DNA-protein interactions in CpG islands and DNAse I sensitive chromatin]

DNA-protein interactions were studied in the chromatin preparations obtained according to different procedures by means of nucleoprotein-celite chromatography. Three discrete fractions dissociating in 1M, 2M and 3M NaCl were observed in all preparations. The 1M fraction prevails in DNaseI-sensitive chromatin and the 2M fraction--in the resistant. Chromatin solubilized by MspI restrictase (the active chromatin) contains the 1M and 3M fractions, one solubilized by AluI (inactive)--the 2M fraction. Distribution of the fractions is different in proliferating and quiescent cells.     

Methylation of estrogen and progesterone receptor gene 5' CpG islands correlates with lack of estrogen and progesterone receptor gene expression in breast tumors

Hormonal factors have a profound influence on the development, treatment, and outcome of breast cancer. The absence of steroid hormone receptors is highly correlated with resistance to antihormonal treatments. Work in cultured human breast cancer cell lines has shown that the absence of estrogen receptor (ER) gene expression in ER- cells is associated with extensive methylation of the ER gene 5' CpG island, and treatment with agents that demethylate the ER gene CpG island results in the production of functional ER protein. The current study shows that CpG islands in the 5' region of the ER and progesterone receptor (PR) genes are methylated in a significant fraction of primary human breast cancer tissues. The ER CpG island is methylated at the methylation-sensitive NotI restriction site in 9 of 39 (25%) of primary ER- breast cancers but remains unmethylated in 53 ER+ breast cancers and 9 normal breast specimens. Three methylation-sensitive restriction sites in the PR gene CpG island are not methylated in normal breast specimens and PR+ human breast cancers but are hypermethylated in 40% of PR- human breast tumors. These data demonstrate that methylation of the ER and PR gene CpG islands is associated with the lack of ER and PR gene expression in a significant fraction of human breast cancers.     

Number of CpG islands and genes in human and mouse

Estimation of gene number in mammals is difficult due to the high proportion of noncoding DNA within the nucleus. In this study, we provide a direct measurement of the number of genes in human and mouse. We have taken advantage of the fact that many mammalian genes are associated with CpG islands whose distinctive properties allow their physical separation from bulk DNA. Our results suggest that there are approximately 45,000 CpG islands per haploid genome in humans and 37,000 in the mouse. Sequence comparison confirms that about 20% of the human CpG islands are absent from the homologous mouse genes. Analysis of a selection of genes suggests that both human and mouse are losing CpG islands over evolutionary time due to de novo methylation in the germ line followed by CpG loss through mutation. This process appears to be more rapid in rodents. Combining the number of CpG islands with the proportion of island-associated genes, we estimate that the total number of genes per haploid genome is approximately 80,000 in both organisms.     

Modulation of chromatin structure regulates cytokine gene expression during T cell differentiation

Brachytherapy boost with external radiation therapy (RT) allows safer delivery to the prostate than conventional techniques. We measured the degree of radiation effect of adenocarcinoma cells in post-RT biopsy specimens and the association with biochemical failure. Forty-six patients with T2b-3c adenocarcinomas underwent 18-month post-RT biopsies, of whom 22 had adenocarcinoma. All biopsy specimens without obvious adenocarcinoma were stained with antibodies to prostate-specific antigen and keratins AE1/AE3 and 34 beta E12. The RT effect to adenocarcinoma cells was scored by adding the scores of the nuclear and cytoplasmic changes. Each adenocarcinoma was assigned 2 scores; the most-common and the least-amount RT effect. Treatment for 7 of the 46 patients failed; 6 of these had residual adenocarcinoma on the post-RT biopsy specimen. Sixteen of 22 patients with adenocarcinoma on the post-RT biopsy specimen did not experience biochemical failure. The presence of adenocarcinoma on the post-RT biopsy specimen was significantly associated with failure. The mean most-common RT-effect score for the 16 patients without failure was 5.2 compared with 4.2 for the 6 patients with failure. The mean least-amount RT-effect score in patients without failure was 4.4 compared with 2.8 (range, 2-4; SD, 0.75) in the failure group. These relatively radiation-resistant foci may be the source of failure. Scoring the RT-effect of adenocarcinoma in post-RT biopsy specimens may be clinically useful in predicting subsequent biochemical failure.     

The unique endometrial expression and genomic organization of the porcine IGFBP-2 gene

Nisin was first introduced commercially as a food preservative in the UK approximately 30 years ago. First established use was as a preservative in processed cheese products and since then numerous other applications in foods and beverages have been identified. It is currently recognised as a safe food preservative in approximately 50 countries. The established uses of nisin as a preservative in processed cheese, various pasteurised dairy products, and canned vegetables will be briefly reviewed. More recent applications of nisin include its use as a preservative in high moisture, hot baked flour products (crumpets) and pasteurised liquid egg. Renewed interest is evident in the use of nisin in natural cheese production. Considerable research has been carried out on the antilisterial properties of nisin in foods and a number of applications have been proposed. Uses of nisin to control spoilage lactic acid bacteria have been identified in beer, wine, alcohol production and low pH foods such as salad dressings. Further developments of nisin are likely to include synergistic action of nisin with chelators and other bacteriocins, and its use as an adjunct in novel food processing technology such as higher pressure sterilisation and electroporation. Production of highly purified nisin preparations and enhancement by chelators has led to interest in the use of nisin for human ulcer therapy, and mastitis control in cattle.     

Demethylation of the progesterone receptor CpG island is not required for progesterone receptor gene expression

In a previous study we have shown that an intravenous infusion of pramlintide (an analogue of human amylin) delayed gastric emptying, but the dose of pramlintide was supraphysiological in relation to the amylin response to food in non-diabetic subjects. The purpose of this study was to examine the dose response relationship of subcutaneous injections of pramlintide on gastric emptying and to determine whether administration of the drug before one meal has an impact on the subsequent meal. Eleven men with insulin-dependent diabetes mellitus were studied in a double-blind, randomised, four-way crossover design. None had autonomic neuropathy. Euglycaemia was maintained overnight before the study day. At -30 min the patients self-injected their usual morning insulin and at -15 min they injected the study drug (either placebo or 30, 60 or 90 microg pramlintide) subcutaneously. At 0 min they ate a standard meal consisting of a pancake, labelled with 99mTc, and a milkshake containing 3-ortho-methylglucose (3-OMG). Gastric emptying images were obtained for the next 8 h. At 240 min the subjects ate a similar meal, but on this occasion the pancake was labelled with (111)In. All three doses of pramlintide delayed emptying of the solid component of the first meal (p < 0.004) with no significant difference between the drug doses. There were no differences between placebo and pramlintide after the second meal. All three doses of pramlintide resulted in a prolongation in the time to peak plasma 3-OMG level (p < 0.0001) after the first meal but there was no difference after the second meal.     

Effects of estrogen on gene expression in the chick oviduct. Isolation and fractionation of chromatin non-histone proteins

Non-histones isolated from hen oviduct chromatin have been fractionated by a variety of methods. Chromatin was dissociated in 2 M NaC1, 5 M Urea, 0.1% beta-mercaptoethanol and 0.01 M Tris - HC1, pH 8.3, and the DNA removed by ultracentrifugation. After desalting by gel filtration the chromatin proteins were separated into three distinct fractions by stepwise elution with 0.10 M NaC1, 0.25 M Na C1 and 15% guanidine - HC1 from Bio-Rex 70 columns. Fractions I and II contain only non-histones and Fraction III contains histones plus a small amount of non-histones. Further fractionation of the non-histones was achieved by ammonium sulfate precipitation and DEAE-cellulose chromatography for Fraction I and phosphocellulose chromatography and gel filtration on Bio-Gel A-15 m for Fraction II. The histone and non-histones present in Fraction III were separated by gel filtration on Bio-Gel A-0.5 m. All fractionation methods have been used preparatively with reasonable recoveries of protein (greater than or equal to 60%). The fractions have been characterized by acrylamide gel electrophoresis. The integrity of the histones was maintained during the fractionation procedure indicating that proteolytic degradation was unlikely to have occurred. There was no selective loss of chromatin proteins during the ultracentrifugation and desalting steps and the non-histones were separated into distinct fractions with enrichment of some species not apparent prior to fractionation of the chromatin proteins.     

DNA damage from oxidants: influence of lesion complexity and chromatin organization

DNA damage by reactive oxygen species results in a spectrum of DNA lesions including single-strand breaks (ssb) and double-strand breaks (dsb). However, most damage is not lethal, and the location and nature of the DNA damage, in addition to total number of breaks, are likely to be critical in determining ultimate survival. Generally associated only with ionizing radiation, multiply damaged sites (i.e., complex lesions and clusters of complex lesions in DNA) are more likely to be lethal because they are less easily repaired. We examined five drugs known to cause DNA adducts, strand breaks, and reactive oxygen species for their ability to produce complex lesions: 4-nitroquinoline-1-oxide (4NQO), H2O2, doxorubicin, Tirapazamine, and etoposide. As indicators of lesion complexity we compared 1) the ratio of ssb to dsb, 2) the rate of rejoining of single-strand breaks, 3) the relative lethality of the breaks (number of breaks per mean lethal dose), and 4) the ability to produce complex lesions. Tirapazamine, etoposide, and doxorubicin gave dsb/ssb ratios similar to that for X-rays, whereas 4NQO and H2O2 showed dsb/ssb ratios of 200 and 3250, respectively. The number of dsb per LD50 varied from 2.5 to 500 for different drugs. There was no apparent relation between ssb rejoining half-time (3.5-85 min) and relative lethality or lesion complexity. A modified (nonionic detergent) filter elution method confirmed that tirapazamine, like ionizing radiation, produced multiple dsb within single chromatin domains. These data indicate that complex lesions can be produced by a number of different chemicals and suggest that the damage that results in killing by these drugs may be related to production of multiply damaged sites in DNA.     

Quick identification and localization of CpG islands in large genomic fragments by partial digestion with Hpa II and Hha I

This study examined features of patients that clinicians identified as good examples of Passive-Aggressive Personality Disorder to identify core features of the disorder and to determine which set of criteria (DSM-III-R, two definitions in the DSM-IV Options Book, or DSM-IV Negativistic) best characterized the identified patients. A national sample of licensed psychologists (N = 68) identified a patient who (based on symptoms) was a good example of Passive-Aggressive Personality Disorder. They then rated the patient on a symptom checklist composed of the Passive-Aggressive and Negativistic criteria, as well as other personality-disorder symptoms that overlap with Passive-Aggressive. Clinicians identified patients they considered exemplars for Passive-Aggressive Personality Disorder, and there was moderate consensus about their characteristic symptoms. DSM-III-R symptoms received the highest ratings, and there was little overlap with other personality disorders. Principal-component factor analysis suggested that a general pattern of passive resistance, along with a behavioral manifestation of procrastination and a second group of symptoms suggesting interpersonal difficulties, were the features of these passive-aggressive patients. More male patients were identified as good examples of the disorder, and female patients presented a more heterogeneous diagnostic picture. Implications and directions for future research are discussed, including the need to integrate research findings from the differing perspectives on personality disorders.     

The organization of histones and DNA in chromatin: evidence for an arginine-rich histone kernel

We have examined the role played by various histones in the organization of the DNA of the nucleosome, using staphylococcal nuclease as a probe of DNA conformation. When this enzyme attacks chromatin, a series of fragments evenly spaced at 10 base pair intervals is generated, reflecting the histone-DNA interactions within the nucleosome structure. To determine what contribution the various histones make to DNA organization, we have studied the staphylococcal nuclease digestion patterns of complexes of DNA with purified histones. Virtually all possible combinations of homogeneous histones were reconstituted onto DNA. Exhaustive digestion of a complex containing the four histones H2A, H2B,H3, and H4 yields a DNA fragment pattern very similar to that of whole chromatin. The only other combinations of histones capable of inducing chromatin-like DNA organization are H2A/H2B/H4 and those mixtures containing both H3 and H4. From an examination of the kinetics of digestion of H3/H4 reconstitutes, we conclude that although the other histones have a role in DNA organization within the nucleosome, the arginine-rich histone pair, H3/H4, can organize DNA segments the length of the nucleosome core in the absence of all other histones.