Forgot your password?
New user?
New Window Opens on the Secret Life of Microbes: Scientists Develop First Microbial Profiles of Ecosystems
CAS announces the release of SciFinder Scholar for Mac OS X
Press Releases
Press Releases
| Check out our New Publishers' Select for Free Articles |
BBA - Gene Regulatory Mechanisms (v.1809, #1)
DNA-mounted self-assembly: New approaches for genomic analysis and SNP detection by Elena V. Bichenkova; Zhaolei Lang; Xuan Yu; Candelaria Rogert; Kenneth T. Douglas (pp. 1-23).
This article presents an overview of new emerging approaches for nucleic acid detection via hybridization techniques that can potentially be applied to genomic analysis and SNP identification in clinical diagnostics. Despite the availability of a diverse variety of SNP genotyping technologies on the diagnostic market, none has truly succeeded in dominating its competitors thus far. Having been designed for specific diagnostic purposes or clinical applications, each of the existing bio-assay systems (briefly outlined here) is usually limited to a relatively narrow aspect or format of nucleic acid detection, and thus cannot entirely satisfy all the varieties of commercial requirements and clinical demands. This drives the diagnostic sector to pursue novel, cost-effective approaches to ensure rapid and reliable identification of pathogenic or hereditary human diseases. Hence, the purpose of this review is to highlight some new strategic directions in DNA detection technologies in order to inspire development of novel molecular diagnostic tools and bio-assay systems with superior reliability, reproducibility, robustness, accuracy and sensitivity at lower assay cost. One approach to improving the sensitivity of an assay to confidently discriminate between single point mutations is based on the use of target assembled, split-probe systems, which constitutes the main focus of this review.Display Omitted► Diagnostic sector requires rapid and reliable approaches for disease identification. ► None of the existing genotyping methods has succeeded in dominating its competitors. ► Advances in new diagnostic strategies often cause undesirable technological issues. ► The goal is to deliver clinical and commercial benefits without associated problems. ► The success will rely on clever combinations of emerging genotyping technologies.
Keywords: Abbreviations; HCV; hepatitis C virus; HIV; human immunodeficiency virus; CCP; cationic conjugated polymer; FRET; fluorescence resonance energy transfer; LCR; ligase chain reaction; LDR; ligase detection reaction; LAR; ligase amplification reaction; MLCT; metal-to-ligand; charge-transfer; MMP; magnetic microparticles; MRSA; methicillin-resistant; Staphylococcus aureus; MSSA; methicillin-sensitive; Staphylococcus aureus; PCR; polymerase chain reaction; SERS; surface-enhanced Raman scattering; SERRS; surface-enhanced resonance Raman scattering; SNP; single nucleotide polymorphisms; sp-FRET; single pair-FRET assay; CFTR; Cystic Fibrosis Transmembrane RegulatorPolymorphism; Fluorescence; Nanoparticle; Exciplex; Excimer; FRET
Long-range DNA interactions are specifically altered by locked nucleic acid-targeting of a CTCF binding site by Jian Qun Ling; Aiju Hou; Andrew R. Hoffman (pp. 24-33).
Long-range DNA interactions play an important role in gene expression. CCCTC-binding factor (CTCF), a ubiquitously expressed and evolutionarily conserved 11-zinc-finger DNA binding protein, is intimately involved in gene regulation, helping to establish and maintain chromatin architecture and long-range DNA interactions. In order to study the effects of manipulating long range chromatin interactions in the regulation of the neurofibromatosis gene NF1, we targeted Zorro locked nucleic acids (Zorro LNA) to a single CTCF binding site at an NF1 locus in human fibroblast cells. Using chromatin immunoprecipitation, we determined that this Zorro LNA altered CTCF and RNA polymerase II binding at three separate and distinct regions in the NF1 gene. This change in protein binding was associated with changes in long-range DNA interactions at the NF1 locus and downregulation of NF1 gene expression. This study describes an efficient and convenient method to manipulate chromatin structure and alter gene expression that is regulated by long-range DNA interactions without changing the DNA sequence. The use of specific Zorro LNA probes may facilitate our efforts to understand the interactions between chromatin architecture and gene expression.►Long-range DNA interactions play an important role in gene expression. ►CTCF is the glue that maintains long range interactions. ►Zorro locked nucleic acids (LNA) can be used to alter long-range DNA interactions. ►LNA can be used to manipulate chromatin structure and alter gene expression.
Keywords: Abbreviations; 3C; chromosome conformation capture; ChIP; chromatin immunoprecipitation; CTCF; CCCTC-binding factor; DMR; differentially methylated region; ECR; evolutionary conserved region; HS; hypersensitive site; ICR; imprinting control region; LCR; locus control region; LNA; locked nucleic acid; miRNA; microRNA; PNA; peptide nucleic acid; PWM; position weight matrix; shRNA; short hairpin RNA; siRNA; small interfering RNA; ZFN; zinc finger nucleaseChromosome conformation capture; NF1; CTCF; Locked nucleic acid
Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation by Sergei Nechaev; Karen Adelman (pp. 34-45).
Proper regulation of gene expression is essential for the differentiation, development and survival of all cells and organisms. Recent work demonstrates that transcription of many genes, including key developmental and stimulus-responsive genes, is regulated after the initiation step, by pausing of RNA polymerase II during elongation through the promoter-proximal region. Thus, there is great interest in better understanding the events that follow transcription initiation and the ways in which the efficiency of early elongation can be modulated to impact expression of these highly regulated genes. Here we describe our current understanding of the steps involved in the transition from an unstable initially transcribing complex into a highly stable and processive elongation complex. We also discuss the interplay between factors that affect early transcript elongation and the potential physiological consequences for genes that are regulated through transcriptional pausing.►Pausing during early elongation is a widespread mechanism for transcription regulation, occurring at active and inactive genes alike. ►The efficiency of early elongation is dictated by the interplay between positive and negative factors. ►Regulation of pause duration through recruitment of the Positive Transcription Factor b (P-TEFb) kinase is a general strategy for modulating gene expression. ►Pausing impacts the dynamics of gene activation and allows for synchronous “bursts” of transcription. ►Transcription output is likely determined by the balance between two potentially rate-limiting steps: Pol II recruitment to a gene promoter and release of Pol II from pausing.
Keywords: RNA polymerase II; Gene regulation; Transcription elongation; Polymerase pausing
Drosophila vigilin, DDP1, localises to the cytoplasm and associates to the rough endoplasmic reticulum by Marta Batlle; Francesc-Xavier Marsellach; Dori Huertas; Azorin Fernando Azorín (pp. 46-55).
Functional characterisation of vigilin, a highly conserved multi-KH-domain protein that binds RNA and ssDNA, remains elusive and, to some extent, controversial. Studies performed in Saccharomyces cerevisiae and human cells indicate that vigilin localises to the cytoplasm, binds ribosomes, associates to RER and regulates mRNA translation. On the other hand, we and others reported a contribution to heterochromatin-mediated gene silencing (PEV) and chromosome segregation in S. cerevisiae, Drosophila and human cells. Whether this contribution is direct remains, however, unclear. Here, we report that Drosophila vigilin, DDP1, vastly localises to the cytoplasm, being largely excluded from the nucleus. We also show that DDP1 preferentially associates to RER and co-purifies with several ribosomal proteins, suggesting a contribution to mRNA translation. In light of these results, the contribution of DDP1 to PEV was re-examined. Here, we show that a newly generated null ddp1Δ mutation is only a weak suppressor of PEV, which is in contrast with our own previous results showing dominant suppression in the presence of a strong hypomorphic ddp1 15.1 mutation. Similar results were obtained in the fission yeast Schizosaccharomyces pombe, where vigilin (Vgl1) also associates to RER, having no significant contribution to PEV at centromeres, telomeres and the mating-type locus. Altogether, these results indicate that cytoplasmic localisation and association to RER, but not contribution to heterochromatin organisation, are evolutionarily conserved features of vigilin, favouring a model by which vigilin acts in the cytoplasm, regulating RNA metabolism, and affects nuclear functions only indirectly.►Vigilin is a highly conserved multi-KH-domain protein whose functional characterisation remains controversial. ►Vigilin was proposed to regulate RNA metabolism as well as to contribute to heterochromatin function and chromosome segregation. ►Our results show that vigilin localises to the cytoplasm, where it associates to the RER and binds ribosomes. ►Vigilin is largely excluded from the nucleus and its contribution to heterochromatin function is indirect. ►From this we conclude that vigilin acts in the cytoplasm and affects nuclear functions only indirectly, clarifying a confusing topic.
Keywords: KH-domain; Vigilin; DDP1; RNA; Heterochromatin; Drosophila
The zinc-sensing transcription factor MTF-1 mediates zinc-induced epigenetic changes in chromatin of the mouse metallothionein-I promoter by Fumika Okumura; Yong Li; Norio Itoh; Tsuyoshi Nakanishi; Masakazu Isobe; Glen K. Andrews; Tomoki Kimura (pp. 56-62).
Metallothionein (MT) is a small, cysteine-rich protein active in zinc homeostasis, cadmium detoxification, and protection against reactive oxygen species. Mouse MT-I gene transcription is regulated by metal response element-binding transcription factor-1 (MTF-1), which is recruited to the promoter by zinc. We examined alterations in the chromatin structure of the MT-I promoter associated with enhanced transcriptional activation. MTF-1 proved essential for zinc-induced epigenetic changes in the MT-I promoter. Chromatin immunoprecipitation assays demonstrated that zinc treatment rapidly decreased Lys4-trimethylated and Lys9-acetylated histone H3 in the promoter and decreased total histone H3 but not histone H3.3. Micrococcal nuclease sensitivity of the MT-I promoter was increased by zinc. Thus, the chromatin structure in the promoter may be locally disrupted by zinc-induced nucleosome removal. Without MTF-1 these changes were not observed, and an MTF-1 deletion mutant recruited to the MT-I promoter by zinc that did not recruit the coactivator p300 or activate MT-I transcription did not affect histone H3 in the MT-I promoter in response to zinc. Interleukin-6, which induces MT-I transcription independently of MTF-1, did not reduce histone H3 levels in the promoter. Rapid disruption of nucleosome structure at the MT-I promoter is mediated by zinc-responsive recruitment of an active MTF-1-coactivator complex.► Zn activates MTF-1 and induces metallothionein (MT) gene transcription. ► Zn disrupts chromatin structure in MT-I promoter by nucleosome removal. ► Interleukin-6 activates MT transcription with MTF-1-independent manner. ► Interleukin-6 does not disrupt the chromatin structure. ► The disruption may be mediated by MTF-1–coactivator complex.
Keywords: Abbreviations; ChIP; chromatin immunoprecipitation; DMEM; Dulbecco's modified Eagle's medium; DTT; dithiothreitol; FBS; fetal bovine serum; GAPDH; glyceraldehyde-3-phosphate dehydrogenase; H3-AcK9; Lys; 9; -acetylated histone H3; H3-triMeK4; Lys; 4; -trimethylated histone H3; IL; interleukin; MEF; mouse embryo fibroblast; MNase; Micrococcal nuclease; MRE; metal response element; MT; metallothionein; MTF-1; metal response element-binding transcription factor-1; MTF-KO; MTF-1 knockout; NP-40; Nonidet P-40; WT; wild-typeMTF-1; Metallothionein; Zinc; p300; Histone
Erratum to “MacroRNA underdogs in a microRNA world: Evolutionary, regulatory, and biomedical significance of mammalian long non-protein-coding RNA” [Biochem. Biophys. Acta 1799 (2010) 597–615]
by Leonard Lipovich; Rory Johnson; Chin-Yo Lin (pp. 63-63).