scholarly journals Nucleosome repeat structure is present in native salivary chromosomes of Drosophila melanogaster.

1982 ◽  
Vol 95 (1) ◽  
pp. 262-266 ◽  
Author(s):  
R J Hill ◽  
M R Mott ◽  
E J Burnett ◽  
S M Abmayr ◽  
K Lowenhaupt ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Electron Microscope ◽  
Micrococcal Nuclease ◽  
Dna Fragments ◽  
Repeat Structure ◽  
Nucleosome Organization ◽  
Micrococcal Nuclease Digestion ◽  
Nuclease Digestion ◽  
Microsurgical Procedure ◽  
5S Gene

The regularly repeating periodic nucleosome organization is clearly resolved in the chromatin of the isolated salivary chromosomes of Drosophila melanogaster. A new microsurgical procedure of isolation in buffer A of Hewish and Burgoyne (1973, Biochem. Biophys. Res. Commun., 52:504-510) yielded native Drosophila salivary chromosomes. These chromosomes were then swollen and spread by a modified Miller procedure, stained or shadowed, and examined in the electron microscope. Individual nucleoprotein fibers were resolved with regularly repeated nucleosomes of approximately 10 nm diameter. Micrococcal nuclease digestion of isolated salivary nuclei gave a family of DNA fragments characteristic of nucleosomes for total chromatin, 5S gene, and simple satellite (rho = 1.688 g/cm3) sequences.

scholarly journals CAM: a quality control pipeline for MNase-seq data

2017 ◽  
Author(s):  
Sheng’en Hu ◽  
Xiaolan Chen ◽  
Ji Liao ◽  
Yiqing Chen ◽  
Chengchen Zhao ◽  
...  
Keyword(s):  
Quality Control ◽  
High Throughput Sequencing ◽  
Micrococcal Nuclease ◽  
Functional Regions ◽  
Nucleosome Organization ◽  
Genome Wide ◽  
Micrococcal Nuclease Digestion ◽  
A Genome ◽  
Nuclease Digestion ◽  
Wide Scale

AbstractNucleosome organization affects the accessibility of cis-elements to trans-acting factors. Micrococcal nuclease digestion followed by high-throughput sequencing (MNase-seq) is the most popular technology used to profile nucleosome organization on a genome-wide scale. Evaluating the data quality of MNase-seq data remains challenging, especially in mammalian. There is a strong need for a convenient and comprehensive approach to obtain dedicated quality control (QC) for MNase-seq data analysis. Here we developed CAM, which is a comprehensive QC pipeline for MNase-seq data. The CAM pipeline provides multiple informative QC measurements and nucleosome organization profiles on different potentially functional regions for given MNase-seq data. CAM also includes 268 historical MNase-seq datasets from human and mouse as a reference atlas for unbiased assessment. CAM is freely available at: http://www.tongji.edu.cn/~zhanglab/CAM

scholarly journals Human SWI/SNF Generates Abundant, Structurally Altered Dinucleosomes on Polynucleosomal Templates

2005 ◽  
Vol 25 (24) ◽  
pp. 11156-11170 ◽  
Author(s):  
Natalia P. Ulyanova ◽  
Gavin R. Schnitzler
Keyword(s):  
Cell Cycle Control ◽  
Micrococcal Nuclease ◽  
Asymmetric Structures ◽  
Micrococcal Nuclease Digestion ◽  
Evolutionarily Conserved ◽  
Nuclease Digestion ◽  
Transcriptional Memory ◽  
Altered Form ◽  
Regulatory Functions ◽  
Negative Supercoils

ABSTRACT Human SWI/SNF (hSWI/SNF) is an evolutionarily conserved ATP-dependent chromatin remodeling complex required for transcriptional regulation and cell cycle control. The regulatory functions of hSWI/SNF are correlated with its ability to create a stable, altered form of chromatin that constrains fewer negative supercoils than normal. Our current studies indicate that this change in supercoiling is due to the conversion of up to one-half of the nucleosomes on polynucleosomal arrays into asymmetric structures, termed “altosomes,” each composed of two histone octamers and bearing an asymmetrically located region of nuclease-accessible DNA. Altosomes can be formed on chromatin containing the abundant mammalian linker histone H1 and have a unique micrococcal nuclease digestion footprint that allows their position and abundance on any DNA sequence to be measured. Over time, altosomes spontaneously revert to structurally normal but improperly positioned nucleosomes, suggesting a novel mechanism for transcriptional attenuation as well as transcriptional memory following hSWI/SNF action.

Chromatin from the unicellular red alga Porphyridium has a nucleosome structure

1982 ◽  
Vol 57 (1) ◽  
pp. 151-160
Author(s):  
K.L. Barnes ◽  
R.A. Craigie ◽  
P.A. Cattini ◽  
T. Cavalier-Smith
Keyword(s):  
Sodium Dodecyl ◽  
Red Alga ◽  
Repeat Length ◽  
Micrococcal Nuclease ◽  
Nucleosome Structure ◽  
Dna Repeat ◽  
Micrococcal Nuclease Digestion ◽  
Nuclease Digestion ◽  
Core Histones ◽  
Higher Eukaryotes

We have isolated a crude nuclear preparation from the unicellular red alga Porphyridium aerugineum and investigated the structure of Porphyridium chromatin. Electrophoresis of deproteinized DNA fragments produced by micrococcal nuclease digestion of Porphyridium nuclei gives a typical ladder pattern, indicative of a repeating structure. The DNA repeat-length, calculated from plots of multimer length against multimer number, varies somewhat between different digestions, ranging from 160 to 180 base-pairs (average 173). We interpret this as evidence of heterogeneity in repeat-length; the calculated repeat-length depends on the extent of digestion because chromatin sub-populations with longer repeat-lengths are on average digested earlier. Polyacrylamide/sodium dodecyl sulphate gel electrophoresis of basic proteins purified from Porphyridium nuclear preparations gives a pattern characteristic of core histones. Although our interpretation is complicated by some degradation, the result strongly suggests that Porphyridium chromatin contains each of the four core histones and that they are similar to those of higher eukaryotes. This, together with the micrococcal nuclease digestion results, demonstrates that Porphyridium chromatin is not fundamentally different from that of higher eukaryotes.

scholarly journals The Effect of Micrococcal Nuclease Digestion on Nucleosome Positioning Data

PLoS ONE ◽  
2010 ◽  
Vol 5 (12) ◽  
pp. e15754 ◽  
Author(s):  
Ho-Ryun Chung ◽  
Ilona Dunkel ◽  
Franziska Heise ◽  
Christian Linke ◽  
Sylvia Krobitsch ◽  
...  
Keyword(s):  
Nucleosome Positioning ◽  
Micrococcal Nuclease ◽  
Micrococcal Nuclease Digestion ◽  
Nuclease Digestion

Hyper(ADP-ribosyl)ation of histone H1

1982 ◽  
Vol 60 (12) ◽  
pp. 1085-1094 ◽  
Author(s):  
R. J. Aubin ◽  
V. T. Dam ◽  
J. Miclette ◽  
Y. Brousseau ◽  
A. Huletsky ◽  
...  
Keyword(s):  
Repeat Unit ◽  
Selective Extraction ◽  
Histone H1 ◽  
Polymerase Activity ◽  
Micrococcal Nuclease ◽  
Micrococcal Nuclease Digestion ◽  
Nuclease Digestion ◽  
Nonionic Detergent ◽  
Minimal Modification ◽  
Triton X

Nucleosomal chains of various repeat unit lengths were generated by a mild micrococcal nuclease digestion of purified pancreatic nuclei. Maximal nucleosome associated poly(ADP-ribose) polymerase activity was recovered in trimeric to tetrameric chromatin fragments, after which the enzyme activity gradually decreased and stabilized towards oligomeric periodicities of 11 to 16 nucleosomes. Electrophoresis of [32P] ADP-ribosylated histones on first-dimension acid–urea or acid–urea–Triton gels and on second-dimension acid – urea – cetyltriammonium bromide gels revealed that, of all histones, only histone H1 could be significantly poly(ADP-ribosyl)ated while only minimal modification could be recovered with histone H10. Furthermore, the extent of ADP-ribosylation present on pancreatic histone H1 is shown to proportionally retard this protein's electrophoretic mobility in all gel systems and to consist of a distinct series of at least 12 modification intermediates which can be evidenced, in nuclei or nucleosomes, and fully recovered along with histone H1 upon its selective extraction with 5% perchloric acid. The generation of these increasingly ADP-ribosylated forms of histone H1 is also demonstrated to be time dependent and the more complex ADP-ribosylated forms of this histone are favored at high NAD+ concentrations. Moreover, the electrophoretic mobilities of all intermediates are unaffected by the presence of the nonionic detergent Triton X-100.

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