidney cells and we believe that our findings of differentially expressed genes served as genetic markers and biological functions can lead to a better understanding of ANP action on the renal protective system and may be used for further therapeutic application.

Uptake, cellular distribution and novel cellular binding proteins of immunostimulatory CpG oligodeoxynucleotides in glioblastoma cells

Glioblastomas are the most malignant and most frequent brain tumors and exciting targets of gene and immunotherapy. Despite rapid development of experimental therapy little is known about the cellular behaviour of therapeutic oligodeoxynucleotides (ODNs). Here we designed uptake, cellular distribution and cellular binding proteins of immunostimulatory CpG-ODNs in glioblastoma cells by flow cytometry, fluorescence microscopy and mass spectrometry. Our data show that the phosphorothioate (PS) CpG-ODNs uptake in T98G and C6 cells is dose-, time-, temperature-dependent and independent of the CpG dinucleotides. Uptake can be inhibited by sodium azide, polyanions but not by chloroquine. After internalisation FITC labelled CpG-ODNs showed a spotted distribution in cytoplasm. Dozens of cellular binding proteins were identified using mass spectrometry. The binding of ODNs to proteins is dependent on modification and sequence but independent on CpG motif. ODNs bind to cellular proteins that are important for RNA processing and transport. Furthermore, three novel membrane proteins were identified, which might contribute to uptake of ODNs. ODNs binding to these proteins might interfere with the physiological function and thus might cause unwanted effects. Such binding also might influence the uptake efficiency or cellular distribution of therapeutic ODNs.

Analysis of gene expression patterns and chromosomal changes associated with aging

Age is the largest single risk factor for the development of cancer in mammals. Age-associated chromosomal changes, such as aneuploidy and telomere erosion, may be vitally involved in the initial steps of tumorigenesis. However, changes in gene expression specific for increased aneuploidy with age have not yet been characterized. Here, we address these questions by using a panel of fibroblast cell lines and lymphocyte cultures from young and old age groups. Oligonucleotide microarrays were used to characterize the expression of 14,500 genes. We measured telomere length and analyzed chromosome copy number changes and structural rearrangements by multicolor interphase fluorescence in situ hybridization and 7-fluorochrome multiplex fluorescence in situ hybridization, and we tried to show a relationship between gene expression patterns and chromosomal changes. These analyses revealed a number of genes involved in both the cell cycle and proliferation that are differently expressed in aged cells. More importantly, our data show an association between age-related aneuploidy and the gene expression level of genes involved in centromere and kinetochore function and in the microtubule and spindle assembly apparatus. To verify that some of these genes may also be involved in tumorigenesis, we compared the expression of these genes in chromosomally stable microsatellite instability and chromosomally unstable chromosomal instability colorectal tumor cell lines. Three genes (Notch2, H2AFY2, and CDC5L) showed similar expression differences between microsatellite instability and chromosomal instability cell lines as observed between the young and old cell cultures suggesting that they may play a role in tumorigenesis.

Differential expression of human replacement and cell cycle dependent H3 histone genes

Histones are the major protein component of chromatin. Except H4, all histone classes consist of several subtypes. The H3 family includes two replacement histone genes, H3.3A and H3.3B, which both encode the same protein and are expressed independently from the cell cycle. Since the two genes encode an identical protein, we analyzed whether they are differentially expressed. Therefore we cloned, sequenced and characterized the regulatory structures of the H3.3A gene and compared these with the corresponding regions in the H3.3B gene. In contrast to the H3.3B promoter, the promoter region of the H3.3A gene revealed neither a TATA nor any CCAAT boxes but an initiator element and several SP1 binding sequence motifs within an overall GC-rich sequence. Northern blot analysis of RNA from six human cell lines revealed that every cell line expressed each of the H3 isoform genes H3.1, H3.3A and H3.3B. In contrast, analysis of total RNA from human tissues showed a differential expression of the H3 isoform genes. The H3.3 genes are essentially only expressed in adult tissue, whereas the H3.1 gene is transcribed just in fetal tissue. The functional relevance of the elements identified by sequence analysis was established using a reporter gene assay with deletion constructs of the H3.3A promoter. In this assay a 256 bp fragment was sufficient for the full promoter activity and three promoter segments, each containing SP1 binding motifs, contribute to the H3.3A gene expression. The possible functional relevance of the differences between the two H3.3 genes in structure and expression is discussed.

Growth regulation of human variant histone genes and acetylation of the encoded proteins

The family of human histone genes consists of replication-dependent and independent subtypes. The replication-independent histone genes, also known as variants, give rise to distinct mRNAs, whose expression is regulated depending on the growth state of the cell, tissue type and developmental stage. In turn, the histone variants are differentially synthesized and modified by acetylation. Consequently, chromatin structure is altered resulting in complex changes in gene expression. The high conservation among histone protein subtypes suggests that they are indispensable. In addition, conservation of the positions of acetylation within subtypes suggests that the location of these sites is functionally important for the eukaryotic cell. For example, the structures of transcriptionally active and repressed chromatin are different depending on the acetylation state of histone proteins [1-3]. In addition, transcriptionally active and repressed chromatin contains distinct histone variants [4]. Specialized histone variants are targeted to the centromere of the chromosome, where they are essential for chromosome segregation [5]. Other specialized histones exist that are essential for development [6]. Changes in histone acetylation have been implicated in the down-regulation of a tumour suppressor gene in human breast cancer [7]. Acetylation also plays an important role in X chromosome inactivation as well as hormone-mediated transcriptional regulation [8, 9]. We propose here a novel model for histone variant gene regulation at the post-transcriptional level, which provides the groundwork to define the pathways regulating the synthesis of these variants.