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At least 1,243 records · Page 69Linked to original sources
PubMed2003

Selective gene regulation by SWI/SNF-related chromatin remodeling factors.

Chromatin is a highly dynamic structure that plays a key role in the orchestration of gene expression patterns during cellular differentiation and development. The packaging of DNA into chromatin generates a barrier to the transcription machinery. The two main strategies by which cells alleviate chromatin-mediated repression are through the action of ATP-dependent chromatin remodeling complexes and enzymes that covalently modify the histones. Various signaling pathways impinge upon the targeting and activity of these enzymes, thereby controlling gene expression in response to physiological and developmental cues. Chromatin structure also underlies many so-called epigenetic phenomena, leading to the mitotically stable propagation of differential expression of genetic information. Here, we will focus on the role of SWI/SNF-related ATP-dependent chromatin remodeling complexes in developmental gene regulation. First, we compare different models for how remodelers can act in a gene-selective manner, and either cooperate or antagonize other chromatin-modulating systems in the cell. Next, we discuss their functioning during the control of developmental gene expression programs.

Animals↗
PubMed1992

Nucleosomal structure and histone H1 subfractional composition of pea (Pisum sativum) root nodules, radicles and callus chromatin.

Higher-order packaging of DNA in chromatin structures could be an essential step in the complex chain of events leading to activation/repression of eukaryotic gene expression. With the goal to investigate this aspect of transcriptional regulation of plant genes involved in symbiotic interactions between legumes and rhizobia we analyze here the molecular parameters of chromatin structure in functioning root nodules, callus and radicles of pea. Morphological intactness and the typical nucleosomal organization are preserved in purified nuclei isolated from all three sources. The calculated values of nucleosomal repeat changed from 185 +/- 5 bp in the nuclei of radicles to 168 +/- 5 bp and 195 +/- 6 bp in nodules and callus respectively. The observed changes are due to alterations in linker DNA lengths. The core histones are identical in all cases, but the subfractional composition of H1 linker histone is subjected to quantitative alterations. The most pronounced is the several-fold increase in content of the lowest-molecular-weight subfraction H1-6 which takes place during nodule development.

Cell Nucleus↗
PubMed1976

Basic chromosomal proteins in lower eukaryotes: relevance to the evolution and function of histones.

The occurence of the basic chromosomal proteins in lower eukaryotes provides a useful approach to the study of histone evolution and function in higher eukaryotes. The histones of higher plants and animals are very similar and some are nearly identical, suggesting a high degree of evolutionary conservation within this group of proteins. However, a literature survey reveals that in the lower eukaryotes the histone situation is quite variable. The ciliates, and the true and cellular slime molds possess basic chromosomal proteins that are very similar to the histones of higher plants and animals. Various other lower eukaryotes possess basic chromosomal proteins that resemble at least some of the major histone fractions, and some microorganisms possess basic chromosomal proteins that bear little or no relationship to higher plant and animal histones. Since histones play a major role in the control of gene expression and the maintenance of chromosome structure in higher organisms, the evolution of these proteins represents a major change in the packaging of DNA and the mode of regulating gene expression in eukaryotes.

Animals↗
PubMedDate not supplied

Hepatitis B virus core protein interacts with the C-terminal region of actin-binding protein.

Hepatitis B viral core protein is present in the nucleus and cytoplasm of infected hepatocytes. There is a strong correlation between the intrahepatic distribution of core protein and the viral replication state and disease activity in patients with chronic hepatitis. To understand the role of core protein in the pathogenesis of HBV, we used a yeast two-hybrid system to search for cellular proteins interacting with the carboxyl terminus of core protein, as this region is involved in a number of important functions in the viral replication cycle including RNA packaging and DNA synthesis. A cDNA encoding the extreme C-terminal region of human actin-binding protein, ABP-276/278, was identified. This interaction was further confirmed both in vitro and in vivo. In addition, the extreme C-terminal region of ABP-276/278 interacted with the nearly full-length HBV core protein. Since this region is present in both the core and the precore proteins, it is likely that both core and precore proteins of HBV can interact with the C-terminal region of ABP-276/278. The minimal region of ABP-276/278 which interacted with the HBV core protein was the C-terminal 199 amino acid residues which correspond to part of the 23rd repeat, the entire 24th repeat and the intervening hinge II region in ABPs. The potential functional outcome of ABP interaction in HBV replication and its contribution to the pathological changes seen in patients with chronic HBV infection are discussed.

Amino Acid Sequence↗
PubMed2001

ATP-dependent chromatin remodeling activities.

Genetic and biochemical approaches have indicated that the packaging of DNA into chromatin can be repressive to transcription. ATP-dependent chromatin remodelling activities can facilitate transcription from chromatin templates. Consistent with this, biochemical assays have shown that the action of ATP-dependent chromatin remodelling activities increase the accessibility of DNA within chromatin templates. However more recent functional studies suggest that many ATP-dependent chromatin remodelling activities can also function as repressors of transcription. Here we review recent advances to our understanding of the biological function of these complexes. We then consider some of the mechanisms by which ATP-dependent chromatin remodelling activities together with other forms of chromatin remodelling or modifying enzymes may act to regulate genomic accessibility either positively or negatively.

Adenosine Triphosphatases↗
PubMed1997

Comparison of a 20 kb region of human herpesvirus 6B with other human beta herpesviruses reveals conserved replication genes and adjacent divergent open reading frames.

The sequence of a 20.15 kb region from human herpesvirus 6 variant B (HHV-6B) strain Z29 is described (GenBank accession number L14772). Determinations of protein homologies for seventeen predicted gene products revealed HHV-6B homologs of six proteins well-conserved both in genetic context and amino acid sequence throughout the alpha-, beta-, and gammaherpesvirus subfamilies. These include proteins involved in viral DNA replication, packaging and nucleotide metabolism, and conserved proteins of undefined function. The close evolutionary relationship of the human betaherpesviruses, HHV-6B, HHV-6A, HHV-7 and human cytomegalovirus (HCMV) was confirmed by identification of several protein sequences encoded only by these viruses, including homologs of the HCMV early phosphoprotein family and a series of HCMV open reading frames predicted to encode glycoprotein exons. Homologs of essential HSV-1 replication proteins, UL8 and UL9, were also identified. Downstream from the conserved replication locus, each betaherpesvirus contains a region of divergent, small open reading frames. The evolution of this region and its potential use in the development of a viral vector system are discussed.

Conserved Sequence↗
PubMed1983

Structure and inherent properties of the bacteriophage lambda head shell. III. Spectroscopic studies on the expansion of the prohead.

The head shell of bacteriophage lambda expands by about 20% in diameter when it packages the DNA molecule in vivo. The expansion reaction is essentially a conformational change of the major head protein molecules to a state of lower free energy and can also be triggered in vitro by treatment with 4 M-urea. In order to investigate the conformational change, we have measured the circular dichroism, fluorescence and difference absorption spectra of the lambda head shell before and after the expansion by the treatment with urea. The far-ultraviolet circular dichroism spectra and the fluorescence spectra show that the expansion is not accompanied by a great change in the secondary structure (29% alpha-helix, 23% beta-structure) and the environment (non-polar) of the tryptophan residues of the major head protein molecule. On the other hand, by measurements of the circular dichroism and difference absorption spectra in the near-ultraviolet region as well as by chemical modification experiments with tetranitromethane, we have found that one or two tyrosine residues of the major head protein are transferred from a polar, solvent-exposed to a non-polar, solvent-unexposed environment during the expansion. Judging from these results, the conformational change seems to be mainly intermolecular or interdomainal rather than intradomainal.

Bacteriophage lambda↗
PubMed1993

A kinetic model of RNA folding.

The RNA folding process is represented as a Markov process with states corresponding to RNA secondary structures and transition probabilities corresponding to transformations of a secondary structure caused by formation or disintegration of a helix. Transition probabilities (kinetic constants) are determined. A notion of a group of structures is introduced, and it allows to reduce the state space. Energetic and kinetic parameters of pseudoknots are estimated. Algorithms for computation of a kinetic ensemble for structures and groups of structures are presented, as well as their modifications that take into account pseudoknots. The described algorithms are implemented as a procedure for prediction of RNA secondary structure that is included in the package DNA-SUN.

Algorithms↗
PubMed1988

Novel eukaryotic expression vectors which permit single-stranded replication in Escherichia coli and in vitro translational analysis of cloned genes.

The ability to express cloned genes transiently is an important technique in the study of eukaryotic gene expression. Numerous useful expression vectors have been constructed for this purpose although many of them share several common drawbacks. In this paper I describe the construction and characterization of novel expression vectors pSVKII and pSVKIII which have 13 and 8 unique restriction sites, respectively, suitable for cloning genes. These vectors have phage M13 ori, which permits them to produce and package ss DNA molecules in Escherichia coli host, thus facilitating the sequencing and site directed mutagenesis of a cloned gene. Expression vector pSVKIII has a T7 phage promoter located between the SV40 promoter and the multiple cloning sites, which permits efficient transcription and in vitro translation of the cloned gene prior to in vivo studies.

Cells↗
PubMed1993

Versatile adeno-associated virus 2-based vectors for constructing recombinant virions.

We have constructed several plasmid vectors with which a more efficient molecular cloning, followed by rescue, replication, and packaging of DNA fragments, can be achieved. The availability of these vectors should facilitate construction of a variety of recombinant adeno-associated virus 2 (AAV)-based virions containing therapeutic genes for potential use in human gene therapy.

Blotting, Southern↗
PubMed1993

Multiple functions of nucleosomes and regulatory factors in transcription.

The in vivo packaging of DNA with histone proteins to form chromatin makes its transcription a difficult process. Biochemical and genetic studies are beginning to reveal mechanistic details of how transcriptional regulatory factors confront at least two hurdles created by nucleosomes, the primary structural unit of chromatin. Regulatory factors must gain access to their respective binding sites and activate the formation of transcription complexes at core promoter elements. Distinct regulatory factors may be specialized to perform these functions.

Animals↗
PubMed2006

Developmental biology: holding pattern for histones.

New research on lipid droplets in Drosophila embryos has led to the surprising conclusion that these poorly understood organelles have a novel role as a regulated storage depot of maternally supplied proteins, particularly histones.

Active Transport, Cell Nucleus↗
PubMed2005

A physical model for the condensation and decondensation of eukaryotic chromosomes.

During the eukaryotic cell cycle, chromatin undergoes several conformational changes, which are believed to play key roles in gene expression regulation during interphase, and in genome replication and division during mitosis. In this paper, we propose a scenario for chromatin structural reorganization during mitosis, which bridges all the different scales involved in chromatin architecture, from nucleosomes to chromatin loops. We build a model for chromatin, based on available data, taking into account both physical and topological constraints DNA has to deal with. Our results suggest that the mitotic chromosome condensation/decondensation process is induced by a structural change at the level of the nucleosome itself.

Cell Cycle↗
PubMed2006

Reciprocal translocation t(7;16)(q21.2;p13.3) in an infertile man.

OBJECTIVE: To report the first case of reciprocal translocation t(7;16)(q21.2;p13.3) associated with male factor infertility. DESIGN: Case report. SETTING: University genetics laboratory and university andrology unit. PATIENT(S): A 38-year-old man with infertility and oligoasthenoteratozoospermia, but otherwise healthy. INTERVENTION(S): Chromosome analyses from peripheral blood lymphocyte cultures using Giemsa (G)-banding (GTG) and C-banding (CBG) and fluorescent in situ hybridization (FISH) were performed. MAIN OUTCOME MEASURE(S): Sperm count, motility, morphology, GTG and CBG banding, and FISH. RESULT(S): We report an apparently unique reciprocal translocation t(7;16)(q21.2;p13.3) confirmed by FISH in an infertile man. Semen analyses showed oligoasthenoteratozoospermia, with sperm count ranging from 2 x 10(6)/mL to 5 x 10(6)/mL and head defects (98%) in sperm morphology. CONCLUSION(S): In the present patient the breakpoint at 16p13.3 could have disrupted or harbored the PRM1, PRM2, or TNP2 genes responsible for the replacement of the histones involved in packaging the DNA into the sperm head. Resulting haploinsufficiency of these genes is likely to be the cause of sperm head defects and infertility in the patient. This case supports the opinion that alterations in the expression of protamine genes may be one of the causes of male factor infertility.

Adult↗
PubMed2006

The emergence of regulated histone proteolysis.

Proliferating cells need to synthesize large amounts of histones to rapidly package nascent DNA into nucleosomes. This is a challenging task for cells because changes in rates of DNA synthesis lead to an accumulation of excess histones, which interfere with many aspects of DNA metabolism. In addition, cells need to ensure that histone variants are incorporated at the correct chromosomal location. Recent discoveries have highlighted the importance of regulated histone proteolysis in preventing both the accumulation of excess histones and the mis-incorporation of histone variants at inappropriate loci.

Animals↗