scholarly journals Micrococcal nuclease digestion of nuclei reveals extended nucleosome ladders having anomalous DNA lengths for chromatin assembled on non-replicating plasmids in transfected cells

1994 ◽  
Vol 22 (3) ◽  
pp. 370-375 ◽  
Author(s):  
ShinWu Jeong ◽  
Arnold Stein
Keyword(s):  
Micrococcal Nuclease ◽  
Transfected Cells ◽  
Micrococcal Nuclease Digestion ◽  
Nuclease Digestion

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.

scholarly journals Slaying the last unicorn - discovery of histones in the microalga Nanochlorum eucaryotum

2020 ◽  
Author(s):  
Valerie WC Soo ◽  
Tobias Warnecke
Keyword(s):  
Exceptional Case ◽  
Micrococcal Nuclease ◽  
Histone Fold ◽  
Histone Mrnas ◽  
Micrococcal Nuclease Digestion ◽  
Eukaryotic Chromatin ◽  
Nuclease Digestion ◽  
Eukaryotic Gene ◽  
Core Histones

ABSTRACTHistones are the principal constituents of eukaryotic chromatin. The four core histones (H2A, H2B, H3, and H4) are conserved across sequenced eukaryotic genomes and therefore thought to be universal to eukaryotes. In the early 1980s, however, a series of biochemical investigations failed to find evidence for histones or nucleosomal structures in the microscopic green alga Nanochlorum eucaryotum. If true, derived histone loss in this lineage would constitute an exceptional case that might help us further understand the principles governing eukaryotic gene regulation. To substantiate these earlier reports of histone loss in N. eucaryotum, we sequenced, assembled and quantified its transcriptome. Following a systematic search for histone-fold domains in the assembled transcriptome, we detect orthologs to all four core histones. We also find histone mRNAs to be highly expressed, comparable to the situation in other eukaryotes. Finally, we obtain characteristic protection patterns when N. eucaryotum chromatin is subjected to micrococcal nuclease digestion, indicating widespread formation of nucleosomal complexes in vivo. We conclude that previous reports of missing histones in N. eucaryotum were mistaken. By all indications, N. eucaryotum has histone-based chromatin characteristic of most eukaryotes.

scholarly journals A chromosomal phosphoprotein is preferentially released by mild micrococcal-nuclease digestion

1984 ◽  
Vol 220 (2) ◽  
pp. 539-545 ◽  
Author(s):  
C C Liew ◽  
M J Halikowski ◽  
M S Zhao
Keyword(s):  
Gradient Centrifugation ◽  
Specific Radioactivity ◽  
Sucrose Density Gradient ◽  
Micrococcal Nuclease ◽  
Chromosomal Protein ◽  
Sucrose Density Gradient Centrifugation ◽  
Micrococcal Nuclease Digestion ◽  
Nuclease Digestion ◽  
32P Incorporation ◽  
Liver Nuclei

[32P]Pi was administered to rats (5mCi/rat) 2h before the isolation of liver nuclei. The isolated nuclei were subjected to mild micrococcal-nuclease digestion for 2.5, 5 and 10 min at 37 degrees C, and the mononucleosomal fraction was subsequently isolated by sucrose-density-gradient centrifugation. The specific radioactivity of 32P-labelled mononucleosomal fractions decreased with increased digestion times. A phosphorylated chromosomal protein, B2 (Mr 68000, pI6.5-8.2), was demonstrated immunologically in the mononucleosomal fraction by using an antibody specific to this electrophoretically purified phosphoprotein. The incorporation of 32P into this phosphoprotein, previously shown to be mainly through covalent linkage, was revealed by antibody precipitation followed by gel electrophoresis. The rate of release of acid-soluble nucleotides by micrococcal-nuclease digestion of liver nuclei from partially hepatectomized rats 16 h after operation was strikingly higher than that for sham-operated controls. After partial hepatectomy, an increase in 32P incorporation into phosphoprotein in the monomer fractions specifically precipitated by this antibody was also found. This suggests that the phosphorylated non-histone chromatin protein B2 is preferentially associated with the transcriptionally active chromatin.

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