Examination of DNA sequences undergoing chromatin conformation changes at a variegating breakpoint in Drosophila melanogaster

Position effect variegation in Drosophila melanogaster is associated with the inability of certain genes to be correctly expressed in a proportion of cells, giving a mosaic phenotype. The lack of expression is thought to be due to alterations in the gene's chromatin structure due to its proximity to a region of heterochromatin. Because of the difficulties involved, there is little biochemical data to support the intuitively appealing model of heterochromatin spreading used to explain this phenomenon.Differences in restriction fragment length were used to distinguish DNA regions from either normal (non-position affected) or rearranged (position affected) chromosomes so as to examine possible changes in gene copy number and the effects of endogenous nucleases. DNA sequences at the breakpoint of In (1)w ^m4, which variegates for the white gene, were assayed under conditions where the chromatin conformation was altered using second site modifier mutations (Su(var) or En(var)). No change in the DNA sequerice copy number was observed at either chromosome breakpoint, relative to wild type, when either suppressor or enhancer mutations were present. Therefore copy number change, through differential polyploidization or somatic gene loss, is not affected by Su(var) or En(var) induced changes in the chromatin conformation.Initial experiments showed a gross difference in the sensitivity of DNA to endogenous nucleases that appeared associated with Su(var) and En(var) mutations. En(var) mutation bearing samples appeared delayed in the digestion, relative to Su(var). This differential sensitivity seemed to be genome-wide as there was no detectable difference between either breakpoint of In(1)w ^m4 or the sequences on the homologous w ^- chromosome. However, after isogenizing the genetic background, the previously noted difference between the Su(var) and En(var) mutations was eliminated. In studies dealing with nuclease digestion of chromatin, the isogenization of genetic background is essential before meaningful comparisons can be made.     

酿酒酵母INO80染色质重塑复合物调控基因表达的研究进展

表观遗传调控是真核生物基因表达精细调控的重要组成部分,主要包括DNA甲基化、组蛋白修饰和染色质重塑。其中,染色质重塑因子可影响组蛋白修饰酶和转录因子与特定位点的结合,在基因表达调控中占有重要地位。INO80复合物是进化上保守的染色质重塑复合物,能利用ATP水解获得的能量促进核小体的滑动和驱逐。INO80复合物除了在DNA复制、修复中发挥重要功能外,还通过改变DNA可及性调控酿酒酵母的基因表达。本文综述了染色质重塑复合物的分类及组成,重点介绍了酿酒酵母多亚基复合物INO80在基因表达调控中的重要功能,包括驱逐RNA聚合酶Ⅱ、响应信号转导途径和改变基因表达水平等,并着重总结了其在酿酒酵母环境胁迫响应机理中的研究进展。深入研究INO80染色质重塑复合物的功能,可为理解真核生物精细代谢调控的机制,并进一步开发基于染色质重塑等表观调控水平的微生物代谢工程和合成生物学改造策略,提高菌株的环境胁迫耐受性和发酵性能提供基础。     

Epigenetic and pharmacological control of pigmentation via Bromodomain Protein 9 (BRD9)

Lineage-specific differentiation programs are activated by epigenetic changes in chromatin structure. Melanin-producing melanocytes maintain a gene expression program ensuring appropriate enzymatic conversion of metabolites into the pigment, melanin, and transfer to surrounding cells. During neuroectodermal development, SMARCA4 (BRG1), the catalytic subunit of SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complexes, is essential for lineage specification. SMARCA4 is also required for development of multipotent neural crest precursors into melanoblasts, which differentiate into pigment-producing melanocytes. In addition to the catalytic domain, SMARCA4 and several SWI/SNF subunits contain bromodomains which are amenable to pharmacological inhibition. We investigated the effects of pharmacological inhibitors of SWI/SNF bromodomains on melanocyte differentiation. Strikingly, treatment of murine melanoblasts and human neonatal epidermal melanocytes with selected bromodomain inhibitors abrogated melanin synthesis and visible pigmentation. Using functional genomics, iBRD9, a small molecule selective for the bromodomain of BRD9 was found to repress pigmentation-specific gene expression. Depletion of BRD9 confirmed a requirement for expression of pigmentation genes in the differentiation program from melanoblasts into pigmented melanocytes and in melanoma cells. Chromatin immunoprecipitation assays showed that iBRD9 disrupts the occupancy of BRD9 and the catalytic subunit SMARCA4 at melanocyte-specific loci. These data indicate that BRD9 promotes melanocyte pigmentation whereas pharmacological inhibition of BRD9 is repressive.     

Development of the large nucleolus in the oocytes of the copepod Acanthocyclops vernalis: an electron microscope study

A central feature of oogenesis in the copepod crustacean, Acanthocyclops vernalis, is the development of a very large nucleolus in the oocytes. This nucleolus appears to be the only source of rRNA for the oocyte, as no helper cells are present. Previous work has suggested that ribosomal DNA sequences other than those found at the morphological nucleolar organizers are participating in the elaboration of this nucleolus. It has been hypothesized that chromatin diminution, which occurs during early embryonic development, may involve the loss of these rDNA sequences, which are needed only for the production of ribosomes during oogenesis. The present study examines the development of the large oocyte nucleolus at the electron microscopic level. Nucleologenesis in A. vernalis was found to proceed through 5 stages. During the first 3 stages nucleolar morphology resembled that described in other organisms. In the last 2, however, nucleolar morphology changed radically and the nucleolus was seen to increase greatly in size while breaking up into multiple subunits. The subunits initially resemble active nucleoli, although in the last stage, synthesis appears to stop, as the nucleolus was found to consist only of dense areas containing ribosome-like particles. These observations are consistent with the hypothesis that diminuted DNA contains ribosomal RNA genes.     

Meiotic chromatin diminution in a vertebrate,the holocephalan fish Hydrolagus collie (Chondrichthyes,Holocephali)

A histochemical, microdensitometric, and electron microscopic study of testes of the ratfish Hydrolagus colliei shows that an instance of the rare phenomenon of germ line chromatin diminution occurs in this vertebrate species. In primary spermatocytes at metaphase I a spherical mass of heterochromatin accumulates at one side of the metaphase plate. At anaphase I the heterochromatic mass is left in the equatorial cytoplasm and is passed into one of the two secondary spermatocytes formed during cytokinesis. As nuclear membranes are being restored, a double membrane envelope is also formed around the heterochromatic mass, which is then termed the ‘chromatin diminution body’ (CDB). At second meiotic division the CDB is included in the cytoplasm of one of the four spermatids and retained there, apparently unchanged, until mid-spermiogenesis. At that time the CDB becomes adherent to the spermatid plasma membrane and is pinched off from the spermatid by a process of apocrine exocytosis, taking a layer of spermatid plasma membrane along with it. Simultaneously this tri-membrane CDB is taken into the adjacent Sertoli cell by endocytosis, thereby acquiring a fourth membrane layer, a part of the Sertoli cell plasma membrane. The CDBs are subsequently phagocytized, possibly first fusing with dense, multilaminate bodies in the Sertoli cell cytoplasm. The CDB chromatin mass is strongly positive with the Feulgen method for DNA and the alkaline fast green method for histones. Microdensitometric analysis shows that the discarded chromatin amounts to about 10% of the diploid nuclear content and that it appears to be part of the normal diploid complement rather than DNA amplified during meiosis.     

从大鼠肝染色质富集具有转录活性的DNA

采用DNase消化法从大鼠肝染色质分离得到富有转录活性的DNA(sDNA)。sDNA琼脂糖凝胶电泳,在0.5—6Kb范围内背景有一片荧光,小于1Kb范围内,出现明显区带。sDNA为探针与大鼠正常肝核RNA杂交百分数(29.5%),为以总核DNA为探针杂交百分数(8.2%)的3.6倍,并高于sDNA与大鼠肝癌核RNA杂交百分数(16.4%).     

Fractionation of the gene-size macronuclear chromatin fragments of the binucleated eukaryote Oxytricha

Summary The macronuclear chromatin of Oxytrichia nova consists of chromatin fragments which are fully soluble in 0.2 mM EDTA and whose DNA length varies from 500–25 000 bp. The DNA migrates electrophoretically as a series of discrete bands, with specific genes present in only one or a few bands. The chromatin fragments are composed of nucleosomes and migrate electrophoretically in proportion to their DNA length. These results suggest schemes for the fractionation of undigested chromatin in order to enrich for specific genes, facilitating analysis of changes in chromatin structure associated with changes in gene expression.     

Probing nucleosome core secondary structure before and after α-chymotrypsin treatment by raman spectroscopy and thermal denaturation

Nucleosome cores were digested with α-chymotrypsin until histone H3 was degraded to a partial histone, CP1. As we reported previously, cleavage occurred at leucine 20 to H3 and resulted in an increase in circular dichroism between 265 to 285 nm. Some modest core unfolding was also observed as determined by a small decrease in the sedimentation coefficient. Studies reported here deal with the analysis of core secondary structure and subsequent perturbation caused by treatment with α-chymotrypsin. Raman spectroscopy indicated that chymotryptic treatment promoted a change in the conformational environment of a population of core histone tyrosines. In addition, a shift from B-form to an intermediate B- or A-form was observed for core DNA. High-resolution thermal denaturation was used to determine alterations in the stabilization of core DNA related to perturbation of the core histones. Brief chymotryptic treatment indicated changes in both pre-melt and irreversible transitions.