scholarly journals Phylogenetic analysis of the core histones H2A, H2B, H3, and H4

1994 ◽  
Vol 22 (2) ◽  
pp. 174-179 ◽  
Author(s):  
Thomas H. Thatcher ◽  
Martin A. Gorovsky
Keyword(s):  
Phylogenetic Analysis ◽  
The Core ◽  
Core Histones

scholarly journals Identification and Characterization of the Genes Encoding the Core Histones and Histone Variants of Neurospora crassa

Genetics ◽  
2002 ◽  
Vol 160 (3) ◽  
pp. 961-973 ◽  
Author(s):  
Shan M Hays ◽  
Johanna Swanson ◽  
Eric U Selker
Keyword(s):  
Neurospora Crassa ◽  
Histone Variants ◽  
Null Alleles ◽  
Histone Genes ◽  
Histone H4 ◽  
Coding Regions ◽  
The Core ◽  
Genomic Arrangement ◽  
Genes Encoding ◽  
Core Histones

Abstract We have identified and characterized the complete complement of genes encoding the core histones of Neurospora crassa. In addition to the previously identified pair of genes that encode histones H3 and H4 (hH3 and hH4-1), we identified a second histone H4 gene (hH4-2), a divergently transcribed pair of genes that encode H2A and H2B (hH2A and hH2B), a homolog of the F/Z family of H2A variants (hH2Az), a homolog of the H3 variant CSE4 from Saccharomyces cerevisiae (hH3v), and a highly diverged H4 variant (hH4v) not described in other species. The hH4-1 and hH4-2 genes, which are 96% identical in their coding regions and encode identical proteins, were inactivated independently. Strains with inactivating mutations in either gene were phenotypically wild type, in terms of growth rates and fertility, but the double mutants were inviable. As expected, we were unable to isolate null alleles of hH2A, hH2B, or hH3. The genomic arrangement of the histone and histone variant genes was determined. hH2Az and the hH3-hH4-1 gene pair are on LG IIR, with hH2Az centromere-proximal to hH3-hH4-1 and hH3 centromere-proximal to hH4-1. hH3v and hH4-2 are on LG IIIR with hH3v centromere-proximal to hH4-2. hH4v is on LG IVR and the hH2A-hH2B pair is located immediately right of the LG VII centromere, with hH2A centromere-proximal to hH2B. Except for the centromere-distal gene in the pairs, all of the histone genes are transcribed toward the centromere. Phylogenetic analysis of the N. crassa histone genes places them in the Euascomycota lineage. In contrast to the general case in eukaryotes, histone genes in euascomycetes are few in number and contain introns. This may be a reflection of the evolution of the RIP (repeat-induced point mutation) and MIP (methylation induced premeiotically) processes that detect sizable duplications and silence associated genes.

Thermodynamic Studies of the Core Histones:  pH and Ionic Strength Effects on the Stability of the (H3−H4)/(H3−H4)2System†

Biochemistry ◽  
1996 ◽  
Vol 35 (6) ◽  
pp. 2037-2046 ◽  
Author(s):  
Vassiliki Karantza ◽  
Ernesto Freire ◽  
Evangelos N. Moudrianakis
Keyword(s):  
Ionic Strength ◽  
Thermodynamic Studies ◽  
The Core ◽  
Core Histones ◽  
The Stability

scholarly journals Nuclear RanGAP Is Required for the Heterochromatin Assembly and Is Reciprocally Regulated by Histone H3 and Clr4 Histone Methyltransferase in Schizosaccharomyces pombe

2006 ◽  
Vol 17 (6) ◽  
pp. 2524-2536 ◽  
Author(s):  
Hitoshi Nishijima ◽  
Jun-ichi Nakayama ◽  
Tomoko Yoshioka ◽  
Ayumi Kusano ◽  
Hideo Nishitani ◽  
...  
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Histone H3 ◽  
Inhibitory Effect ◽  
Stable Complex ◽  
Gtpase Activating Protein ◽  
Ran Gtpase ◽  
The Core ◽  
Trimeric Complex ◽  
Core Histones ◽  
Heterochromatin Assembly

Although the Ran GTPase-activating protein RanGAP mainly functions in the cytoplasm, several lines of evidence indicate a nuclear function of RanGAP. We found that Schizosaccharomyces pombe RanGAP, SpRna1, bound the core of histone H3 (H3) and enhanced Clr4-mediated H3-lysine 9 (K9) methylation. This enhancement was not observed for methylation of the H3-tail containing K9 and was independent of SpRna1–RanGAP activity, suggesting that SpRna1 itself enhances Clr4-mediated H3-K9 methylation via H3. Although most SpRna1 is in the cytoplasm, some cofractionated with H3. Sprna1ts mutations caused decreases in Swi6 localization and H3-K9 methylation at all three heterochromatic regions of S. pombe. Thus, nuclear SpRna1 seems to be involved in heterochromatin assembly. All core histones bound SpRna1 and inhibited SpRna1–RanGAP activity. In contrast, Clr4 abolished the inhibitory effect of H3 on the RanGAP activity of SpRna1 but partially affected the other histones. SpRna1 formed a trimeric complex with H3 and Clr4, suggesting that nuclear SpRna1 is reciprocally regulated by histones, especially H3, and Clr4 on the chromatin to function for higher order chromatin assembly. We also found that SpRna1 formed a stable complex with Xpo1/Crm1 plus Ran-GTP, in the presence of H3.

Reconstruction of complexes of histone and superhelical nuclear DNA

1981 ◽  
Vol 50 (1) ◽  
pp. 209-224
Author(s):  
J.M. Levin ◽  
P.R. Cook
Keyword(s):  
Nuclear Dna ◽  
Micrococcal Nuclease ◽  
Base Pairs ◽  
The Core ◽  
Ionic Detergent ◽  
Nuclear Rna ◽  
Core Histones ◽  
Non Destructive ◽  
Rna And Dna ◽  
General Method

When HeLa cells are lysed in solutions containing a non-ionic detergent and 2 M-NaCl, structures are released that retain many of the morphological features of nuclei. These nucleoids contain all the nuclear RNA and DNA but few of the proteins characteristic of chromatin. Their DNA is supercoiled and so intact. Using a simple and rapid procedure we have reconstructed nucleohistone complexes from nucleoids and the ‘core’ histones without breaking the DNA. We have probed the integrity and structure of the reconstructed complexes using a non-destructive fluorometric approach, which provides a general method for detecting agents that bind to DNA and alter its supercoiling. The superhelical status of the DNA in the reconstructed complexes is indistinguishable from that found in control nucleoids containing core histones. Experiments with micrococcal nuclease confirm that the DNA in the reconstructed complexes is organized into nucleosome-like structures. These, however, are spaced 145 base-pairs apart and not 200 base-pairs apart as is found in native chromatin.

Molecular evolution of the actin family

2002 ◽  
Vol 115 (13) ◽  
pp. 2619-2622 ◽  
Author(s):  
Holly V. Goodson ◽  
William F. Hawse
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Evolution ◽  
Chromatin Remodeling ◽  
The Core ◽  
Nuclear Process ◽  
Core Set ◽  
Eukaryotic Proteins ◽  
Related Proteins

Members of the actin family have well-characterized cytoskeletal functions,but actin and actin-related proteins (ARPs) have also been implicated in nuclear activities. Previous analyses of the actin family have identified four conserved subfamilies, but many actin-related proteins (ARPs) do not fall into these groups. A new systematic phylogenetic analysis reveals that at least eight ARP subfamilies are conserved from humans to yeast, indicating that these ARPs are part of the core set of eukaryotic proteins. Members of at least three subfamilies appear to be involved in chromatin remodeling,suggesting that ARPs play ancient, fundamental roles in this nuclear process.

Histone Variants: The Nexus of Developmental Decisions and Epigenetic Memory

2020 ◽  
Vol 54 (1) ◽  
pp. 121-149 ◽  
Author(s):  
Benjamin Loppin ◽  
Frédéric Berger
Keyword(s):  
Cell Differentiation ◽  
Cell Fate ◽  
Histone Variants ◽  
Epigenetic Memory ◽  
The Core ◽  
Nucleosome Dynamics ◽  
Nucleosome Structure ◽  
Core Histones ◽  
And Function ◽  
The Impact

Nucleosome dynamics and properties are central to all forms of genomic activities. Among the core histones, H3 variants play a pivotal role in modulating nucleosome structure and function. Here, we focus on the impact of H3 variants on various facets of development. The deposition of the replicative H3 variant following DNA replication is essential for the transmission of the epigenomic information encoded in posttranscriptional modifications. Through this process, replicative H3 maintains cell fate while, in contrast, the replacement H3.3 variant opposes cell differentiation during early embryogenesis. In later steps of development, H3.3 and specialized H3 variants are emerging as new, important regulators of terminal cell differentiation, including neurons and gametes. The specific pathways that regulate the dynamics of the deposition of H3.3 are paramount during reprogramming events that drive zygotic activation and the initiation of a new cycle of development.

scholarly journals Trypanosoma brucei brucei: differences in the nuclear chromatin of bloodstream forms and procyclic culture forms

Parasitology ◽  
1993 ◽  
Vol 107 (3) ◽  
pp. 237-247 ◽  
Author(s):  
W. Schlimme ◽  
M. Burri ◽  
K. Bender ◽  
B. Betschart ◽  
H. Hecker
Keyword(s):  
Life Cycle ◽  
Trypanosoma Brucei ◽  
Dna Interaction ◽  
Trypanosoma Brucei Brucei ◽  
The Core ◽  
Sds Page ◽  
Core Histones ◽  
Liver Chromatin ◽  
Two Stages ◽  
New Evidence

SummaryNucleosome filaments of two stages of the life-cycle of Trypanosoma brucei brucei, namely bloodstream forms and procyclic culture forms, were investigated by electron microscopy. Chromatin of bloodstream forms showed a salt-dependent condensation. The level of condensation was higher than that shown by chromatin from procyclic culture forms, but 30 nm fibres as formed in rat liver chromatin preparations were not found. Analysis of histones provided new evidence for the existence of H1-like proteins, which comigrated in the region of the core histones in SDS–PAGE and in front of the core histones in Triton acid urea gels. Differences were found between the H1-like proteins of the two trypanosome stages as well as between the core histones in their amount, number of bands and banding pattern. It can be concluded that T. b. brucei contains a full set of histones, including H1-like proteins, and that the poor condensation of its chromatin is not due to the absence of H1, but most probably due to histone–DNA interaction being weak. It is obvious that structural and functional differences of the chromatin exist not only between T. b. brucei and higher eukaryotes, but also between various stages of the life-cycle of the parasite. It is therefore not adequate to investigate the chromatin only of the procyclic culture forms as a model for all stages of the life-cycle of T. b. brucei.

scholarly journals Distribution of the core histones H2AH2B, H3and H4during cell replication

1982 ◽  
Vol 10 (2) ◽  
pp. 735-748 ◽  
Author(s):  
Elizabeth Fowler ◽  
Roderick Farb ◽  
Salma El-Saidy
Keyword(s):  
Cell Replication ◽  
The Core ◽  
Core Histones

Diversification of the Histone Fold Motif in Plants: Evolution of New Functional Roles

2016 ◽  
Vol 1 (1) ◽  
pp. 63 ◽  
Author(s):  
Amish Kumar ◽  
Gitanjali Yadav
Keyword(s):  
Gene Families ◽  
Chromatin Accessibility ◽  
Core Histone ◽  
Alpha Helices ◽  
Functional Roles ◽  
Histone Fold ◽  
Nuclear Factor Y ◽  
The Core ◽  
Large Gene ◽  
Core Histones

<p>The Histone fold motif (HFM) is one of the most conserved structural motifs in biology, mainly found in the core histone sub-units of all eukaryotes. The HFM represents a helix-strand-helix motif having three alpha helices connected by two loops/beta strands. This helix-strand-helix motif has the unique property of binding strongly with proteins as well as with DNA. Apart from core histones, the HFM has been reported in a variety of other proteins in all forms of life. In this work, we review the various classes of proteins that contain the HFM, as well as the diverse roles played by these proteins in the plant kingdom. As will be clear from this review, formation of the core histones through multi-merisation is not the only role played by this conserved fold, although the characteristic ability of the HFM to dimerize with suitable partner proteins has been used by nature to perform several non-core-histone functions. Most of the information about plant HFM containing proteins, such as identification and classification, has been done based on homology with yeast and animal counterparts. However, the ability of plants genomes to duplicate extensively has led to the existence of large gene families of the HFM containing proteins, unlike other eukaryotes. Plant HFM containing proteins can broadly be classified under the following major categories; TBP-associated factors (TAF), Nuclear Factor Y (NF-Y), Dr1/DrAp1 proteins and the chromatin accessibility complex (CHRAC). These proteins families are known to be involved in transcriptional regulation, co-activation and chromosome maintenance. Partner recognition through dimer formation remains a major conserved feature of these groups when compared with core histone sub-units.</p>

scholarly journals Phosphorylation of histones in cells treated with hypertonic and acidic media.

1984 ◽  
Vol 4 (6) ◽  
pp. 1186-1188 ◽  
Author(s):  
P Pantazis ◽  
M H West ◽  
W M Bonner
Keyword(s):  
Cell Lines ◽  
Growth Media ◽  
Acidic Media ◽  
Normal Medium ◽  
The Core ◽  
Core Histones ◽  
Extracellular Environment ◽  
Mass Pattern ◽  
In Cells

Factors in the extracellular environment, specifically hypertonic or acidic growth media, are shown to alter the modification of histones in several cell lines. For histone 2A, changes in modification were visible in the mass pattern and were found to be primarily changes in phosphorylation. The increased modification of the core histones was quickly reversed when cells were returned to normal medium.

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