Comparison of the early histone H4 gene sequence of Strongylocentrotus purpuratus with maternal, early, and late histone H4 mRNA sequences.
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Amino Acid Sequence↗
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Reiteration frequency of the gene for tissue-specific histone H5 in the chicken genome.
Chicken erythroid cells contain a tissue specific histone known as H5 in addition to the five major histone species found in other organisms. The mRNA coding for this histone has been isolated by indirect immunoprecipitation from immature, non-dividing reticulocytes in which this is the only histone synthesised. The mRNA has been modified by the enzymatic addition of a 3' polyadenylic acid tract, and transcribed into complementary DNA (cDNA) using the RNA-dependent DNA-polymerase from avian myeloblastosis virus. Studies on the hybridisation of this cDNA indicate that the gene coding for the H5 histone is reiterated 10 times in the chicken genome.
Alleles↗
Histone gene expression during sea urchin spermatogenesis: an in situ hybridization study.
The expression of testis-specific and adult somatic histone genes in sea urchin testis was investigated by in situ hybridization. The testis-specific histone genes (Sp H2B-1 of Strongylocentrotus purpuratus and Sp H2B-2 of Lytechinus pictus) were expressed exclusively in a subset of male germ line cells. These cells are morphologically identical to replicating cells pulse-labelled with 3H-thymidine. Genes coding for histones expressed in adult somatic and late embryo cells (H2A-beta for S. purpuratus and H3-1 for L. pictus) were expressed in the same germ line cells, as well as in the supportive cells (nutritive phagocytes) of the gonad. All histone mRNAs detected in the male germ lineage declined precipitously by the early spermatid stage, before cytoplasmic reduction. The data suggest that both testis-specific and adult somatic histone genes are expressed in proliferating male germ line cells. Testis-specific gene expression is restricted to spermatogonia and premeiotic spermatids, but somatic histone expression is not. The decline of histone mRNA in nondividing spermatids is not merely a consequence of cytoplasmic shedding, but probably reflects mRNA turnover.
Animals↗
Amino acid substitutions in the structured domains of histones H3 and H4 partially relieve the requirement of the yeast SWI/SNF complex for transcription.
Transcription of many yeast genes requires the SWI/SNF regulatory complex. Prior studies show that reduced transcription of the HO gene in swi and snf mutants is partially relieved by mutations in the SIN1 and SIN2 genes. Here we show that SIN2 is identical to HHT1, one of the two genes coding for histone H3, and that mutations in either can result in a Sin- phenotype. These mutations are partially dominant to wild type and cause amino acid substitutions in three conserved positions in the structured domain of histone H3. We have also identified partially dominant sin mutations that affect two conserved positions in the histone-fold domain of histone H4. Three sin mutations affect surface residues proposed to interact with DNA and may reduce affinity of DNA for the histone octamer. Two sin mutations affect residues at or near interfaces between (H2A-H2B) dimer and (H3-H4)2 tetramer subunits of the histone octamer and may affect nucleosome stability or conformation. The ability of mutations affecting the structure of the histone octamer to relieve the need for SWI and SNF products supports the proposal that the SWI/SNF complex stimulates transcription by altering chromatin structure and can account for the apparent conservation of SWI and SNF proteins in eukaryotes other than yeast.
Amino Acids↗
Molecular characterization of a beta-type proteasome subunit from Arabidopsis thaliana co-expressed at a high level with an alpha-type proteasome subunit early in the cell cycle.
Proteasomes are the essential components of complexes involved in an extralysosomal energy- and ubiquitin-dependent proteolytic pathway. The first alpha-type proteasome subunit in plants has recently been described. In this work, the sequence of the first beta-type proteasome subunit in plants, isolated from Arabidopsis thaliana cDNA libraries is reported. The mRNA accumulation of both subunits was analysed and compared with those of the ubiquitin and histone mRNAs, in different tissues and during re-initiation of mitotic activity. It is demonstrated that in plants, as in animal cells, the transcripts of both the alpha-type and beta-type proteasome subunits accumulate to high levels during cell proliferation, in parallel with mRNAs coding for a ubiquitin fusion protein and several polyubiquitins, but earlier than those coding for histone H4 whose expression is known to be coupled to DNA synthesis. These results suggest that, as in animal cells, proteasomes may be involved in the progression of the cell cycle.
Amino Acid Sequence↗
Acetylation in histone H3 globular domain regulates gene expression in yeast.
In Saccharomyces cerevisiae, known histone acetylation sites regulating gene activity are located in the N-terminal tails protruding from the nucleosome core. We report lysine 56 in histone H3 as a novel acetylation site that is located in the globular domain, where it extends toward the DNA major groove at the entry-exit points of the DNA superhelix as it wraps around the nucleosome. We show that K56 acetylation is enriched preferentially at certain active genes, such as those coding for histones. SPT10, a putative acetyltransferase, is required for cell cycle-specific K56 acetylation at histone genes. This allows recruitment of the nucleosome remodeling factor Snf5 and subsequent transcription. These findings indicate that histone H3 K56 acetylation at the entry-exit gate enables recruitment of the SWI/SNF nucleosome remodeling complex and so regulates gene activity.
Acetylation↗
Role of chromatin in estrogen action in the uterus. II. Hormone-induced synthesis of nonhistone acidic proteins which restore histone-inhibited DNA-dependent RNA synthesis.
Nonhistone acidic proteins were isolated, by equilibrium density centrifugation in 4 M cesium chloride, from the chromatin isolated and purified from the uterus of the ovariectomized rat or from calf endometrium. Evidence is presented to show (1) that arginine-rich histones are more effective inhibitors of chromatin-directed RNA synthesis in vitor than lysine-rich histones, (2) that the nonhistone acidic proteins of chromatin do not inhibit the synthesis of RNA directed by chromatin in vitro, (3) that added nonhistone acidic chromatin proteins effect a restoration of histone-inhibited RNA synthesis directed by chromatin in vitro, and (4) that the synthesis of nonhistone acidic chromatin proteins is under estrogen control in the uterus, but not in the liver. It is concluded that a major feature of the early action of estrogen in the uterus of the ovariectomized rat is the stimulation of synthesis and the accumulation in the interphase chromosomes of nonhistone acidic proteins which counter the inhibitory effect of histone on transcription by RNA polymerase. Presumably this would permit more and perhaps a new synthesis of RNA programmed for transport to the cytoplasm.
Animals↗
A transposon-like DNA fragment interrupts a Physarum polycephalum histone H4 gene.
A recombinant DNA library was screened for histone H4 genes using a sea urchin probe. One recombinant was analysed by restriction enzyme mapping and Southern blotting. The complete DNA sequence of the H4 histone locus was determined. An 86 base pair interrupting sequence was found within the histone H4 coding sequence. The inserted DNA fragment has some characteristics of a transposable element.
Amino Acid Sequence↗
Genome-Wide Profiling of Histone Modifications in Fission Yeast Using CUT&Tag.
Eukaryotic DNA is organized in the nucleus in the form of chromatin. Nucleosomes, the fundamental unit of chromatin, are subject to many posttranslational modifications (PTMs) as well as compositional variations through incorporation of histone variants. These alterations play important roles in regulation of genome structure and activity. Genome-wide profiling of these regulatory features is essential for understanding of genome function. Chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-Seq) is a widely used method to assay genome-wide localization in fission yeast but suffers from the requirement for a large amount of input chromatin, antibodies, and a cumbersome experimental pipeline. New methods such as Cleavage Under Targets and Tagmentation (CUT&Tag), which combine the specificity of targeted cleavage and adapter insertion with the sensitivity of next-generation sequencing, enable identification and characterization of various epigenetic marks affording low input requirement as well as more streamlined protocols. However, these approaches have not been adapted for use in fission yeast, Schizosaccharomyces pombe. Here, we describe an adapted CUT&Tag protocol for epigenomic profiling in fission yeast using the heterochromatin-associated histone H3K9 methylation PTM for benchmarking.
Schizosaccharomyces↗
Identification of a second conserved element within the coding sequence of a mouse H3 histone gene that interacts with nuclear factors and is necessary for normal expression.
Replication-dependent histone genes of all four nucleosomal classes are coordinately up-regulated at the beginning of S phase of the eukaryotic cell cycle. The universality and importance of this process in eukaryotic cells suggest that common regulatory mechanisms are involved in controlling the high level of expression of these histone genes. We have previously identified the alpha element within mouse H2a.2 and H3.2 coding region activating sequences (CRAS), which is involved in regulation of these two replication-dependent genes. Here we report the identification of a second element within the mouse histone CRAS, the omega element. This element interacts with nuclear proteins and we present in vivo evidence that this sequence is required for normal expression. Omega nucleotides involved in interaction with nuclear proteins have been precisely mapped by menas of DNase I footprinting and methylation interference assays. A naturally occurring mutation in the omega sequence is found in a replication-independent H3.3 gene. Mutation of the H3.2 omega element to that of the H3.3 sequence (3 nt changes) caused a 4-fold drop in in vivo expression of the H3.2 gene in stably transfected CHO cells, equally the effect of mutation of all 7 nt of the element. By UV cross-linking we have determined the approximate molecular weight of the omega binding protein to be 45 kDa. Finally, we identify putative omega sequences in the coding region of mouse H2B and H4 histone genes.
Animals↗
The nucleotide and amino acid coding sequence of a gene for H1 histone that interacts with euchromatin. The early embryonic H1 gene of the sea urchin Strongylocentrotus purpuratus.
We have determined the nucleotide sequence of the gene that codes for an H1 histone associated with euchromatin in the sea urchin Strongylocentrotus purpuratus. The gene codes for a protein of 205 amino acids. The nucleotide sequence of this gene is homologous to the sequence of H1 mRNA that is expressed during early embryonic development. We have compared the nucleotide and protein coding sequences of this H1 gene to those of the early H1 histone gene of the sea urchin Psammechinus miliaris. There is considerable drift by nucleotide substitution between the two genes randomly distributed across the mRNA coding region. Despite this divergence of nucleotide sequence, there are local constraints on amino acid substitutions throughout the molecule and especially in its central region. We have also compared the amino acid sequence in this central hydrophobic region of the euchromatic S. purpuratus H1 histone to the same region in H1 and H5 histones associated with heterochromatin. We show that certain amino acids are conserved and aligned in frameworks in all the sequenced H1 proteins.
Amino Acid Sequence↗
Isolation of yeast histone genes H2A and H2B.
Analysis of cloned sequences for yeast histone genes H2A and H2B reveals that there are only two copies of this pair of genes within the haploid yeast genome. Within each copy, the genes for H2A and H2B are separated by approximately 700 bp of spacer DNA. The two copies are separated from one another in the yeast genome by a minimum distance of 35-60 kb. Sequence homology between the two copies is restricted to the genes for H2A and H2B; the spacer DNA between the genes is nonhomologous. In both copies, the genes for H2A and H2B are divergently transcribed. In addition, both plasmids code for other nonhistone proteins. Sequences coding for histones H3 and H4 have not been detected in the immediate vicinity of the genes for H2A and H2B.
Base Sequence↗
[Epigenetics of specific chromosome regions].
Investigation of protein complexes, various types of protein modifications and the structure of the chromatin of specific chromosome regions, such as centromeres, telomeres, and adjacent heterochromatic regions, considerably complicated the notion on DNA, prevailing five decades ago, as molecules that exclusively control coding and realization of genetic information. Striking plasticity of the primary structure of centromeric and telomeric DNA suggests a variety of molecular mechanisms underlying fundamental and universal functions of these key chromosome regions. The present review is an attempt to consider the current concepts on the structure of the DNA and protein components, as well as the structure of the chromatin of specific chromosome regions in eukaryotes, and the concerted evolution of these components, leading to the formation of a hierarchy of coordinated DNA-protein complexes.
Animals↗
Histone gene number in relation to C-value in amphibians.
We have compared the number of copies of sequences complementary to a cloned Xenopus histone H4 coding sequence in the genomes of Xenopus, Triturus and Ambystoma, amphibian species with widely different C-values (3, 23 and 38pg DNA/haploid genome respectively). Quantitative autoradiography indicates that H4 sequence constitute a greater proportion of the genome the larger that genome is. Measurement of the absolute copy-number by reassociation kinetic analysis indicated 47 +/- 10, 636 +/- 21 2685 +/- 349 copies per haploid genome each in Xenopus, Triturus and Ambystoma respectively. Whilst this confirms a trend of increasing copy-number with increasing C-value, the two are not directly proportional and some other factors must contribute to determining the number of copies of these genes.
Ambystoma↗
Coupling cAMP signaling to transcription in the liver: pivotal role of CREB and CREM.
Transcriptional factors binding to cAMP-responsive elements (CREs) in the promoters of various genes belong to the basic domain-leucine zipper superfamily and are composed of three genes in mammals, CREB, CREM, and ATF-1. A large number of CREB, CREM, and ATF-1 proteins are generated by posttranscriptional events, mostly alternative splicing, and regulate gene expression by acting as activators or repressors. Activation is classically brought about by signaling-dependent phosphorylation of a key acceptor site (Ser133 in CREB) by a number of possible kinases, including PKA, CamKIV, and Rsk-2. Phosphorylation is the prerequisite for the interaction of CBP (CREB-binding protein), a co-activator that has also histone acetyltransferase activity. Repression may involve dynamic dephosphorylation of the activators and thus decreased association with CBP. Another pathway of transcriptional repression on CRE sites implicates the inducible repressor ICER (inducible cAMP early repressor), a product of the CREM gene. Being an inducible repressor, ICER is involved in autoregulatory feedback loops of transcription that govern the down-regulation of early response genes, such as the proto-oncogene c-fos. The liver represents a remarkable physiological setting where cAMP-responsive signaling plays a major role. Indeed, a finely tuned program of gene expression is triggered by partial hepatectomy, so that through specific checkpoints a coordinated regeneration of the tissue is obtained. Temporal kinetics of transcriptional activation after hepatectomy reveals a pattern of early induction for several genes, some of them controlled by the CREB/CREM transcription factors. An important role of CREM in liver physiology was suggested by the robust induction of ICER after partial hepatectomy. The delay in tissue regeneration in CREM-deficient mice confirmed the important function of this factor in regulating hepatocyte proliferation. As gene induction is accompanied by critical changes in chromatin organization, the deciphering of the specific modification codes that histones display during liver regeneration and physiology will provide exciting new insights into the dynamics of chromatin architecture.
Animals↗
Brain non-adenylated mRNAs.
Most eukaryotic messenger RNA (mRNA) species contain a 3'-poly(A) tract. The histone mRNAs are a notable exception although a subclass of histone-encoding mRNAs is polyadenylated. A class of mRNAs lacking a poly(A) tail would be expected to be less stable than poly(A)+ mRNAs and might, like the histones, have a half-life that varied in response to changes in the intracellular milieu. Brain mRNA exhibits an unusually high degree of sequence complexity; studies published ten years ago suggested that a large component of this complexity might be present in a poly(A)- mRNA population that was expressed postnatally. The question of the existence of a complex class of poly(A)- brain mRNAs is particularly tantalizing in light of the heterogeneity of brain cells and the possibility that the stability of these poly(A)- mRNAs might vary with changes in synaptic function, changing hormonal stimulation or with other modulations of neuronal function. The mRNA complexity analyses, although intriguing, did not prove the existence of the complex class of poly(A)- brain mRNAs. The observed mRNA complexity could have resulted from a variety of artifacts, discussed in more detail below. Several attempts have been made to clone members of this class of mRNA. This search for specific poly(A)- brain mRNAs has met with only limited success. Changes in mRNA polyadenylation state do occur in brain in response to specific physiologic stimuli; however, both the role of polyadenylation and de-adenylation in specific neuronal activities and the existence and significance of poly(A)- mRNAs in brain remain unclear.
Animals↗
Multiomics Reveal Associations Between CpG Methylation, Histone Modifications and Transcription in a Species That has Lost DNMT3, the Colorado Potato Beetle.
Insects display exceptional phenotypic plasticity, which can be mediated by epigenetic modifications, including CpG methylation and histone modifications. In vertebrates, both are interlinked and CpG methylation is associated with gene repression. However, little is known about these regulatory systems in invertebrates, where CpG methylation is mainly restricted to gene bodies of transcriptionally active genes. A widely conserved mechanism involves the co-transcriptional deposition of H3K36 trimethylation and the targeted methylation of unmethylated CpGs by the de novo DNA methyltransferase DNMT3. However, DNMT3 has been lost multiple times in invertebrate lineages raising the question of how the links between CpG methylation, histone modifications and gene expression are affected by its loss. Here, we report the epigenetic landscape of Leptinotarsa decemlineata, a beetle species that has lost DNMT3 but retained CpG methylation. We combine RNA-seq, enzymatic methyl-seq and CUT&Tag to study gene expression, CpG methylation and patterns of H3K36me3 and H3K27ac histone modifications on a genome-wide scale. Despite the loss of DNMT3, H3K36me3 mirrors CpG methylation patterns. Together, they give rise to signature profiles for expressed and not expressed genes. H3K27ac patterns show a prominent peak at the transcription start site that is predictive of expressed genes irrespective of their methylation status. Our study provides new insights into the evolutionary flexibility of epigenetic modification systems that urge caution when generalizing across species.
Animals↗
Constitutive heterochromatin in Microtus agrestis: binding of actinomycin-D and transcriptional inactivity.
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Animals↗