Peptide nucleic acid (PNA) binding-mediated gene regulation

Peptide nucleic acids (PNAs) are synthetic oligonucleotides with chemically modified backbones. PNAs can bind to both DNA and RNA targets in a sequence-specific manner to form PNA/DNA and PNA/RNA duplex structures. When bound to double-stranded DNA (dsDNA) targets, the PNA molecule replaces one DNA strand in the duplex by strand invasion to form a PNA/DNA/PNA [or (PNA)2/DNA] triplex structure and the displaced DNA strand exists as a singlestranded D-loop. PNA has been used in many studies as research tools for gene regulation and gene targeting. The Dloops generated from the PNA binding have also been demonstrated for its potential in initiating transcription and inducing gene expression. PNA provides a powerful tool to study the mechanism of transcription and an innovative strategy to regulate target gene expression. An understanding of the PNA-mediated gene regulation will have important clinical implications in treatment of many human diseases including genetic, cancerous, and age-related diseases.

Structural components of the nuclear body in nuclei of Allium cepa cells

Nuclear bodies have long been noted in interphase nuclei of plant cells, but their structural component, origin and function are still unclear by now. The present work showed in onion cells the nuclear bodies appeared as a spherical structure about 0.3 to 0.8 microm in diameter. They possibly were formed in nucleolus and subsequently released, and entered into nucleoplasm. Observation through cytochemical staining method at the ultrastructural level confirmed that nuclear bodies consisted of ribonucleoproteins (RNPs) and silver-stainable proteins. Immunocytochemical results revealed that nuclear bodies contained no DNA and ribosomal gene transcription factor (UBF). Based on these data, we suggested that nuclear bodies are not related to the ribosome or other gene transcription activities, instead they may act as subnuclear structures for RNPs transport from nucleolus to cytoplasm, and may also be involved in splicing of pre-mRNAs.

Rice Mitochondrial Genes Are Transcribed by Multiple Promoters That Are Highly Diverged

Plant mitochondrial genes are often transcribed into complex sets of mRNA. To characterize the transcription initiation and promoter structure, the transcript termini of four mitochondrial genes, atpl, atp6, cob, rps7, in rice （Oryza sativa L.）, were determined by using a modified circularized RNA reverse transcription- polymerase chain reaction method. The results revealed that three genes （atp1, atp6, rps7） were transcribed from multiple initiation sites, indicating the presence of multiple promoters. Two transcription termination sites were detected in three genes （atp6, cob, rps7）, respectively. Analysis on the promoter architecture showed that the YRTA （Y=T or C, R=A or G） motifs that are widely present in the mitochondrlal promoters of other monocot and dicot plant species were detected only in two of the 12 analyzed promoters. Our data suggest that the promoter sequences in the rice mitochondrial genome are highly diverged in comparison to those in other plants, and the YRTA motif is not an essential element for the promoter activity.

High-Sensitivity Transcriptome Data Structure and Implications for Analysis and Biologic Interpretation

Novel microarray technologies such as the AB1700 platform from Applied Biosysterns promise significant increases in the signal dynamic range and a higher sensitivity for weakly expressed transcripts. We have compared a representative set of AB1700 data with a similarly representative Affymetrix HG-U133A dataset. The AB1700 design extends the signal dynamic detection range at the lower bound by one order of magnitude. The lognormal signal distribution profiles of these highsensitivity data need to be represented by two independent distributions. The additional second distribution covers those transcripts that would have gone undetected using the Affymetrix technology. The signal-dependent variance distribution in the AB1700 data is a non-trivial function of signal intensity, describable using a composite function. The drastically different structure of these highsensitivity transcriptome profiles requires adaptation or even redevelopment of the standard microarray analysis methods. Based on the statistical properties, we have derived a signal variance distribution model for AB1700 data that is necessary for such development. Interestingly, the dual lognormal distribution observed in the AB1700 data reflects two fundamentally different biologic mechanisms of transcription initiation.

Control of ribosome synthesis in bacteria:the important role of rRNA chain elongation rate

Bacteria growth depends crucially on protein synthesis,which is limited by ribosome synthesis.Ribosomal RNA(rRNA)transcription is the rate-limiting step of ribosome synthesis.It is generally proposed that the transcriptional initiation rate of rRNA operon is the primary factor that controls the r RNA synthesis.In this study,we established a convenient GFP-based reporter approach for measuring the bacterial rRNA chain elongation rate.We showed that the rRNA chain elongation rate of Escherichia coli remains constant under nutrient limitation and chloramphenicol inhibition.In contrast,rRNA chain elongation rate decreases dramatically under low temperatures.Strikingly,we found that Vibrio natriegens,the fastest growing bacteria known,has a 50%higher rRNA chain elongation rate than E.coli,which contributes to its rapid ribosome synthesis.Our study demonstrates that r RNA chain elongation rate is another important factor that affects the bacterial ribosome synthesis capacity.