MNase Digestion Protection Patterns of the Linker DNA in Chromatosomes.

The compact nucleosomal structure limits DNA accessibility and regulates DNA-dependent cellular activities. Linker histones bind to nucleosomes and compact nucleosomal arrays into a higher-order chromatin structure. Recent developments in high throughput technologies and structural computational studies provide nucleosome positioning at a high resolution and contribute to the information of linker histone location within a chromatosome. However, the precise linker histone location within the chromatin fibre remains unclear. Using monomer extension, we mapped core particle and chromatosomal positions over a core histone-reconstituted, 1.5 kb stretch of DNA from the chicken adult ß-globin gene, after titration with linker histones and linker histone globular domains. Our results show that, although linker histone globular domains and linker histones display a wide variation in their binding affinity for different positioned nucleosomes, they do not alter nucleosome positions or generate new nucleosome positions. Furthermore, the extra ~20 bp of DNA protected in a chromatosome is usually symmetrically distributed at each end of the core particle, suggesting linker histones or linker histone globular domains are located close to the nucleosomal dyad axis.

Telomeric and Sub-Telomeric Structure and Implications in Fungal Opportunistic Pathogens.

Telomeres are long non-coding regions found at the ends of eukaryotic linear chromosomes. Although they have traditionally been associated with the protection of linear DNA ends to avoid gene losses during each round of DNA replication, recent studies have demonstrated that the role of these sequences and their adjacent regions go beyond just protecting chromosomal ends. Regions nearby to telomeric sequences have now been identified as having increased variability in the form of duplications and rearrangements that result in new functional abilities and biodiversity. Furthermore, unique fungal telomeric and chromatin structures have now extended clinical capabilities and understanding of pathogenicity levels. In this review, telomere structure, as well as functional implications, will be examined in opportunistic fungal pathogens, including Aspergillus fumigatus, Candida albicans, Candida glabrata, and Pneumocystis jirovecii.

Accumulation of unacetylatable Snf2p at the INO1 promoter is detrimental to remodeler recycling supply for CUP1 induction.

Chromatin structure plays a decisive role in gene regulation through the actions of transcriptional activators, coactivators, and epigenetic machinery. These trans-acting factors contribute to gene expression through their interactions with chromatin structure. In yeast INO1 activation, transcriptional activators and coactivators have been defined through intense study but the mechanistic links within these trans-acting factors and their functional implications are not yet fully understood. In this study, we examined the crosstalk within transcriptional coactivators with regard to the implications of Snf2p acetylation during INO1 activation. Through various biochemical analysis, we demonstrated that both Snf2p and Ino80p chromatin remodelers accumulate at the INO1 promoter in the absence of Snf2p acetylation during induction. Furthermore, nucleosome density and histone acetylation patterns remained unaffected by Snf2p acetylation status. We also showed that cells experience increased sensitivity to copper toxicity when remodelers accumulate at the INO1 promoter due to the decreased CUP1 expression. Therefore, our data provide evidence for crosstalk within transcriptional co-activators during INO1 activation. In light of these findings, we propose a model in which acetylation-driven chromatin remodeler recycling allows for efficient regulation of genes that are dependent upon limited co-activators.

Vma3p protects cells from programmed cell death through the regulation of Hxk2p expression.

In yeast, the vacuolar proton-pumping ATPase (V-ATPase) acidifies vacuoles to maintain pH of cytoplasm. Yeast cells lacking V-ATPase activity, due to a disruption of any VMA (vacuolar membrane ATPase) gene, remain viable but demonstrate growth defects. Although it has been suggested that VMA genes are critical for phospholipid biosynthesis, the link between VMA genes and phospholipid biosynthesis is still uncertain. Here, we found that cells lacking Vma3p, one of the major V-ATPase assembly genes, had a growth defect in the absence of inositol, suggesting that Vma3p is important in phospholipid biosynthesis. Through real-time PCR, we found that cells lacking Vma3p down-regulated HXK2 expression. Furthermore, acetic acid sensitivity assay showed that cells lacking Vma3p were more sensitive to acetic acid than WT cells. HXK2 encodes hexokinase 2 which can phosphorylate glucose during phospholipid biosynthesis. Since cells lacking HXK2 are sensitive to acetic acid and this is an indicator of programmed cell death, our observations suggest that Vma3p plays an important role in programmed cell death. Taken together, we have proposed a working model to describe how Vma3p protects cells against apoptosis through the regulation of HXK2 expression.

Pah1p negatively regulates the expression of V-ATPase genes as well as vacuolar acidification.

In yeast, PAH1 plays an important role in cell homeostasis and lipid biosynthesis. PAH1 encodes for the PA phosphatase, Pah1p, which is responsible for de novo TAG and phospholipid synthesis. It has been suggested that the lack of Pah1p causes irregular vacuolar morphology and dysfunctional V-ATPase pump activity. However, the molecular connection between Pah1p and V-ATPase activity has remained unclear. Through real-time PCR, we have shown that PAH1 is maximally induced at the stationary stage in the presence of inositol. We also found that vacuoles were less fragmented when PAH1 is maximally expressed. Subsequently, we observed that vacuoles from pah1Δ cells were more acidic than those in WT cells. Furthermore, V-ATPase genes were upregulated in the absence of Pah1p. These results suggest that Pah1p plays an important role in vacuolar activity by negatively regulating the expression of V-ATPase genes. As such, we provide evidence to show the role of Pah1p in vacuolar acidification and fragmentation.

The effects of serotonin1A receptor on female mice body weight and food intake are associated with the differential expression of hypothalamic neuropeptides and the GABAA receptor.

Both common eating disorders anorexia nervosa and bulimia nervosa are characteristically diseases of women. To characterize the role of the 5-HT1A receptor (5-HT1A-R) in these eating disorders in females, we investigated the effect of saline or 8-hydroxy-2-(di-n-propylamino) tetralin (8-OH-DPAT) treatment on feeding behavior and body weight in adult WT female mice and in adult 5-HT1A-R knockout (KO) female mice. Our results showed that KO female mice have lower food intake and body weight than WT female mice. Administration of 8-OH-DPAT decreased food intake but not body weight in WT female mice. Furthermore, qRT-PCR was employed to analyze the expression levels of neuropeptides, γ-aminobutyric acid A receptor subunit ß (GABAA ß subunits) and glutamic acid decarboxylase in the hypothalamic area. The results showed the difference in food intake between WT and KO mice was accompanied by differential expression of POMC, CART and GABAA ß2, and the difference in body weight between WT and KO mice was associated with significantly different expression levels of CART and GABAA ß2. As such, our data provide new insight into the role of 5-HT1A-R in both feeding behavior and the associated expression of neuropeptides and the GABAA receptor.

Co-dependent recruitment of Ino80p and Snf2p is required for yeast CUP1 activation.

In yeast, Ace1p-dependent induction of CUP1 is responsible for protecting cells from copper toxicity. Although the mechanism of yeast CUP1 induction has been studied intensively, it is still uncertain which chromatin remodelers are involved in CUP1 transcriptional activation. Here, we show that yeast cells are inviable in the presence of copper when either chromatin remodeler, Ino80p or Snf2p, is not present. This inviability is due to the lack of CUP1 expression in ino80Δ and snf2Δ cells. Subsequently, we observe that both Ino80p and Snf2p are present at the promoter and they are responsible for recruiting chromatin remodeling activity to the CUP1 promoter under induced conditions. These results suggest that they directly participate in CUP1 transcriptional activation. Furthermore, the codependent recruitment of both INO80 and SWI/SNF depends on the presence of the transcriptional activator, Ace1p. We also demonstrate that both remodelers are required to recruit RNA polymerase II and targeted histone acetylation, indicating that remodelers are recruited to the CUP1 promoter before RNA polymerase II and histone acetylases. These observations provide evidence for the mechanism of CUP1 induction. As such, we propose a model that describes novel insight into the order of events in CUP1 activation.

Neuroprotective role of taurine during aging.

Aging of the brain is characterized by several neurochemical modifications involving structural proteins, neurotransmitters, neuropeptides and related receptors. Alterations of neurochemical indices of synaptic function are indicators of age-related impairment of central functions, such as locomotion, memory and sensory performances. Several studies demonstrate that ionotropic GABA receptors, glutamate decarboxylase (GAD), and somatostatinergic subpopulations of GABAergic neurons are markedly decreased in experimental animal brains during aging. Additionally, levels of several neuropeptides co-expressed with GAD decrease during aging. Thus, the age-related decline in cognitive functions could be attributable, at least in part, to decrements in GABA inhibitory neurotransmission. In this study, we showed that chronic supplementation of taurine to aged mice significantly ameliorated the age-dependent decline in spatial memory acquisition and retention. We also demonstrated that concomitant with the amelioration in cognitive function, taurine caused significant alterations in the GABAergic and somatostatinergic system. These changes included (1) increased levels of the neurotransmitters GABA and glutamate, (2) increased expression of both isoforms of GAD (65 and 67) and the neuropeptide somatostatin, (3) decreased hippocampal expression of the ß3 subunits of the GABAA receptor, (4) increased expression in the number of somatostatin-positive neurons, (5) increased amplitude and duration of population spikes recorded from CA1 in response to Schaefer collateral stimulation and (6) enhanced paired pulse facilitation in the hippocampus. These specific alterations of the inhibitory system caused by taurine treatment oppose those naturally occurring in the aging brain, suggesting a protective role of taurine in this process. An increased understanding of age-related neurochemical changes in the GABAergic system will be important in elucidating the underpinnings of the functional changes of aging. Taurine supplementation might help forestall the age-related decline in cognitive functions through interaction with the GABAergic system.

Changes in gene expression at inhibitory synapses in response to taurine treatment.

We have previously shown that chronic supplementation of taurine to mice significantly ameliorated the age-dependent decline in memory acquisition and retention. We also showed that concomitant with the amelioration in cognitive function, taurine caused significant alterations in the GABAergic and somatonergic system. These changes include increased levels of the neurotransmitters GABA and glutamate, increased expression of both isoforms of GAD and the neuropeptide somatostatin, decreased hippocampal expression of the beta (ß) 2/3 subunits of the GABA(A) receptor, an increase in the number of somatostatin-positive neurons, and an increase in the amplitude and duration of population spikes recorded from CA1 in response to Schaefer collateral stimulation and enhanced paired pulse facilitation in the hippocampus. These specific alterations of the inhibitory system caused by taurine treatment oppose those naturally induced by aging, suggesting a protective role of taurine in this process. In this study, we further investigated the effects of taurine on gene expression of relevant proteins of the inhibitory synapses using qRT-PCR method and found that taurine affects gene expression of various subunits of the GABA(A) receptors and GAD. Increased understanding the effects of taurine on gene expression will increase our understanding of age-related taurine-mediated neurochemical changes in the GABAergic system and will be important in elucidating the underpinnings of the functional changes of aging. Taurine might help forestall the age-related decline in cognitive functions through interaction with the GABAergic system.

Chromatin repositioning activity and transcription machinery are both recruited by Ace1p in yeast CUP1 activation.

The relationship among transcriptional activators, nucleosome repositioning activity and transcription machinery at the yeast CUP1 gene was addressed. CUP1 encodes a cysteine-rich, copper-binding metallothionein that protects cells against copper toxicity through its ability to sequester copper. The induction of CUP1 requires the presence of Ace1p and the binding of Ace1p at the CUP1 promoter during activation provides evidence that Ace1p is directly involved in CUP1 induction. Furthermore, transcriptional activation of CUP1 resulted in nucleosome repositioning at the CUP1 promoter and sequences further downstream in the coding region, suggesting a gene-wide chromatin remodeling activity. Such remodeling activity depends on the presence of transcription activator Ace1p. The recruitment of RNA polymerase II also requires the presence of Ace1p. Therefore, these observations provide insight into the molecular mechanism of CUP1 activation.

INO1 induction requires chromatin remodelers Ino80p and Snf2p but not the histone acetylases.

Transcriptional co-activators contribute to gene expression through different mechanisms. We used various biochemical tools available for Saccharomyces cerevisiae to examine the mechanism of INO1 expression. INO1 encodes inositol-3-phosphate synthase, which catalyzes the rate-limiting step in the synthesis of inositol, a key player in phospholipid biosynthesis. Herein, we had demonstrated that the recruitment of histone acetylases Gcn5p and Esa1p mainly relied on the presence of transcriptional activator Ino2p during INO1 activation. However, the presence of the chromatin remodelers, Ino80p and Snf2p, may contribute to the additive effect of Gcn5p recruitment. We also showed that the recruitment of chromatin remodelers, Ino80p and Snf2p, is independent of the presence of histone acetylases. Furthermore, INO1 expression can be activated exclusively by the activator and chromatin remodelers, suggesting a dispensable role of histone acetylases in INO1 induction. Therefore, our data provide a mechanism for cross talk within transcriptional co-activators during INO1 activation.

Downregulation of GABA(A) ß subunits is transcriptionally controlled by Fmr1p.

Fragile X mental retardation syndrome is caused by the transcriptional silence of FMR1. Here, a quantitative PCR technique was used to examine the effect of Fmr1p on the expression of GABA(A) ß subunits in different mouse brain regions. Our results demonstrated the reduction of GABA(A) ß2 mRNA in all brain regions assessed, and the reduction of GABA(A) ß3 mRNA in the cortex, suggesting that the expression of GABA(A) ß subunits is transcriptionally regulated by Fmr1p. This finding may help to establish the link between the transcriptional profile of the GABAergic inhibitory system and the development of fragile X mental retardation syndrome.

Transcriptional control of genes involved in yeast phospholipid biosynthesis.

Phospholipid biosynthetic genes encode enzymes responsible for phospholipid biosynthesis. They are coordinately regulated by the availability of phospholipid precursors through the inositol-sensitive upstream activating sequence (UAS(INO)). However, not all phospholipid genes are UAS(INO)-containing genes and not all UAS(INO)-containing genes have the same response to the phospholipid precursors. Therefore, the transcriptional regulation of phospholipid genes in response to the availability of phospholipid precursors is still unclear. Here, 22 out of 47 phospholipid biosynthetic genes were identified as UAS(INO)-containing genes, including EKI1, EPT1, INM1, IPK2, KCS1, PAH1, and PIK1 which have never been reported before. We also showed, using qRT-PCR technique, that 12 UAS(INO)-containing genes are down-regulated by 100 µM inositol in the wild type cells and up-regulated by 100 µM inositol in the ino2Δ cells. Therefore, it is possible that these genes are transcriptionally regulated by the UAS(INO) through the negative response of Ino2p to inositol. One other UAS(INO)-containing gene might be regulated by the positive response of Ino2p to 100 µM inositol. Surprisingly, we found 9 UAS(INO)-containing genes are not dependent on the response of Ino2p to 100 µM inositol, indicating that they may be regulated by other pathway. Furthermore, we identified 9 and 3 non-UAS(INO)-containing genes that are possibly regulated by the negative and positive response of Ino2p to 100 µM inositol, respectively. Therefore, these observations provide insight into the understanding of the co-regulated phospholipid biosynthetic genes expression.

Gene-wide histone acetylation at the yeast INO1 requires the transcriptional activator Ino2p.

The relationship between histone acetylation and transcriptional activation at the yeast INO1 gene was addressed. INO1 encodes a key enzyme required for the de novo synthesis of phosphatidylinositol. Induction of INO1 resulted in acetylation of both histones H3 and H4 at the INO1 promoter and sequences farther downstream in the coding region, suggesting a gene-wide acetylation in response to transcriptional activation. Such chromatin remodeling activity requires the presence of transcriptional activator Ino2p. This indicates that histone acetylation is an activator-dependent event. Furthermore, the increase of histone acetylation is due to the increase of acetylation levels per nucleosome rather than the increase of nucleosome density. Therefore, these observations constitute evidence for the molecular mechanism of the correlation between histone acetylation and INO1 activity.

Altered expression of Autism-associated genes in the brain of Fragile X mouse model.

Autism is a severe neurodevelopmental disorder, which typically emerges in early childhood. Most cases of autism have not been linked to mutations in a specific gene, and the etioloty of the disorder remains to be established [S.S. Moy, J.J. Nadler, T.R. Magnuson, J.N. Crawley, Mouse models of autism spectrum disorders: the challenge for behavioral genetics, Am. J. Med. Genet. 142 (2006) 40-51]. Fragile X syndrome is caused by mutation in the FMR1 gene and is characterized by mental retardation, physical abnormalities, and, in most case, autistic-like behavior [R.J. Hagerman, A.W. Jackson, A. Levitas, B. Rimland, M. Braden, An analysis of autism in fifty males with the Fragile X syndrome, Am. J. Med. Genet. 23 (1986) 359-374, C.E. Bakker, C. Verheij, R. Willemsen, R. van der Helm, F. Oerlemans, M. Vermeij, A. Bygrave, A.T. Hoogeveen, B.A. Oostra, E. Reyniers, K. De Boulle, R. D'Hooge, P. Cras, D. van Velzen, G. Nagels, J.J. Marti, P. De Deyn, J.K. Darby, P.J. Willems, Fmr1 knockout mice: a model to study Fragile X mental retardation, Cell 78 (1994) 23-33]. The FMR1 knockout (KO) mouse is one of the best characterized animal models for human disorders associated with autism [S.S. Moy, J.J. Nadler, T.R. Magnuson, J.N. Crawley, Mouse models of autism spectrum disorders: the challenge for behavioral genetics, Am. J. Med. Genet. 142 (2006) 40-51]. We have used real-time PCR to investigate changes in expression levels of three genes: WNT2, MECP2, and FMR1 in different brain regions of Fagile X mice and litter mate controls. We found major changes in the expression pattern for the three genes examined. FMR1, MECP2, and WNT2 expression were drastically down regulated in the Fragile X mouse brain.

Activator-dependent recruitment of SWI/SNF and INO80 during INO1 activation.

Transcriptional activation of yeast INO1 requires SWI/SNF and INO80 for nucleosome disruption at the promoter. However, the cooperative interplay among remodelers and their recruitment dynamics in activation have thus far been vague. Here, we showed, using chromatin immunoprecipitation, that both SWI/SNF and INO80 are present at the promoter and are restricted to the promoter, indicating that they directly participate in localized INO1 chromatin remodeling. Furthermore, both SWI/SNF and INO80 are absent at the INO1 promoter in ino2Delta cells, suggesting that these are activator-dependent remodelers. We have also found that the presence of INO80 is required for SWI/SNF recruitment, indicating that INO80 arrives first at the promoter followed by SWI/SNF. In light of these findings, we proposed a model which describes the order of events in INO1 activation.

A SWI/SNF- and INO80-dependent nucleosome movement at the INO1 promoter.

Transcriptional activation in yeast INO1 chromatin was studied using the indirect end-labeling technique. INO1 chromatin is organized into an ordered, overlapping nucleosomal array under repressing conditions. Nucleosome positions were only disrupted at the promoter region under inducing conditions in the presence of SWI/SNF and INO80. Mutants lacking either remodeler demonstrated identical positioning patterns as the wild type under repressing conditions. This indicates that these two remodelers are responsible and essential for local nucleosomal mobilization at the INO1 promoter. The area of local nucleosome movement is consistent with the previously identified region of histone deacetylation activity. In light of these findings, we suggest that nucleosomes subject to local mobilization are also targets for local histone modifications.

Mapping histone modifications by nucleosome immunoprecipitation.

Studies of histone modification patterns and their role in gene regulation have led to the proposal that there is a "histone code." We have developed a method for nucleosome immunoprecipitation that can precisely identify the specific nucleosomes that carry a posttranslational modification of interest. The process involves the isolation and micrococcal nuclease digestion of minichromosomes to generate nucleosome core particles. These are then used in immunoprecipitation reactions with an antibody directed against the histone modification of interest. Subsequently, nucleosome core particle DNA is purified and end labeled. The original locations of the nucleosomes in the immunoprecipitate can be determined at low resolution (using a modified Southern blot hybridization procedure) or at maximal resolution (using the monomer extension method). Using the latter method, the positions of specific nucleosomes that carry the posttranslational modification of interest can be identified precisely. This method is sensitive, provides maximal resolution, and is inexpensive. The approach described here may serve as a paradigm for the study of histone-modifying patterns.

The DNA-binding domain of the yeast Spt10p activator includes a zinc finger that is homologous to foamy virus integrase.

The yeast SPT10 gene encodes a putative histone acetyltransferase that binds specifically to pairs of upstream activating sequence (UAS) elements found only in the histone gene promoters. Here, we demonstrate that the DNA-binding domain of Spt10p is located between residues 283 and 396 and includes a His(2)-Cys(2) zinc finger. The binding of Spt10p to the histone UAS is zinc-dependent and is disabled by a zinc finger mutation (C388S). The isolated DNA-binding domain binds to single histone UAS elements with high affinity. In contrast, full-length Spt10p binds with high affinity only to pairs of UAS elements with very strong positive cooperativity and is unable to bind to a single UAS element. This implies the presence of a "blocking" domain in full-length Spt10p, which forces it to search for a pair of UAS elements. Chromatin immunoprecipitation experiments indicate that, unlike wild-type Spt10p, the C388S protein does not bind to the promoter of the gene encoding histone H2A (HTA1) in vivo. The C388S mutant has a phenotype similar to that of the spt10Delta mutant: poor growth and global aberrations in gene expression. Thus, the C388S mutation disables the DNA-binding function of Spt10p in vitro and in vivo. The zinc finger of Spt10p is homologous to that of foamy virus integrase, perhaps suggesting that this integrase is also a sequence-specific DNA-binding protein.

Global regulation by the yeast Spt10 protein is mediated through chromatin structure and the histone upstream activating sequence elements.

The yeast SPT10 gene encodes a putative histone acetyltransferase (HAT) implicated as a global transcription regulator acting through basal promoters. Here we address the mechanism of this global regulation. Although microarray analysis confirmed that Spt10p is a global regulator, Spt10p was not detected at any of the most strongly affected genes in vivo. In contrast, the presence of Spt10p at the core histone gene promoters in vivo was confirmed. Since Spt10p activates the core histone genes, a shortage of histones could occur in spt10Delta cells, resulting in defective chromatin structure and a consequent activation of basal promoters. Consistent with this hypothesis, the spt10Delta phenotype can be rescued by extra copies of the histone genes and chromatin is poorly assembled in spt10Delta cells, as shown by irregular nucleosome spacing and reduced negative supercoiling of the endogenous 2mum plasmid. Furthermore, Spt10p binds specifically and highly cooperatively to pairs of upstream activating sequence elements in the core histone promoters [consensus sequence, (G/A)TTCCN(6)TTCNC], consistent with a direct role in histone gene regulation. No other high-affinity sites are predicted in the yeast genome. Thus, Spt10p is a sequence-specific activator of the histone genes, possessing a DNA-binding domain fused to a likely HAT domain.