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 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 Slaying the last unicorn: discovery of histones in the microalga Nanochlorum eucaryotum

2021 ◽  
Vol 8 (2) ◽  
pp. 202023
Author(s):  
Valerie W. C. Soo ◽  
Tobias Warnecke
Keyword(s):  
Exceptional Case ◽  
Micrococcal Nuclease ◽  
Histone Fold ◽  
Histone Mrnas ◽  
Micrococcal Nuclease Digestion ◽  
Eukaryotic Chromatin ◽  
Nuclease Digestion ◽  
Eukaryotic Gene ◽  
Core Histones

Histones 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 orthologues 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, Nanochlorum eucaryotum has histone-based chromatin characteristic of most eukaryotes.

scholarly journals The variation with age of nuclear phosphoproteins released during micrococcal-nuclease digestion and nucleosomal phosphoproteins in three cell types from rat liver

1981 ◽  
Vol 194 (3) ◽  
pp. 963-974
Author(s):  
V Zongza ◽  
A P Mathias
Keyword(s):  
Rat Liver ◽  
Cell Types ◽  
Micrococcal Nuclease ◽  
Dna Repeat ◽  
Micrococcal Nuclease Digestion ◽  
Different Types ◽  
Nuclease Digestion ◽  
Old Rats ◽  
Parenchymal Cells ◽  
Nuclear Phosphoproteins

The nucleosomal non-histone phosphoproteins, and phosphoproteins released during the digestion of nuclei by micrococcal nuclease, were studied in three rat liver nuclear populations, namely diploid stromal, diploid parenchymal, and tetraploid parenchymal nuclei, which were separated by zonal centrifugation, in 3-week-old rats in which the parenchymal cells contain diploid nuclei and in 2- and 4-month-old rats with increasing proportions of parenchymal tetraploid nuclei. Qualitative and quantitative differences in nucleosomal phosphoprotein band patterns were found among different types of nuclei and ages. More phosphoprotein bands were found in nucleosomes derived from parenchymal than stromal nuclei. The number of phosphoproteins released during micrococcal-nuclease digestion increased with age for parenchymal nuclei. The significance of these results, considered in conjunction with the increase of DNA repeat length and decrease of nuclease accessibility with age, is discussed.

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.

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

scholarly journals The variation with age of the structure of chromatin in three cell types from rat liver

1979 ◽  
Vol 179 (2) ◽  
pp. 291-298 ◽  
Author(s):  
V Zongza ◽  
A P Mathias
Keyword(s):  
Rat Liver ◽  
Cell Types ◽  
Repeat Length ◽  
Micrococcal Nuclease ◽  
Dna Repeat ◽  
Old Rats ◽  
Parenchymal Cells ◽  
Kinetics Of

The organization of chromatin in three rat liver nuclear populations, namely diploid stromal, diploid parenchymal, and tetraploid parenchymal nuclei, which were separated by zonal centrifugation, was studied by digestion with micrococcal nuclease and pancreatic deoxyribonuclease in 3-week-old rats in which the parenchymal cells contain diploid nuclei and in 2-and 4-month-old rats with a high proportion of tetraploid nuclei. Digestion by micrococcal nuclease allowed the estimation of DNA-repeat length in chromatin. Parenchymal nuclei have shorter repeat length than stromal nuclei and DNA-repeat length increases with the age in all three nuclei populations. The kinetics of digestion by micrococcal nuclease showed that nuclei with shorter repeat length are more sensitive to micrococcal nuclease and that the sensitivity of chromatin decreases with age for all the types of nuclei in this study. The kinetics of digestion by pancreatic deoxyribonuclease showed that sensitivity of chromatin is related to the repeat length and that the sensitivity decreases with the ages.

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