Methidlumpropyl-EDTA-iron(II) cleavage of ribosomal DNA chromatin from<i>Dictyostetium dhcoideum</i>

Parish, Roger W.; Banz, Elizabeth; Ness, Penelope J.

doi:10.1093/nar/14.5.2089

Cited by 10 publications

(5 citation statements)

References 49 publications

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“…Transcriptional activity of genes can be correlated to a series of modifications in chrcnatin structure such as ENase I (hyper)sensitivity (7)(8)(9), disruption of the nmcl nal pattern (10), Sl nuclease sensitivity (11), restriction enzyme accessibility (12) and protein-ENA bindirs sites (13). lThese modifications are associated with actively expressed genes, potentially active genes, and genes that were once active (for review see (14)).…”

Section: Nucleic Acids Researchmentioning

confidence: 99%

In vivoprotein binding sites and nuclease hypersensitivity in the promoter region of a cell cycle regulated human H3 histone gene

et al. 1989

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The chromatin structure and protein-DNA interactions of a cell cycle regulated human H3 histone gene have been examined at different levels of resolution. Using traditional Southern blot analysis we have investigated the accessibility of the H3 coding region and its flanking sequences to DNase I, S1 nuclease and restriction endonuclease digestion. Using the native genomic blotting method recently developed in our laboratory, two sites of protein-DNA interaction in the proximal 240 bp of the promoter region of this H3 gene were established. Further in vivo analysis of protein-DNA binding sites in intact cells by genomic sequencing revealed, with single nucleotide resolution, the guanine contacts and footprints of the proteins bound to the promoter. The relative locations of protein-DNA interactions in this H3 gene are similar to those identified in vivo and in vitro in a cell cycle dependent human H4 histone gene. The proteins complexed with the H3 histone gene promoter can be dissociated between 0.16 and 0.28 M NaCl. The protein-DNA contacts persist throughout the cell cycle and thus may have a functional relationship with the basal level of transcription of this H3 gene that occurs during and outside of S phase.

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Section: Nucleic Acids Researchmentioning

confidence: 99%

In vivoprotein binding sites and nuclease hypersensitivity in the promoter region of a cell cycle regulated human H3 histone gene

et al. 1989

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“…The nuclear genome of D. discoideum is about 34 Mb in length and distributed over 6 chromosomes ranging from 4.5 Mb to 7 Mb. Additionally, a palindromic linear DNA molecule (inverted repeat) of about 90 kb is contained in the nucleus, which encodes for the rRNA genes [47]. This palindrome is amplified and represents about 20 % of all nucleotides in D. discoideum.…”

Section: P Falciparum Has a Nuclear Genome Of About 30mentioning

confidence: 99%

Large Scale Sequencing and Analysis of AT Rich Eukaryote Genomes

Glöckner¹

2000

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Environmental pressures can direct genomes from a normal to a more or less pronounced imbalance in the base composition. These pressures seem to occur relatively often since genomes with a deviation from a normal base composition are widespread throughout lower eukaryotes. These genomes show altered codon usage and enrichment for the preferred bases in intron and intergenic regions. Techniques designed for large scale sequencing and assembly of genomes with normal base composition will fail with these unusual genomes. Additionally, the currently available analysis tools are mainly suitable for gene finding in genomes with normal base composition. In recent years some large scale genome analysis projects involving species with a skew directed to a very high AT content were initiated. These projects are encountered with sequencing, assembly, and gap closure problems due to the high AT content. These problems can only be overcome with additional techniques, which partly were developed and used in the ongoing projects. In this review some characteristic aspects of AT rich genomes, the progress of the Dictyostelium discoideum and the Plasmodium falciparum projects, as well as techniques specifically used for the sequencing of these genomes are highlighted.

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“…The active genes are particularly sensitive to micrococcal nuclease. We found a continuous distribution of rDNA fragments was produced following digestion of Dictyostelium discoideum nucleoli with micrococcal nuclease (6,7) or methidiumpropyl-EDTA-iron(II) (11). The loss of periodicity may result from changes in nucleosome structure but also from an undefined linker length between the nucleosomes.…”

Section: Introductionmentioning

confidence: 97%

The effects of transcription on the nucleosome structure of fourDictyosteliumgenes

Pavlovic¹,

Banz²,

Parish³

1989

Nucl Acids Res

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Micrococcal nuclease digestion of Dictyostelium discoideum nuclei from various developmental stages was used to investigate transcription-related changes in the chromatin structure of the coding region of four genes. Gene activity was determined by Northern blotting and nuclear run on experiments. During strong transcription of the developmentally regulated cysteine proteinase I gene, a smear superimposed on a nucleosomal ladder was observed, indicating perturbation of nucleosomal structure was occurring. However, two other developmentally regulated genes, discoidin I and pSC253, showed only slight nucleosome disruption during high levels of transcription. The chromatin structure of a fourth gene (pCZ22) was disrupted throughout development, even at those stages where transcription was greatly reduced. We suggest that although nucleosome structure can be transiently perturbed by the passage of the transcription complex in vivo, the degree of perturbation and the speed with which nucleosomes reassemble is also influenced by the DNA sequence.

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Methidlumpropyl-EDTA-iron(II) cleavage of ribosomal DNA chromatin fromDictyostetium dhcoideum

Cited by 10 publications

References 49 publications

In vivoprotein binding sites and nuclease hypersensitivity in the promoter region of a cell cycle regulated human H3 histone gene

In vivoprotein binding sites and nuclease hypersensitivity in the promoter region of a cell cycle regulated human H3 histone gene

Large Scale Sequencing and Analysis of AT Rich Eukaryote Genomes

The effects of transcription on the nucleosome structure of fourDictyosteliumgenes

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