The genes for protamine 1 and 2 (PRM1 and PRM2) and transition protein 2 (TNP2) are closely linked in the mammalian genome

Sequence variability of CatSper1 and TNP2 gene in indigenous and crossbred cattle in Bangladesh

CatSper1 and TNP2 genes are known to affect semen quality and fertility parameters, including sperm motility and maturation. However, studies are yet to examine the genes in indigenous and crossbred cattle in Bangladesh. Therefore, this study was conducted to determine the genetic variants of CatSper1 and TNP2 in indigenous and crossbred cattle in Bangladesh. Blood samples were collected from 130 indigenous and 70 crossbred (Holstein Friesian × indigenous) cattle. Nucleotide variation was evaluated by PCR-RFLP and sequencing. The results of the study showed that the indigenous cattle possessed only TT genotype (1.0), whereas the crossbreds possessed both TT (0.91) and CT (0.09) genotypes, which was validated by gene sequencing. Additionally, the CatSper1 was conserved in both the indigenous and crossbred cattle, suggesting good semen quality and fertility. However, the TNP2 was conserved in the indigenous breeds and mostly conserved in the crossbreds. The findings of this study reveal the diversity of CatSper1 and TNP2 genes in indigenous and crossbred cattle.

Identifying loci under positive selection in complex population histories

Detailed modeling of a species’ history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method—called graph-aware retrieval of selective sweeps (GRoSS)—has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish, and human population genomic data containing panels of multiple populations related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in understudied human populations, as well as muscle mass, milk production, and tameness in specific bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation owing to inversions in the history of Atlantic codfish.

Association of TNP2 gene polymorphisms of the bta-miR-154 target site with the semen quality traits of Chinese Holstein bulls

Transition protein 2 (TNP2) participates in removing nucleohistones and the initial condensation of spermatid nucleus during spermiogenesis. This study investigated the relationship between the variants of the bovine TNP2 gene and the semen quality traits of Chinese Holstein bulls. We detected three single nucleotide polymorphisms (SNPs) of the TNP2 gene in 392 Chinese Holstein bulls, namely, g.269 G>A (exon 1), g.480 C>T (intron 1), and g.1536 C>T (3′-UTR). Association analysis showed that the semen quality traits of the Chinese Holstein bulls was significantly affected by the three SNPs. The bulls with the haplotypic combinations H6H4, H6H6, and H6H8 had higher initial semen motility than those with the H7H8 and H8H4 haplotypic combinations (P<0.05). SNPs in the microRNA (miRNA) binding region of the TNP2 gene 3′-UTR may have contributed to the phenotypic differences. The phenotypic differences are caused by the altered expression of the miRNAs and their targets. Bioinformatics analysis predicted that the g.1536 C>T site in the TNP2 3′-UTR is located in the bta-miR-154 binding region. The quantitative real-time polymerase chain reaction results showed that the TNP2 mRNA relative expression in bulls with the CT and CC genotypes was significantly higher than those with the TT genotype (P<0.05) in the g.1536 C>T site. The luciferase assay also indicated that bta-miR-154 directly targets TNP2 in a murine Leydig cell tumor cell line. The SNP g.1536 C>T in the TNP2 3′-UTR, which altered the binding of TNP2 with bta-miR-154, was found to be associated with the semen quality traits of Chinese Holstein bulls.

Quantitative Assessment of Transition Proteins 1, 2 Spermatid-Specific Linker Histone H1-Like Protein Transcripts in Spermatozoa from Normozoospermic and Asthenozoospermic Men

Spermatid-specific linker histone H1-like protein (HILS1), transition proteins 1 and 2 (TNP1 and TNP2), and protamines 1 and 2 (PRM1 and PRM2) contribute to considerable dense packing of spermatid chromatin during spermiogenesis. We evaluated the HILS1, TNP1, and TNP2 transcript levels in spermatozoa isolated from normozoospermic and asthenozoospermic men. Human ejaculates from normozoospermic (n = 70) and asthenozoospermic (n = 100) donors were purified by centrifugation through a discontinuous Percoll density gradient. RNA was isolated from spermatozoa according to the Chomczynski and Sacchi method, treated with DNase I and reverse-transcribed into cDNA. Quantitative analysis of HILS1, TNP1, and TNP2 transcripts was performed by real-time quantitative (RQ-PCR) SYBR green I analysis. We found significantly lower levels of HILS1, TNP1, and TNP2 transcripts in spermatozoa from asthenozoospermic men compared to normozoospermic men. Our observations suggest that a reduction in HILS1, TNP1, and TNP2 transcripts may be associated with asthenozoospermia.

The KLAB Toolbox: a suite of in-house software applications for epigenetic analysis

Systems biology presents a new paradigm for elucidating the processes required to organize and sustain life. We now have access to whole genome sequences, gene expression data for multiple cell types, and databases for regulatory elements governing these genes. These resources make it feasible to identify conserved genomic sequences across multiple species, transcription factors regulating the expression of genes with similar expression patterns within a given cell type and to compare expression levels of specific genes between normal and diseased cellular states. In order to utilize this wealth of information, new computational tools that integrate these datasets in a genome-wide context are required. Using the protamine cluster as an example, we present a series of in-house applications that we have developed to integrate, contextualize and visualize datasets across multiple hierarchies.

Prm3, the fourth gene in the mouse protamine gene cluster, encodes a conserved acidic protein that affects sperm motility

The protamine gene cluster containing the Prm1, Prm2, Prm3, and Tnp2 genes is present in humans, mice, and rats. The Prm1, Prm2, and Tnp2 genes have been extensively studied, but almost nothing is known about the function and regulation of the Prm3 gene. Here we demonstrate that an intronless Prm3 gene encoding a distinctive small acidic protein is present in 13 species from seven orders of mammals. We also demonstrate that the Prm3 gene has not generated retroposons, which supports the contention that genes that are expressed in meiotic and haploid spermatogenic cells do not generate retroposons. The Prm3 mRNA is first detected in early round spermatids, while the PRM3 protein is first detected in late spermatids. Thus, translation of the Prm3 mRNA is developmentally delayed similar to the Prm1, Prm2, and Tnp2 mRNAs. In contrast to PRM1, PRM2, and TNP2, PRM3 is an acidic protein that is localized in the cytoplasm of elongated spermatids and transfected NIH-3T3 cells. To elucidate the function of PRM3, the Prm3 gene was disrupted by homologous recombination. Sperm from Prm3(-/-) males exhibited reductions in motility, but the fertility of Prm3(-/-) and Prm3(+/+) males was similar in matings of one male and one female. We have developed a competition test in which a mutant male has to compete with a rival wild-type male to fertilize a female; the implications of these results are also discussed.

Mammalian sperm chromatin structure and assessment of DNA fragmentation

This review article illustrates the biology of mammalian sperm chromatin structure. The possible causes of DNA (deoxyribonucleic acid) fragmentation are discussed. Also available molecular techniques for assessment of mammalian sperm DNA damage are described.

Mutations in the protamine 1 gene associated with male infertility

In elongating spermatids, human sperm chromatin undergoes a complex compaction in which the transition proteins are extensively replaced by the protamine proteins. Several human studies demonstrate that expression of the protamine proteins is altered in some men with male infertility. For this study, we screened the PRM1 (protamine 1) gene for mutations in a large cohort of 281 men seeking infertility treatment. We identified the c.102G>T transversion that results in an p.Arg34Ser amino acid change in two men. One of these patients presented with oligozoospermia associated with increased sperm DNA fragmentation. The second individual was normospermic but together with his partner sought treatment for idiopathic couple infertility. We also identified a novel missense mutation (c.119G>A, p.Cys40Tyr) in a man with oligoasthenozoospermia. These mutations were not observed in control populations. Interestingly, we also detected variants both 5' and 3' to the PRM1 open-reading frame specifically in infertile individuals. Four individuals with unexplained severe oligozoospermia were heterozygote for a c.-107G>C change that is located at -15 bp from the transcription initiation site of the gene. This mutation may influence PRM1 expression. In addition, a c.*51G>C variant was detected in the 3'UTR of PRM1 specifically in a man with severe oligoasthenozoospermia.

Protamines and male infertility

Protamines are the major nuclear sperm proteins. The human sperm nucleus contains two types of protamine: protamine 1 (P1) encoded by a single-copy gene and the family of protamine 2 (P2) proteins (P2, P3 and P4), all also encoded by a single gene that is transcribed and translated into a precursor protein. The protamines were discovered more than a century ago, but their function is not yet fully understood. In fact, different hypotheses have been proposed: condensation of the sperm nucleus into a compact hydrodynamic shape, protection of the genetic message delivered by the spermatozoa, involvement in the processes maintaining the integrity and repair of DNA during or after the nucleohistone-nucleoprotamine transition and involvement in the epigenetic imprinting of the spermatozoa. Protamines are also one of the most variable proteins found in nature, with data supporting a positive Darwinian selection. Changes in the expression of P1 and P2 protamines have been found to be associated with infertility in man. Mutations in the protamine genes have also been found in some infertile patients. Transgenic mice defective in the expression of protamines also present several structural defects in the sperm nucleus and have variable degrees of infertility. There is also evidence that altered levels of protamines may result in an increased susceptibility to injury in the spermatozoan DNA causing infertility or poor outcomes in assisted reproduction. The present work reviews the articles published to date on the relationship between protamines and infertility.

Chromosomal proteins in the spermatogenesis of Drosophila

Chromatin constitution in the male germ line of Drosophila is discussed with respect to the substitution of somatic histones by protamines or other basic proteins. The specific properties of germ line chromatin include the initiation and completion of the spermatogenic pathway and the reprogramming of the genome for embryonic development. During meiotic prophase cell cycle-regulated H3 histones appear to a large extent to be substituted by the histone H3.3 replacement variant protein, which is generally found associated with transcriptionally active chromatin. Condensation of the chromosomes during meiosis and the subsequent compaction for packaging in the sperm head require suitable proteins, but the cell cycle-regulated histones are not available as their expression is limited to S-phase. It is, therefore, proposed that any basic protein with a limited range of sequence requirements may take over this packaging function. Suitable proteins may have evolved by divergence from histone variants not restricted in their expression to S-phase, similar to the testes-predominant histone H3.3A of Drosophila.

Roles of transition nuclear proteins in spermiogenesis

The transition nuclear proteins (TPs) constitute 90% of the chromatin basic proteins during the steps of spermiogenesis between histone removal and the deposition of the protamines. We first summarize the properties of the two major transition nuclear proteins, TP1 and TP2, and present concepts, based on their time of appearance in vivo and in vitro properties, regarding their roles. Distinct roles for the two TPs in histone displacement, sperm nuclear shaping, chromatin condensation, and maintenance of DNA integrity have been proposed. More definitive information on their roles in spermiogenesis has recently been obtained using mice with null mutations in the Tnp1 or Tnp2 genes for TP1 and TP2, respectively. In these mice, histone displacement and sperm nuclear shaping appear to progress quite normally. Spermatid nuclear condensation occurs, albeit in an abnormal fashion, and the mature sperm of the Tnp -null mutants are not as condensed as wild-type sperm. There is also evidence that sperm from these mutant mice contain an elevated level of DNA strand breaks. The mutant sperm showed several unexpected phenotypes, including a high incidence of configurational defects, such as heads bent back on midpieces, midpieces in hairpin configurations, coils, and clumps, other midpiece defects, reduced levels of proteolytic processing of protamine 2 during maturation, and reduced motility. The two TPs appear partly to compensate for each other as both Tnp1 - and Tnp2 -null mice were able to produce offspring, and appear to have largely overlapping functions as the two mutants had similar phenotypes.

Biochemical and hematological changes in low-level aluminum intoxication

The aim of this study was to investigate the biochemical and hematological changes in patients on routine hemodialysis treatment when they were accidentally exposed to moderately high serum aluminum concentrations during a period of time of less than four months. We studied the changes in biochemical and hematological measurements in 33 patients on dialysis in our hospital before and during the exposure to about 0.85 pmol/l of aluminum in dialysis water due to a malfunction of the reverse osmosis system of water purification. Patients showed a decrease in the hemoglobin concentration from 115+/-12.4 g/l to 108+/-12.2 g/l (p=0.026) and in the mean corpuscular hemoglobin concentration from 5.15+/-0.22 to 5.02+/-0.30 mmol/l (p=0.014). Ferritin was decreased from 243+/-192 microg/l to 196+/-163 microg/l (p=0.047) and transferrin saturation from 0.20+/-0.06 to 0.15+/-0.07 (p=0.004). Biochemical measurements related to calcium-phosphate metabolism did not change. Otherwise, all patients showed an increase in serum aluminum from 0.56+/-0.44 to 1.63+/-0.52 micromol/l (p<0.001). No differences were detected in serum aluminum between patients receiving and not receiving oral aluminum salts. Even moderately high aluminum concentrations maintained during a short period of time could produce significant hematological alterations and a depletion of body iron stores before clinical manifestations were evident.

The genes for human brain factor 1 and 2, members of the fork head gene family, are clustered on chromosome 14q

Brain factor-1 (BF-1) is a member of the fork head gene family which shows expression restricted to the neurons of the developing telencephalon in rodents and man. We have isolated a second human gene (HBF-2), which is also strongly expressed in embryonic brain and has very high homology to both the rat and human brain factor-1 genes and the retroviral oncogene qin. The HBF-2 cDNA was isolated from a human fetal brain expression library and contains a putative open reading frame of 479 amino acids. The HBF-2 gene is strongly expressed in fetal brain and also with lower levels of expression in several adult tissues. At the genomic level the gene for HBF-1 contains an 500 bp intron situated between the DNA binding domain II and the fork head domain while that of HBF-2 is intronless. The two genes are clustered on human chromosome 14q11-13.

Computer assisted promoter analysis of a human sperm specific nucleoprotein gene cluster

The promoter regions of the clustered human spermatid-specific nucleoprotein PRM1, PRM2 arid TNP2 genes were compared to define regulatory elements that may govern their expression. Sequence alignment revealed two wll conserved motifs, despite a lack of extensive homology. They are located at similar positions within the first 400 nt of their 5' UTRs. Conservation of these motifs may reflect selective evolutionary pressure to maintain their structure. This supports the view that these elements assume a central role in the coordinate regulation of this gene cluster during spermiogenesis. The distribution of binding sites of known transcription factors was also assessed within the regions flanking the 5' ends of these genes. This analysis should prove useful in directing studies that define the signals necessary for the coordinate regulation of this spermatid specific gene cluster.

The nuclear status of human sperm cells

In the last decade, and in particular since the development of in vitro fertilization techniques, the nuclear status of human sperm cells has shown to be a key parameter in the assessment of male fertility. The shape and condensed state of the mature sperm nucleus are determined by structural and functional events that occur during spermiogenesis. This paper reviews essential findings on re-organization of the nucleus during sperm differentiation and maturation, and reports recent data on the architecture, biochemical composition and stability of the nucleus in human ejaculated spermatozoa. Different methods used to evaluate nuclear maturity in relation to male fertility are critically appraised.

Linkage maps of porcine chromosomes 3, 6, and 9 based on 31 polymorphic markers

Linkage maps of porcine Chromosomes (Chrs) 3, 6, and 9, based on 31 polymorphic markers, are reported. The markers include 14 microsatellites, 12 RFLPs, three protein polymorphisms, and two blood group loci. The genetic interpretations of 11 RFLPs are documented. The markers were scored in a three-generation Wild Boar/Large White pedigree, and genetic maps were constructed on the basis of two-point and multi-point linkage analysis. Altogether the maps span a genetic distance of 216 cM, and previous physical assignments indicate that the linkage groups cover major parts of the three chromosomes. Significant differences in recombination rates between the sexes were observed for all three chromosomes. The recombination rate on the q arm of Chr 6 was markedly low. Sixteen loci are informative with regard to comparative mapping, that is, they have previously been mapped in the human and/or mouse genomes.

Evolution of the monotremes. The sequences of the protamine P1 genes of platypus and echidna

The protamine P1 genes from two monotremes, platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus) were isolated after polymerase-chain-reaction amplification then cloned and sequenced. The two protamine P1 genes are of 290 bp and 311 bp for platypus and echidna, respectively, and are clearly orthologous to the published sequences of protamine P1 genes of eutherian mammals and birds. Both genes contain an intron, like the mammals and marsupials and unlike the bird P1 genes that are intronless. The deduced protein sequences from the coding areas of the platypus and echidna protamine P1 genes do not contain any cysteine residues. This absence of cysteine residues leaves the sperm nuclei susceptible to disruption in vitro by exposure to increasing ionic strength and is a characteristic of fish, birds and marsupials. In contrast, the P1 protamines of placental mammals invariably contain 6-9 cysteine residues that, as a result of the formation of intermolecular and intramolecular disulfide bridges, significantly increase the stability of the sperm nuclei that can only be disrupted following disulfide-bond cleavage. Phylogenetic analysis of the protamine P1 gene sequences indicates that the monotremes occupy a position half-way between the eutherian mammals and birds. From the DNA sequences we estimate the time of divergence of the platypus and the echidna to be around 22 million years ago. This date agrees very well with the published estimates of divergence based on other criteria.

Evolution of pro-protamine P2 genes in primates

Protamines P1 and P2 form a family of small basic peptides that represent the major sperm proteins in placental mammals. In human and mouse protamine P2 is one of the most abundant sperm proteins. The protamine P2 gene codes for a P2 precursor, pro-P2 which is later processed by proteolytic cleavages in its N-terminal region to form the mature P2 protamines. We have used polymerase chain amplification to directly sequence the pro-P2 genes of the five major primate families: red howler (Alouatta seniculus) is a New World monkey (Cebidae); the two macaque species, Macaca mulatta and M. nemistrina are Old World monkeys (Cercopithecidae), the gibbon, Hylobates lar, represents one branch of the apes (Hylobatidae); the orangutan, Pongo pygmaeus, gorilla, Gorilla gorilla and two species of chimpanzee Pan paniscus and Pan troglodytes represent a second ape family (Pongidae). These pro-P2 genes are compared with that of human [Domenjoud, L., Nussbaum, G., Adham, I. M., Greeske, G. & Engel, W. (1990) Genomics 8, 127-133]. The overall size and organization of the genes are conserved within the group. The mean length of pro-P2 is 101 residues, with an increase to 102 in M. nemistrina and a decrease to 99 residues in red howler (A. seniculus). In gorilla and red howler one of two 79-bp tandem repeats that occurs 3' of the gene is deleted. Of the 101 deduced amino acids examined, an amino acid change occurs in one or more primates at 45 positions. Considering only the most recently diverged group, the human/gorilla/chimpanzee clade, this represents a very high mutation rate of 0.99 changes/100 sites in 10(6) years. This rapid mutation rate is characteristic of both members of the protamine gene family, P1 and P2. Consideration of the variable nature of the sequences at the multiple sites of proteolysis during the processing of the pro-P2 indicates either that there are several processing enzymes of differing specificities, or more likely that the folded structure of the pro-P2 limits accessibility of a non-specific protease to certain exposed sites.

The gene for human transition protein 2: nucleotide sequence, assignment to the protamine gene cluster, and evidence for its low expression

We have isolated the gene for transition protein 2 (TNP2) from a human cosmid clone that contains the genes for protamines 1 and 2. A nucleotide sequence of 1776 bp that comprises 268 bp of the 5'-noncoding region, 400 bp of exon 1, 849 bp of an intron, 17 bp of exon 2, and 242 bp of the 3'-noncoding region was determined. A modified CAT box, a TATAA box, and two possible polyadenylation sites were identified. Transcripts in testicular RNA could be detected only by RT-PCR and RNase protection assays. By direct sequencing of the PCR products, a cDNA sequence was established. It can be deduced from these results that, in contrast to other mammalian genes, the human TNP2 gene is expressed at a very low level. The human gene differs from that of other mammalian species by the absence of a conserved GCCATCAC nucleotide sequence in the 3'-untranslated region. Since both protamine genes are known to be localized on chromosome 16p13.3, this chromosomal localization holds true for the human TNP2 gene as well. The genes for both protamines and TNP2 are arranged in a DNA stretch of 13 kb.