Protein-DNA interactions within the rat histone H4t promoter

Histone variant innovation in a rapidly evolving chordate lineage

Background

Histone variants alter the composition of nucleosomes and play crucial roles in transcription, chromosome segregation, DNA repair, and sperm compaction. Modification of metazoan histone variant lineages occurs on a background of genome architecture that shows global similarities from sponges to vertebrates, but the urochordate, Oikopleura dioica, a member of the sister group to vertebrates, exhibits profound modification of this ancestral architecture.

Results

We show that a histone complement of 47 gene loci encodes 31 histone variants, grouped in distinct sets of developmental expression profiles throughout the life cycle. A particularly diverse array of 15 male-specific histone variants was uncovered, including a testes-specific H4t, the first metazoan H4 sequence variant reported. Universal histone variants H3.3, CenH3, and H2A.Z are present but O. dioica lacks homologs of macroH2A and H2AX. The genome encodes many H2A and H2B variants and the repertoire of H2A.Z isoforms is expanded through alternative splicing, incrementally regulating the number of acetylatable lysine residues in the functionally important N-terminal "charge patch". Mass spectrometry identified 40 acetylation, methylation and ubiquitylation posttranslational modifications (PTMs) and showed that hallmark PTMs of "active" and "repressive" chromatin were present in O. dioica. No obvious reduction in silent heterochromatic marks was observed despite high gene density in this extraordinarily compacted chordate genome.

Conclusions

These results show that histone gene complements and their organization differ considerably even over modest phylogenetic distances. Substantial innovation among all core and linker histone variants has evolved in concert with adaptation of specific life history traits in this rapidly evolving chordate lineage.

Birth-and-death long-term evolution promotes histone H2B variant diversification in the male germinal cell line

The rich diversity within each of the five histone families (H1, H2A, H2B, H3, and H4) can hardly be reconciled with the notion of homogenizing evolution. The prevalence of birth-and-death long-term evolution over concerted evolution has already been demonstrated in the linker histone H1 family as well as for the H2A, H3, and H4 core histone families. However, information about histone H2B is lacking. In the present work, we have analyzed the diversity of the members of this histone family across different eukaryotic genomes and have characterized the mechanisms involved in their long-term evolution. Our results reveal that, quite in contrast with other histones, H2B variants are subject to a very rapid process of diversification that primarily affects the male germinal cell lineage and involves their functional specialization probably as a consequence of neofunctionalization and subfunctionalization events after gene duplication. The overall parallelism observed between the molecular phylogenies and the relationships among the electrostatic potentials of the different variants suggests that the latter may have played a major structural selective constraint during H2B evolution. It thus seems that the reorganization of chromatin structure during spermiogenesis might have affected the evolutionary constraints driving histone H2B evolution, leading to an increase in diversity.

H1t/GC-box and H1t/TE1 element are essential for promoter activity of the testis-specific histone H1t gene

The testis-specific linker histone H1t gene is transcribed exclusively in mid to late pachytene primary spermatocytes. Tissue-specific expression of the gene is mediated primarily through elements located within the proximal promoter. Previous work in transgenic animals identified a unique 40-base pair promoter element designated H1t/TE that is essential for spermatocyte-specific expression. The H1t/TE element contains three subelements designated TE2, GC-box, and TE1 based on in vitro footprinting and electrophoretic mobility shift assays. Because GC-box is a consensus site for binding of Sp transcription-factor family members, experiments were performed demonstrating that two Sp family members, Sp1 and Sp3, were present in testis cells from 9-day-old and adult rats and in pachytene primary spermatocytes and early spermatids. A 95- to 105-kDa form of Sp1 is most abundant in the tissues and cell lines examined, but a 60-kDa form of Sp1 is the most abundant species in spermatocytes and early spermatids. Further examination of Sp1 and Sp3 from adult testis, primary spermatocytes, and early spermatids showed that they can bind to the H1t/TE element. In order to determine the contributions of the subelements to H1t transcription, we mutated each of them in H1t promoter luciferase reporter vectors. Mutation of the GC-box and TE1 subelement reduced expression 77% and 49%, respectively, compared with the wild-type H1t promoter in transient expression assays in a testis GC-2spd cell line that was derived from germinal cells. These studies suggest that Sp transcription factors may be involved in transcription of the H1t gene and the GC-box and the TE1 subelement are required for activation of the H1t promoter.

Biological activity in the repopulating rat spermatocyte after the withdrawal of gossypol treatment. VI. Alteration in nuclear factors for interaction with histone gene promoter

This article reports the effects of gossypol at the genomic level in rat spermatogenic cells. After gossypol treatment for various times (8, 12, and 19 weeks), the spermatogonial cells were allowed to rest for 2 to 4 weeks. The function of histone H4 gene promoter (H4GP) in the repopulating pachytene spermatocytes (RPS) was investigated. The sequences of the oligonucleotides for the H4GP binding sites 1 and 2 were synthesized by an ABI-392 DNA synthesizer. RPS and the control pachytene spermatocytes (CPS) were obtained by centrifugal elutriation and subsequently they were used for the preparation of nuclear protein extracts (NPE). The NPE interaction with the DNA fragment of site 1 or 2 was studied by an electrophoresis mobility shift assay (EMSA). EMSA with NPE-CPS revealed ten major gel shift bands for site 1 and 2. The presence of extra unlabelled DNA fragments competed with 6 of the bands. After 2 to 4 weeks recovery from 8, 12, and 19 weeks of gossypol treatment, NPE-RPS failed to shift four bands (b through e) in site 1. These results suggested that gossypol treatment affected the transcription factors for interaction with site 1. On the contrary, no effect was demonstrated in NPE that interacted with site 2. Furthermore, gossypol treatment did not change the nucleotide sequence in the H4GP site 1 and 2.

Characterization of proteoglycans produced by rat pleural mesothelial cells in vitro

The mesothelial cell envelopes the surface of the parietal and visceral pleura. These cells are known to synthesize most of the protein constituents of the pleural basement membrane and interstitium. This study examined the ability of a rat pleural mesothelial cell line to synthesize proteoglycans in vitro. Cells were labeled with inorganic 35SO4 to label the glycosaminoglycan moiety of proteoglycans. The medium and combined cell membrane/extracellular matrix fractions contained 73 and 25% of the proteoglycan radioactivity, respectively. The medium contained a single chondroitin/dermatan sulfate proteoglycan of approximately 190 kDa, consistent with biglycan. As determined by Northern analysis of steady-state levels of messenger RNA, the cells contained message for biglycan. Stimulation of the cells with epidermal growth factor resulted in the appearance of a second chondroitin/dermatan sulfate proteoglycan of approximately 97 kDa, characteristic of decorin. The cell membrane/matrix contained a biglycan-like chondroitin/dermatan proteoglycan and several heparan sulfate proteoglycans. Pleural mesothelial cells in vitro are capable of synthesizing a variety of interstitial and basement membrane proteoglycans.

Cell cycle controlled histone H1, H3, and H4 genes share unusual arrangements of recognition motifs for HiNF-D supporting a coordinate promoter binding mechanism

Cell cycle and growth control of the DNA binding and transactivation functions of regulatory factors provides a direct mechanism by which cells may coordinate transcription of a multitude of genes in proliferating cells. The promoters of human DNA replication dependent histone H4, H3, and H1 genes interact with at least seven distinct proteins. One of these proteins is a proliferation-specific nuclear factor, HiNF-D, that interacts with a key cis-regulatory element (H4-Site II; 41 bp) present in H4 genes. Here we describe binding sites for HiNF-D in the promoters of H3 and H1 genes using cross-competition, deletion analysis, and methylation interference assays, and we show that HiNF-D recognizes intricate arrangements of at least two sequence elements (CA- and AG-motifs). These recognition motifs are irregularly dispersed and distantly positioned in the proximal promoters (200 bp) of both the H3 and H1 genes. In all cases, these motifs either overlap or are in close proximity to other established transcriptional elements, including ATF and CCAAT sequences. Although HiNF-D can interact with low affinity to a core recognition domain, auxiliary elements in both the distal and proximal portions of each promoter cooperatively enhance HiNF-D binding. Thus, HiNF-D appears to bridge remote regulatory regions, which may juxtapose additional trans-activating proteins interacting within histone gene promoters. Consistent with observations in many cell culture systems, the interactions of HiNF-D with the H4, H3, and H1 promoters are modulated in parallel during the cessation of proliferation in both osteosarcoma cells and normal diploid osteoblasts, and these events occur in conjunction with concerted changes in histone gene expression. Thus, HiNF-D represents a candidate participant in coordinating transcriptional control of several histone gene classes.

Histone H1t: a tissue-specific model used to study transcriptional control and nuclear function during cellular differentiation

One of the most prominent and best studied family of genes is the histone gene family. In recent years, histone gene regulation during the cell cycle of somatic cells has been studied extensively. This paper is intended to highlight and emphasize recent data concerning the tissue-specific expression of histone H1t using spermatogenesis as a model system. In this article we describe a unique DNA element within the proximal promoter of the histone H1t gene. This element has been shown to bind exclusively to nuclear proteins from pachytene spermatocytes and early spermatids. Thus, there is a strong temporal correlation between the appearance of the testis-specific DNA-binding protein and the onset of transcription of the testis-specific histone H1t gene.

Tissue-specific binding of testis nuclear proteins to a sequence element within the promoter of the testis-specific histone H1t gene

The rat histone H1t gene is transcribed only in testis germinal cells. This testis-specific chromosomal protein is first synthesized during spermatogenesis in pachytene spermatocytes and the entire complement of testis histones is replaced during the midspermatid stage of spermiogenesis by positively charged transition nuclear proteins TP1 and TP2. Mobility shift assays conducted using crude nuclear protein extracts from different tissues and an 18-bp DNA sequence element within the H1t promoter as a probe reveal binding only with nuclear proteins from testis. The binding is specifically competed with an excess of the same unlabeled DNA fragment but not with heterologous competitors. A larger oligonucleotide corresponding to the same sequence element plus 18 bp of the adjacent downstream H1/CCAAT element binds nuclear proteins from all tissues tested, but a unique low mobility band is formed only with testis extracts. Protein-DNA crosslinking experiments reveal that two major polypeptides with molecular weights of approximately 13 and 30 kDa bind to the 18-bp H1t promoter sequence element. This strong correlation between the tissue where the H1t gene is transcribed and the presence of testis-specific nuclear proteins that bind to a sequence element within the testis histone H1t promoter supports the possibility that these DNA-binding proteins may participate in formation of an active transcription initiation complex with the testis H1t promoter.

Temporal correlation between the appearance of testis-specific DNA-binding proteins and the onset of transcription of the testis-specific histone H1t gene

The histone H1t gene is transcribed only in testis. Northern blot analyses reveal that transcription of the H1t gene occurs first in pachytene primary spermatocytes. Thus, there is a temporal correlation between onset of transcription of the gene and synthesis of histone H1t in primary spermatocytes during spermatogenesis. Previous studies revealed that replacement of most H1t and core histones occurs during the midspermatid stage of spermiogenesis by transition proteins TP1 and TP2. In this paper we extend our study of the specific binding of testis nuclear proteins to a unique sequence element within the H1t promoter. The relatively tight binding is competed with an excess of homologous DNA but not with a mutated element. Testis proteins from prepubertal animals do not bind to the 18-bp promoter element out proteins from enriched populations of primary spermatocytes do bind. Therefore, the temporal correlation between onset of transcription of the H1t gene and the time when the specific H1t promoter-binding proteins are detected in primary spermatocytes suggests that the DNA-binding proteins might be germinal cell-specific transcription factors that participate in formation of an active H1t transcription initiation complex. These studies present the first analysis of binding sites for testis nuclear proteins from primary spermatocytes within the promoter of a gene expressed only during this stage of spermatogenesis.