Isolation, characterization, and expression of the gene encoding the late histone subtype H1-gamma of the sea urchin Strongylocentrotus purpuratus

Multiple SSAP binding sites constitute the stage-specific enhancer of the sea urchin late H1beta gene

The sea urchin late histone H1 genes are expressed at low levels up until mid-blastula stage of development when an enhancer element activates transcription to higher levels. Stage-specific activator protein (SSAP) was previously identified as the transcription factor that binds to a sequence motif within the late H1-specific enhancer, USE IV, and mediates this stage-specific activation. However, another conserved late H1-specific element, USE III, was also shown to contribute to the activated expression of the late H1 genes. To attain a better understanding of the mechanism of blastula stage activation an extended analysis of the late H1-specific DNA sequences of the SpH1beta gene was performed. Our findings indicate that this region, located between positions -320 and -200, consists of three SSAP binding sites, USE IV, USE III, and another site located between the two, termed Site 2. Although SSAP binds to USE IV in vitro with 10-15-fold higher affinity than to either of the other two sites, multiple sites are necessary for activation. Multimers of either USE IV or USE III activate mid-blastula stage transcription to similar levels in the context of a functional H1beta basal promoter, but not with a TATA box alone. In addition, multimers of USE IV activate expression of a reporter construct containing an early histone H1 promoter at an embryonic stage when it is normally repressed. We propose a mechanism for mid-blastula activation of the late histone H1 genes where SSAP binding sites activate expression, but require the presence of the cis sequences of the basal promoter to function.

Histone H1 diversity: bridging regulatory signals to linker histone function

Genes encoding linker histone variants have evolved to link their expression to signals controlling the proliferative capacities of cells, i.e. cycling and growth-arrested cells express distinct and specific H1 subtypes. In metazoan, these variants show a tripartite structure, with considerably divergent sequences in their amino and carboxyl terminus domains. The aim of this review is to show how specific regulatory signals control the expression of an individual H1 and to discuss the functional significance of the two variables associated with a linker histone: its primary sequence and the timing of its expression.

Isolation and amino acid sequence analysis reveal an ancient evolutionary origin of the cleavage stage (CS) histones of the sea urchin

The cleavage stage (CS) H1, H2A, and H2B histones of the sea urchin, which have previously been identified by their distinct electrophoretic mobility on Triton/acid/urea gels, are known to be maternally expressed during oogenesis and have been implicated in chromatin remodeling of the male pronucleus following fertilization. Here, we describe the isolation of these three CS histones by reverse-phase HPLC chromatography. Moreover, a novel CS H3 protein was identified by the same purification procedure. A low incorporation of radioactive amino acids into the CS histones during early development revealed that the bulk of these proteins in the blastula embryo are derived from the maternal pool of the egg. Amino acid analysis, together with the previously described electrophoretic mobilities, unequivocally identified the purified proteins as CS histones. Peptide sequence analysis confirmed the novel nature of the CS variants as they are distantly related to the early, late, and sperm histone subtypes of the sea urchin. The CS H1 protein displays highest sequence similarity with the H1M (B4) histone of Xenopus laevis, indicating that the frog H1M protein may be a vertebrate homologue of the CS H1 histone. These data suggest an ancient evolutionary origin and wide distribution of the CS histone variants.

Decreased heterogeneity of CS histone variants after hydrolysis of the ADP-ribose moiety

Sea urchin CS histone variants are electrophoretically heterogeneous when analyzed in two dimensional polyacrylamide gels (2D-PAGE). Previous results suggested that this heterogeneity is due to the poly (ADP-ribosylation) of these proteins. Consequently, native CS histone variants were subjected to different treatments to remove the ADP-ribose moiety. The incubation in 1 M hydroxylamine was not effective in eliminating the polymers of ADP-ribose from CS variants, and the treatment with sodium hydroxide was deleterious to the proteins. In contrast, the ADP-ribose moiety was successfully removed from the CS variants by incubation with phosphodiesterase (PDE). To eliminate contamination of CS histone variants with PDE extract, the enzyme was covalently bound to Sepharose 4B prior to its utilization. Treatment of native CS histone variants with this immobilized phosphodiesterase removed around 85% of the total ADP-ribose moiety from these proteins. After S-PDE treatment the complex electrophoretic pattern of CS histone variants in 2-D PAGE decreases to five major fractions. From these results we conclude that the electrophoretic heterogeneity of native CS histone variants is mainly due to the extent to which five main CS histone variants are poly(ADP)-ribosylated).

Analysis of the charge distribution in the C-terminal region of histone H1 as related to its interaction with DNA

We have studied the net positive charge distribution in the C-terminal region of histone H1. We find that it is not random, but rather uniform. In most histone H1 sequences, 4 +/- 1 positive charges are found in this region of the molecule in over 95% of all possible segments that are 10 amino acids long. Neither alternating sequences (basic-nonbasic) nor more complex repeating sequences are ever found. Clusters of three or more basic amino acids are seldom observed in somatic H1s, yet their presence increases in sperm histones and even more so in protamines. It is concluded that the C-terminal region of histone H1 has a remarkably uniform distribution of charge, in spite of its apparent variations in sequence in different proteins and within individual molecules. The functional significance of these findings is discussed, suggesting a purely electrostatic role for the C-terminal region of histone H1, which may be evenly wrapped around individual segments of DNA molecules, thus decreasing its net charge. A likely candidate for a long alpha-helical region in the C-terminal region of histone H1 from sea urchin spermatozoa also has been located. This region may contribute to the aggregating properties of this histone in sperm chromatin.

Identification of a Caenorhabditis elegans histone H1 gene family. Characterization of a family member containing an intron and encoding a poly(A)+ mRNA

The isolation and properties of a gene encoding a histone H1 protein of Caenorhabditis elegans, his-24, are described. The predicted protein sequence is similar to histone H1 proteins of other eukaryotes. However, the gene structure of his-24 is atypical for a histone H1 gene; it contains an intron and encodes a polyadenylated mRNA. A family of approximately five histone H1 genes is defined by cross-hybridization to his-24. All appear to encode polyadenylated mRNAs. One gene is expressed specifically in male germ cells. These histone H1 genes are dispersed individually in the genome, apart from the previously described clusters of core histone genes (H2A, H2B, H3 and H4), which probably all encode non-polyadenylated mRNAs. This histone gene organization, with clustered core histone genes, encoding non-polyadenylated transcripts, and dispersed, histone H1 genes from which it appears only polyadenylated messages arise, suggests that C. elegans is at a stage of evolution of the histone gene family intermediate between lower eukaryotes (e.g. yeast) and the most advanced forms.

Developmental regulation of micro-injected histone genes in sea urchin embryos

The developmental behavior of cloned histone genes of Psammechinus miliaris was studied by injection into eggs of two related sea urchin species followed by fertilization. All five early histone genes were faithfully expressed in early blastula embryos as shown by SP6 RNA mapping. A 5-10 times lower expression rate was estimated for the injected early H2A gene from its competition strength with the endogenous gene. Transcripts of this early H2A gene accumulated during the cleavage stages and decayed in late embryos in parallel with the endogenous early H2A mRNA. However, an introduced late H2B gene was incorrectly regulated, since its mRNA level did not increase from the blastula to the gastrula stage. The sperm H2B-1 gene, normally inactive in development, was 80 times less well expressed than the early H2A gene in transformed blastulae. A fusion gene with the early H2A promoter linked to the structural sperm H2B gene was, however, efficiently transcribed suggesting that all essential information for an early expression pattern is contained within the 5' region of the early H2A gene.

Molecular characterization of the histone gene family of Caenorhabditis elegans

The core histone genes (H2A, H2B, H3 and H4) of Caenorhabditis elegans are arranged in approximately 11 dispersed clusters and are not tandemly arrayed in the genome. Three well-characterized genomic clones, which contain histone genes, have one copy of each core histone gene per cluster. One of the clones (lambda Ceh-1) carries one histone cluster surrounded by several thousand base-pairs of non-histone DNA, and another clone (lambda Ceh-3) contains a histone cluster duplication surrounded by non-histone DNA. A third clone (lambda Ceh-2) carries a cluster of core histone genes flanked on one side (12,000 base-pairs away) by a single H2B gene and on the other by non-histone DNA. A fourth cluster (clone BE9) has one copy each of H3 and H4 and two copies each of H2A and H2B. This cluster is also flanked by non-histone DNA. Analysis of cosmid clones which overlap three of the clusters shows that no other histone clusters are closer than 8000 to 60,000 base-pairs, although unidentified non-histone transcription units are present on the flanking regions. Gene order within the histone clusters varies, and histone mRNAs are transcribed from both DNA strands. No H1 sequences are found on these core histone clones. Restriction fragment length polymorphisms between two related nematode strains (Bristol and Bergerac) were used as phenotypic markers in genetic crosses to map one histone cluster to linkage group V and another to linkage group IV. Hybridization of gene-specific probes from sea urchin to C. elegans RNA identifies C. elegans core histone messenger RNAs of sizes similar to sea urchin early stage histone mRNAs (H2A, H2B, H3 and H4). The organization of histone genes in C. elegans resembles the clustering found in most vertebrate organisms and does not resemble the tandem patterns of the early stage histone gene family of sea urchins or the major histone locus of Drosophila.