Detection of Novel BEST1 Variations in Autosomal Recessive Bestrophinopathy Using Third-generation Sequencing

OBJECTIVE

Autosomal recessive bestrophinopathy (ARB), a retinal degenerative disease, is characterized by central visual loss, yellowish multifocal diffuse subretinal deposits, and a dramatic decrease in the light peak on electrooculogram. The potential pathogenic mechanism involves mutations in the BEST1 gene, which encodes Ca2+-activated Cl- channels in the retinal pigment epithelium (RPE), resulting in degeneration of RPE and photoreceptor. In this study, the complete clinical characteristics of two Chinese ARB families were summarized.

METHODS

Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing was performed on the probands to screen for disease-causing gene mutations, and Sanger sequencing was applied to validate variants in the patients and their family members.

RESULTS

Two novel mutations, c.202T>C (chr11:61722628, p.Y68H) and c.867+97G>A, in the BEST1 gene were identified in the two Chinese ARB families. The novel missense mutation BEST1 c.202T>C (p.Y68H) resulted in the substitution of tyrosine with histidine in the N-terminal region of transmembrane domain 2 of bestrophin-1. Another novel variant, BEST1 c.867+97G>A (chr11:61725867), located in intron 7, might be considered a regulatory variant that changes allele-specific binding affinity based on motifs of important transcriptional regulators.

CONCLUSION

Our findings represent the first use of third-generation sequencing (TGS) to identify novel BEST1 mutations in patients with ARB, indicating that TGS can be a more accurate and efficient tool for identifying mutations in specific genes. The novel variants identified further broaden the mutation spectrum of BEST1 in the Chinese population.

Various phenotypes of autosomal dominant cone-rod dystrophy with cone-rod homeobox mutation in two Chinese families

AIM: To present the clinical manifestations of 5 autosomal dominant cone-rod dystrophy (adCORD) patients from two Chinese families with cone-rod homeobox (CRX) mutation (p.R41W), and to explore the clinical heterogeneity of adCORD with CRX mutation (p.R41W). METHODS: Interrogation and ophthalmological examinations were undertaken in all patients and unaffected members. Analysis of clinical features was performed by visual acuity, slit lamp examination, visual field examination, fundoscopy, autofluorescence and spectral domain optical coherence tomography. Targeted next-generation sequencing was applied as a useful tool to identify the causative mutation of CORD genes. RESULTS: A CRX missense mutation c.121C>T was identified in all patients, resulting in an amino acid change from arginine acid to tryptophan (p.R41W). The patients presented with early onset, progressive and different severities with CORD. CONCLUSION: This is the first report of the clinical phenotype of CRX mutation (p.R41W) in Chinese families, and the mutation can lead to a wide range of various retinal phenotypes.

[Early mortality and risk analysis in adult patients with maintenance hemodialysis]

Objective: To retrospectively analyze the early mortality and related risk factors in adult patients with maintenance hemodialysis (MHD). Methods: Adult MHD patients from 2008 to 2018 were enrolled and divided into training data group and validation data group. In training data group, multivariate logistic regression was used to analyze the risk factors of early death within 120 days after hemodialysis and establish a prediction model. The receiver operating characteristic (ROC) curve was applied to evaluate the prediction ability of the model. Results: A total of 4 885 patients were included. The cumulative mortality within 120 days was 20.97/100 person years, and that within 365 days was 12.25/100 person years. A total of 3 603 patients in the training data group were analyzed. The following risk factors were correlated with early mortality (all P<0.05), including age at start of dialysis over 60 years old (OR=1.792), non-chronic glomerulonephritis (OR=2.214), cardio-cerebrovascular disease (OR=2.695), plasma albumin less than 35 g/L (OR=1.358), platelet count less than 120×10⁹/L (OR=2.194), serum creatinine less than 600 μmol/L (OR=1.652), blood urea nitrogen over 30 mmol/L (OR=1.887), blood phosphorus less than 1.13 mmol/L (OR=1.783), pulse pressure over 55 mmHg(1 mmHg=0.133 kPa) (OR=1.656), low density lipoprotein less than 1.5 mmol/L (OR=1.873), and blood calcium over 2.5 mmol/L (OR=1.876). Risk prediction model was established. The other 1 282 cases in the validation data group were verified. The area under ROC curve was 0.810, with sensitivity 85.7%, and specificity 62.5%. Conclusion: The mortality rate of adult MHD patients within 120 days after dialysis is high. The established prediction model can effectively predict the risk of early death.

Haplotype analysis of association of the MYOC gene with primary angle-closure glaucoma in a Han Chinese population

PURPOSE

The aim of this study is to examine whether or not myocilin (MYOC) genetic variations are associated with susceptibility to primary angle-closure glaucoma (PACG) in the Han Chinese population.

METHODS

Four single-nucleotide polymorphisms (SNPs)-rs235913, rs183532, rs12076134, and rs235875-in the MYOC gene were genotyped in 212 adult patients with PACG and 255 age-, sex-, and ethnic-matched healthy controls by using a polymerase chain reaction-restriction fragment length polymorphism assay. Data were analyzed by chi-square analysis.

RESULTS

The four SNPs in the MYOC gene were in the Hardy-Weinberg equilibrium in all the subjects. The frequencies of A allele rs183532 were significantly different between the PACG patients and the controls (0.238 vs. 0.169, p=0.008; OR=1.541; 95% CI: 1.117-2.127). The frequencies of the AA genotype and A allele of rs235913 were increased in PACG patients compared with controls, but the difference was not significant (p=0.037, p=0.017, respectively). A comparison of the distributions of the genotypes and alleles of rs12076134 and rs235875 showed no statistically significant differences between the PACG patients and the controls (p>0.05). Haplotype analysis indicated that the frequency of the AATG and AATA haplotypes was significantly higher for PACG patients than for control subjects (both p<0.001). However, the frequency of CGGA and CGTG haplotypes was lower for PACG patients than for control subjects (p<0.001).

CONCLUSIONS

Our study suggests that rs183532 is associated with an increased risk of PACG in the Chinese Han population.

Phenotype of Usher syndrome type II assosiated with compound missense mutations of c.721 C>T and c.1969 C>T in MYO7A in a Chinese Usher syndrome family

AIM

To identify the pathogenic mutations in a Chinese pedigree affected with Usher syndrome type II (USH2).

METHODS

The ophthalmic examinations and audiometric tests were performed to ascertain the phenotype of the family. To detect the genetic defect, exons of 103 known RDs -associated genes including 12 Usher syndrome (USH) genes of the proband were captured and sequencing analysis was performed to exclude known genetic defects and find potential pathogenic mutations. Subsequently, candidate mutations were validated in his pedigree and 100 normal controls using polymerase chain reaction (PCR) and Sanger sequencing.

RESULTS

The patient in the family occurred hearing loss (HL) and retinitis pigmentosa (RP) without vestibular dysfunction, which were consistent with standards of classification for USH2. He carried the compound heterozygous mutations, c.721 C>T and c.1969 C>T, in the MYO7A gene and the unaffected members carried only one of the two mutations. The mutations were not present in the 100 normal controls.

CONCLUSION

We suggested that the compound heterozygous mutations of the MYO7A could lead to USH2, which had revealed distinguished clinical phenotypes associated with MYO7A and expanded the spectrum of clinical phenotypes of the MYO7A mutations.

Detecting novel genetic mutations in Chinese Usher syndrome families using next-generation sequencing technology

Usher syndrome (USH) is the most common cause of combined blindness and deafness inherited in an autosomal recessive mode. Molecular diagnosis is of great significance in revealing the molecular pathogenesis and aiding the clinical diagnosis of this disease. However, molecular diagnosis remains a challenge due to high phenotypic and genetic heterogeneity in USH. This study explored an approach for detecting disease-causing genetic mutations in candidate genes in five index cases from unrelated USH families based on targeted next-generation sequencing (NGS) technology. Through systematic data analysis using an established bioinformatics pipeline and segregation analysis, 10 pathogenic mutations in the USH disease genes were identified in the five USH families. Six of these mutations were novel: c.4398G > A and EX38-49del in MYO7A, c.988_989delAT in USH1C, c.15104_15105delCA and c.6875_6876insG in USH2A. All novel variations segregated with the disease phenotypes in their respective families and were absent from ethnically matched control individuals. This study expanded the mutation spectrum of USH and revealed the genotype-phenotype relationships of the novel USH mutations in Chinese patients. Moreover, this study proved that targeted NGS is an accurate and effective method for detecting genetic mutations related to USH. The identification of pathogenic mutations is of great significance for elucidating the underlying pathophysiology of USH.

A novel mutation in C5L2 gene was associated with hyperlipidemia and retinitis pigmentosa in a Chinese family

Background

Previous studies indicated that hyperlipidemia was associated with retinitis pigmentosa (RP). We aimed to identify the mutations in the C5L2 gene which was reported to be associated with hyperlipidemia in a Chinese family with (RP).

Methods

The Proband from the family was screened for mutations in the C5L2 gene that was known to cause hyperlipidemia. Cosegregation analysis was performed in the available family members. Linkage analysis was performed for one missense mutation to calculate the likelihood of its pathogenicity. One hundred and fifty unrelated, healthy Chinese subjects were screened to exclude nonpathogenic polymorphisms.

Results

By direct sequencing method, we identified a novel mutation (Thr196Asn) in C5L2 gene. In this family, each affected family members with RP showed a heterozygous mutation in the C5L2 gene. And all the carriers with heterozygous mutation have increased serum lipid levels in this family.

Conclusions

The present study has extended the mutation spectrum of C5L2, and Thr196Asn mutations in C5L2 were associated with RP and serum lipid levels.

Process of aerenchyma formation and reactive oxygen species induced by waterlogging in wheat seminal roots

The development and regulation of aerenchyma in waterlogged conditions were studied in the seminal roots of wheat. Evans blue staining and the first cell death position indicated that the cortical cell death began at the root mid-cortex cells in flooding conditions. Continuous waterlogging treatment caused the spread of cell death from the mid-cortex to the neighboring cells and well-developed aerenchyma was formed after 72 h. Meanwhile, the formation of radial oxygen loss barrier was observed in the exodermis owing to the induction of Casparian bands and lignin deposition. Analysis of aerenchyma along the wheat root revealed that aerenchyma formed at 10 mm from the root tip, significantly increased toward the center of the roots, and decreased toward the basal region of the root. In situ detection of radial oxygen species (ROS) showed that ROS accumulation started in the mid-cortex cells, where cell death began indicating that cell death was probably accompanied by ROS production. Further waterlogging treatments resulted in the accumulation of ROS in the cortical cells, which were the zone for aerenchyma development. Accumulation and distribution of H₂O₂ at the subcellular level were revealed by ultracytochemical localization, which further verified the involvement of ROS in the cortical cell death process (i.e., aerenchyma formation). Furthermore, gene expression analysis indicated that ROS production might be the result of up-regulation of genes encoding for ROS-producing enzymes and the down-regulation of genes encoding for ROS-detoxifying enzymes. These results suggest that aerenchyma development in wheat roots starts in the mid-cortex cells and its formation is regulated by ROS.

Cell wall degradation and the dynamic changes of Ca2+ and related enzymes in the developing aerenchyma of wheat (Triticum aestivum L.) under waterlogging

This research was aimed to study the cell wall degradation and the dynamic changes of Ca2+ and related enzymes in developing aerenchyma of wheat root under waterlogging. An examination of morphological development by light and electron microscope revealed that the structure of cell wall in middle cortical cells remained intact after 12 h of waterlogging and turned thinner after waterlogging for 24 h. At 48 h, the aerenchyma has been formed. The cellulase activity gradually increased in middle cortical cells within 24 h of waterlogging, and decreased with the formation of aerenchyma. Fluorescence detection and subcellular localization of Ca2+ showed the dynamic changing of Ca2+ at the cellular and subcellular levels during the development of aerenchyma. The activity of Ca2+-ATPase enhanced markedly in intercellular space, plasma membrane and tonoplast of some middle cortical cells after 8 h of waterlogging and remained high after 24 h, but it decreased after 48 h of waterlogging. All these suggests that cellulase, Ca2+ and Ca2+-ATPase show a dynamic distribution during the aerenchyma development which associated with the cell wall degradation of middle cortical cells. Moreover, there is a feedback regulation between Ca2+ and Ca2+-ATPase.

Assessment of hepatitis B virus DNA and hepatitis C virus RNA in the common bedbug (Cimex lectularius L.) and kissing bug (Rodnius prolixus)

OBJECTIVE

Historical clinical studies suggest the potential for insect-borne transmission of human hepatitis viruses. Studies of hepatitis B virus (HBV) persistence in insects were performed before the advent of molecular techniques, and studies to assess possible insect-borne transmission of hepatitis viruses have not yet been performed. The aim of this study was to determine, using molecular techniques, whether HBV and hepatitis C virus (HCV) persist in and are excreted in the feces of the bedbug Cimex lectularius L. and kissing bug Rodnius prolixus after an infectious meal.

METHODS

Blood-feeding insects from the insect order Hemiptera (Cimex lectularius L. and Rhodnius prolixus) were fed on blood from infected patients with high titers of HBV, HCV, and control uninfected patients. Insects and insect excrement were collected at weekly intervals and tested for HBV DNA and HCV RNA using the polymerase chain reaction.

RESULTS

HBV DNA was detected in bedbugs and excrement up to 6 wk after feeding on an infectious meal. HBV DNA was also detected in most kissing bugs and excrement up to 2 wk after feeding. HCV RNA was not detected in bedbugs at any time after feeding.

CONCLUSIONS

We did not detect HCV RNA in bedbugs after feeding on an infectious meal. Our data provide molecular evidence to suggest that HBV may persist in Hemiptera. Additional studies are ongoing to determine whether this viral persistence is capable of infection.

DNA-binding and photocleavage studies of cobalt(III) mixed-polypyridyl complexes containing 2-(2-chloro-5-nitrophenyl)imidazo [4,5-f][1,10]phenanthroline

The ligand 2-(2-chloro-5-nitrophenyl)imidazo[4,5-f][1,10]phenanthroline(CNOIP) and its complexes [Co(bpy)(2)(CNOIP)](3+) (1) and [Co(phen)(2)(CNOIP)](3+) (2) (bpy=2,2'-bipyridine; phen=1,10-phenanthroline) have been synthesized and characterized. Binding of the two complexes with calf thymus DNA has been investigated by spectroscopic methods, cyclic voltammetry, viscosity, and electrophoresis measurements. The experimental results indicate that both complexes bind to DNA through an intercalative mode. In comparison with their parent complexes containing PIP ligand (PIP=2-phenylimidazo[4,5-f][1,10]phenanthroline), the introduction of NO(2) and Cl groups to the PIP ligand decreased the binding affinity of complexes 1 and 2 to CT DNA. Both complexes have also been found to promote the photocleavage of plasmid pBR 322 DNA, the hydroxyl radical (OH*) is suggested to be the reactive species responsible for the cleavage.

Identification of 10 novel snoRNA gene clusters from Arabidopsis thaliana

Ten novel small nucleolar RNA (snoRNA) gene clusters, consisting of two or three snoRNA genes, respectively, were identified from Arabidopsis thaliana. Twelve of the 25 snoRNA genes in these clusters are homologous to those of yeast and mammals according to the conserved antisense sequences that guide 2'-O-ribose methylation of rRNA. The remaining 13 snoRNA genes, including two 5.8S rRNA methylation guides, are new genes identified from A.thaliana. Interestingly, seven methylated nucleotides, predicted by novel snoRNAs Z41a-Z46, are methylated neither in yeast nor in vertebrates. Using primer extension at low dNTP concentration the six methylation sites were determined as expected. These snoRNAs were recognized as specific guides for 2'-O:-ribose methylation of plant rRNAs. Z42, however, did not guide the expected methylation of 25S rRNA in our assay. Thus, its function remains to be elucidated. The intergenic spacers of the gene clusters are rich in uridine (up to 40%) and most of them range in size from 35 to 100 nt. Lack of a conserved promoter element in each spacer and the determination of polycistronic transcription from a cluster by RT-PCR assay suggest that the snoRNAs encoded in the clusters are transcribed as a polycistron under an upstream promoter, and individual snoRNAs are released after processing of the precursor. Numerous snoRNA gene clusters identified from A.thaliana and other organisms suggest that the snoRNA gene cluster is an ancient gene organization existing abundantly in plants.

Seven novel methylation guide small nucleolar RNAs are processed from a common polycistronic transcript by Rat1p and RNase III in yeast

Through a computer search of the genome of the yeast Saccharomyces cerevisiae, the coding sequences of seven different box C/D antisense small nucleolar RNAs (snoRNAs) with the structural hallmarks of guides for rRNA ribose methylation have been detected clustered over a 1.4-kb tract in an inter-open reading frame region of chromosome XIII. The corresponding snoRNAs have been positively identified in yeast cells. Disruption of the nonessential snoRNA gene cluster specifically suppressed the seven cognate rRNA ribose methylations but did not result in any growth delay under the conditions of yeast culture tested. The seven snoRNAs are processed from a common polycistronic transcript synthesized from an independent promoter, similar to some plant snoRNAs but in marked contrast with their vertebrate functional homologues processed from pre-mRNA introns containing a single snoRNA. Processing of the polycistronic precursor requires nucleases also involved in rRNA processing, i.e., Rnt1p and Rat1p. After disruption of the RNT1 gene, the yeast ortholog of bacterial RNase III, production of the seven mature snoRNAs was abolished, while the polycistronic snoRNA precursor accumulated. In cells lacking functional Rat1p, an exonuclease involved in the processing of both pre-rRNA and intron-encoded snoRNAs, several processing intermediates of the polycistronic precursor accumulated. This allowed for the mapping in the precursor of the presumptive Rnt1p endonucleolytic cuts which provide entry sites for subsequent exonucleolytic trimming of the pre-snoRNAs. In line with known properties of double-stranded RNA-specific RNase III, pairs of Rnt1p cuts map next to each other on opposite strands of long double-helical stems in the secondary structure predicted for the polycistronic snoRNA precursor.

Intron-encoded, antisense small nucleolar RNAs: the characterization of nine novel species points to their direct role as guides for the 2'-O-ribose methylation of rRNAs

A growing number of small nucleolar RNAs (snoRNAs) are intron-encoded, contain the characteristic box C (UGAUGA) and box D (CUGA) motifs and exhibit long complementarities to conserved sequences in mature rRNAs. We have identified nine additional members of this family, U32 to U40. All but one are encoded in introns of ribosomal protein genes in vertebrates: U32 to U35 in rpL13a, U36 in rpL7a and U38 to U40 in rpS8. By contrast, U37 is encoded in elongation factor 2 gene. Interestingly, U32 and U36 each contain two complementarities (one to 18 S and the other to 28 S rRNA). U32 to U40 are fibrillarin-associated, devoid of a 5'-trimethyl-cap and display an exclusively nucleolar localization. They are all metabolically stable and roughly as abundant as previously reported members of this family. Characterization of their homologs in distant species shows that their 10 to 14 nt long rRNA complementarities are conserved. A clue on the function of this snoRNA family is provided by the comparative analysis of the largely expanded collection of their conserved duplexes with rRNA. Not only does each duplex span at least one site of 2'-O-ribose methylation in the rRNA but the modification site is always at the same position in the duplex, paired to the fifth nucleotide upstream from a box D motif in the snoRNA. Consistent with the notion that each snoRNA of this family guides one particular methylation along the rRNA sequence, we have detected several pairs of snoRNAs with overlapping complementarities to rRNA tracts with vicinal sites of ribose methylations. In each case, the two overlapping complementarities are shifted from each other by a distance equal to the spacing between the methylated sites which are thus found at the same position within each of the mutually exclusive duplexes. Finally, we have also identified, within three previously known snoRNAs, novel antisense elements able to form a canonical duplex around ribose-methylated sites in rRNA, which further supports the conclusion that the duplex structure provides the 2'-O-methyltransferase with the appropriate site-specificity on the substrate.

SnoRNA U21 is also intron-encoded in Drosophila melanogaster but in a different host-gene as compared to warm-blooded vertebrates

U21 is an intron-encoded snoRNA in vertebrates which contains a 13-nt tract of complementarity to an invariant sequence in eukaryotic 28S rRNA. Here, we report the characterization of its Drosophila melanogaster homolog which is the first case of an intron-encoded snoRNA in an invertebrate metazoan. In D. melanogaster, U21 is encoded within the ARF-1 (ADP ribosylation factor 1) gene, whereas in chicken and mammals it is found in the ribosomal protein L5 gene. In D. melanogaster, like in vertebrates, U21 is devoid of a 5' trimethylguanosine cap, thus, likely resulting from processing of intronic RNA. The only portion of U21 sequence preserved between D. melanogaster and vertebrates, in addition to the hallmark box C and box D motifs, corresponds precisely to the 13-nt complementary to rRNA, pointing to an important role of the pairing of U21 to pre-rRNA.

Novel intron-encoded small nucleolar RNAs with long sequence complementarities to mature rRNAs involved in ribosome biogenesis

Recently, several new snoRNAs encoded in introns of genes coding for ribosomal, ribosome-associated, or nucleolar proteins have been discovered. We are presently studying four of these intronic snoRNAs. Three of them, U20, U21, and U24, are closely related to each other on a structural basis. They are included in genes encoding nucleolin and ribosomal proteins L5 and L7a, respectively, in warm-blooded vertebrates. These three metabolically stable snoRNAs interact with nucleolar protein fibrillarin. In addition, they display common features that make them strikingly related to snoRNA U14. U14 contains two tracts of complementarity to 18S rRNA, which are required for the production of 18S rRNA. U20 displays a 21 nucleotide (nt) long complementarity to 18S rRNA. U21 contains a 13 nt complementarity to an invariant sequence in eukaryotic 28S rRNA. U24 has two separate 12 nt long complementarities to a highly conserved tract of 28S rRNA. Phylogenetic evidences support the fundamental importance of the pairings of these three snoRNAs to pre-rRNA, which could be involved in a control of pre-rRNA folding during preribosome assembly. By transfection of mouse cells, we have also analyzed the processing of U20 and found that the -cis acting signals for its processing from intronic RNA are restricted to the mature snoRNA sequence. Finally, we have documented changes of host genes for these three intronic snoRNAs during the evolution of eukaryotes.

U24, a novel intron-encoded small nucleolar RNA with two 12 nt long, phylogenetically conserved complementarities to 28S rRNA

Following computer searches of sequence banks, we have positively identified a novel intronic snoRNA, U24, encoded in the ribosomal protein L7a gene in humans and chicken. Like previously reported intronic snoRNAs, U24 is devoid of a 5'-trimethyl-cap. U24 is immunoprecipitated by an antifibrillarin antibody and displays an exclusively nucleolar localization by fluorescence microscopy after in situ hybridization with antisense oligonucleotides. In vertebrates, U24 is a 76 nt long conserved RNA which is metabolically stable, present at approximately 14,000 molecules per human HeLa cell. U24 exhibits a 5'-3' terminal stem-box C-box D structure, typical for several snoRNAs, and contains two 12 nt long conserved sequences complementary to 28S rRNA. It is, therefore, strikingly related to U14, U20 and U21 snoRNAs which also possess long sequences complementary to conserved sequences of mature 18S or 28S rRNAs. In 28S rRNA the two tracts complementary to U24 are adjacent to each other, they involve several methylated nucleotides and are surprisingly close, within the rRNA secondary structure, to complementarities to snoRNAs U18 and U21. Identification of the yeast Saccharomyces cerevisiae U24 gene directly confirms the outstanding conservation of the complementarity to 28S rRNA during evolution, suggesting a key role of U24 pairing to pre-rRNA during ribosome biogenesis, possible in the control of pre-rRNA folding. Yeast S.cerevisiae U24 is also intron-encoded but not in the same host-gene as in humans or chicken.

U21, a novel small nucleolar RNA with a 13 nt. complementarity to 28S rRNA, is encoded in an intron of ribosomal protein L5 gene in chicken and mammals

Following a search of sequence data bases for intronic sequences exhibiting structural features typical of snoRNAs, we have positively identified by Northern assays and sequence analysis another intron-encoded snoRNA, termed U21. U21 RNA is a 93 nt. long, metabolically stable RNA, present at about 10(4) molecules per HeLa cell. It is encoded in intron 5 of the ribosomal protein L5 gene, both in chicken and in the two mammals studied so far, human and mouse. U21 RNA is devoid of a 5'-trimethyl-cap and is likely to result from processing of intronic RNA. The nucleolar localization of U21 has been established by fluorescence microscopy after in situ hybridization with digoxigenin-labeled oligonucleotide probes. Like most other snoRNAs U21 contains the box C and box D motifs and is precipitated by anti-fibrillarin antibodies. By the presence of a typical 5'-3' terminal stem, U21 appears more particularly related to U14, U15, U16 and U20 intron-encoded snoRNAs. Remarkably, U21 contains a long stretch (13 nt.) of complementarity to a highly conserved sequence in 28S rRNA. Sequence comparisons between chicken and mammals, together with Northern hybridizations with antisense oligonucleotides on cellular RNAs from more distant vertebrates, point to the preferential preservation of this segment of U21 sequence during evolution. Accordingly, this complementarity, which overlaps the complementarity of 28S rRNA to another snoRNA, U18, could reflect an important role of U21 snoRNA in the biogenesis of large ribosomal subunit.

In humans all U3 genes map to chromosome 17p12-->p11, but in mouse the U3A and U3B genes are located on different chromosomes

U3 small nucleolar RNA, which participates in eukaryotic rRNA processing, is encoded by a small multigene family in mammals. In humans, the four to six gene copies code for an identical U3 RNA molecule; rodents, however, have two variant forms of these genes, U3A and U3B. We show that all U3 genes in humans map to a single chromosomal locus, 17p12-->-p11, which corresponds exactly to the region of mouse Chromosome 11 where the four U3B genes are clustered. By contrast, in mouse the unique U3A gene copy is not linked to the U3B gene cluster but maps to another chromosome (the B2-B4 region of Chromosome 10).

A sequence dimorphism in a conserved domain of human 28S rRNA. Uneven distribution of variant genes among individuals. Differential expression in HeLa cells

In humans, cellular 28S rRNA displays a sequence dimorphism within an evolutionarily conserved motif, with the presence, at position +60, of either a A (like the metazoan consensus) or a G. The relative abundance of the two forms of variant genes in the genome exhibit large differences among individuals. The two variant forms are generally represented in cellular 28S rRNA in proportion of their relative abundance in the genome, at least for leucocytes. However, in some cases, one form of variant may be markedly underexpressed as compared to the other. Thus, in HeLa cells, A-form genes contribute to only 1% of the cellular content in mature 28S rRNA although amounting to 15% of the ribosomal genes. The differential expression seems to result from different transcriptional activities rather than from differences in pre-rRNA processing efficiency or in stabilities of mature rRNAs. G-form ribosomal genes were not detected in other mammals, including chimpanzee, which suggests that the fixation of this variant type is a rather recent event in primate evolution.

Presence of a differentially expressed U3A RNA variant in mouse. Structure and evolutive implications

A U3 RNA variant has been identified in mouse, the abundance of which relative to the previously characterized major form (U3B) appears to vary to a large extent depending upon the cell origin. Its partial sequence analysis shows that it is clearly related to the U3A form previously described in rat. Sequence comparisons suggest that the separation of the two forms of U3 genes now found in rat and mouse represent a relatively ancient event in rodent evolution. While mouse U3B RNA is encoded by four clustered genes, the U3A variant is encoded by a unique gene. Both mouse U3 RNAs differ substantially in primary structure (more than 10% divergence). Although rodent U3 RNAs exhibit a largely similar secondary structure, a specific difference between the A and B form can nevertheless be observed.

Evolution of large-subunit rRNA structure. The diversification of divergent D3 domain among major phylogenetic groups

During evolution, the potential for sequence (and length) variation of large-subunit rRNA has been mostly restricted over 12 divergent domains (termed D1-D12) interspersed along the molecule. Here, we have focused our attention onto the D3 divergent domain, through a detailed analysis of its pattern of variation in the phylogeny, both in terms of primary and secondary structures. We have systematically compared all the procaryotic and eucaryotic sequences published so far (i.e. 36 species), together with a series of 10 additional eucaryotic specimens, which were determined by direct RNA sequencing. Secondary structures supported by comparative evidence have been derived for archaebacteria, eubacteria and eucaryotes respectively, which shows that the D3 domain contains a subset of universally conserved structural features interspersed with four variable subdomains. Within the four portions where a structural diversification has taken place, elementary structures specific of large phylogenetic groups can be identified. Remarkably such diversified structures appear to be preserved despite sequence divergence, suggesting they correspond to functionally important structures. Accordingly, the mode of sequence variation of the D3 domain suggests this region of the molecule may encode elementary functions of rRNA which could have significantly diversified during the evolution of the major groups of organisms.

Origin of the algae

Eukaryotic algae are traditionally separated into three broad divisions: the rhodophytes, the chromophytes and the chlorophytes. The evolutionary relationships between these groups, their links with other eukaryotes and with other photosynthetic groups, such as euglenophytes and cryptophytes, have been the subject of much debate and speculation. Here we analyse partial sequences of the large (28S) cytoplasmic ribosomal RNA from ten new species of protists belonging to various groups of unicellular algae. By combining them with the homologous sequences from 14 other unicellular and multicellular eukaryotes, we show that rhodophytes, chromophytes and chlorophytes emerge as three distinct groups late among eukaryotes, that is, close to the metazoa-metaphytes radiation. This implies a relatively late occurrence of eukaryotic photosynthetic symbiosis. We also provide details of intra- and inter-phyla relationships.

Phylogenetic calibration of the 5' terminal domain of large rRNA achieved by determining twenty eucaryotic sequences

Due to their high information content and their particular mode of variation, large rRNA molecules potentially represent powerful indicators of phylogenetic relationships. Even partial sequences may suffice to generate reliable estimations, provided they correspond to well-chosen portions of the molecule. We have systematically analyzed a specific portion of the large rRNA (the region extending over nearly 400 nucleotides from the 5' end) as a general index of eucaryotic phylogeny. By means of fast and direct rRNA sequencing, we have determined the sequence of this region for 20 additional eucaryotes, including several representatives of each vertebrate class, an invertebrate metazoan (mussel), a fungus (Schizosaccharomyces pombe), and three higher plants. Comparative treatment of these new data and previously reported rRNA sequences shows that this region can serve as an indicator of eucaryotic phylogeny for evaluating both long-range and short-range relationships. Its conservative domains appear to possess a rather uniform rate of nucleotide changes in all the eucaryotic lineages analyzed and the phylogenetic tree we derived agrees with classical views.

Partial phylogeny of the unicellular eukaryotes based on rapid sequencing of a portion of 28S ribosomal RNA

Using a rapid rRNA sequencing technique, we have determined the sequence of the 400 nucleotides located at the 5' end of the large subunit rRNA molecule from eight species of unicellular eukaryotes (protists). This region contains a pair of conservative domains well-suited for long-range phylogenetic evaluations among eukaryotes, due both to their substantia, length and to their intrinsic rate of sequence variation during evolution. It also comprises a central more rapidly evolving portion, which allows for a fine tuning of distance evaluation between closely related species. Molecular distances were computed between the aligned nucleotides of all presently available protist sequences and were used to derive a tentative dendrogram. Within the limitations inherent to this approach, a number of interesting observations emerge: The various protist groups appear to have separated very early from each other. The most deeply divergent protists belong to a number of orders of flagellates (mastigotes), suggesting a very ancient origin for organelles containing a 9 + 2 microtubular arrangement. Ciliates emerged late among eukaryotes, suggesting that their peculiar genetic code was derived secondarily. Moreover, a dinoflagellate clusters with ciliates, thus making it likely that the unusual features of nuclear organization and mitosis of this group are not primitive but derived characters. Finally, within groups, taxonomic and evolutionary inferences appear to be feasible using this portion of the rRNA.

Phylogeny of Onchocerca volvulus and related species deduced from rRNA sequence comparisons

A rapid, direct method for determining the partial nucleotide sequence of large subunit ribosomal RNA was adapted and applied to a group of helminth parasites. Small samples of total, unfractionated cellular RNA isolated from each organism were analysed and the nucleotide sequences of equivalent portions of the large subunit ribosomal RNA compared. The data obtained were used to construct a phylogenetic tree showing the evolutionary relationships within this group of organisms.

Molecular evolution of the 5'-terminal domain of large-subunit rRNA from lower eukaryotes. A broad phylogeny covering photosynthetic and non-photosynthetic protists

This paper summarizes the present status of an analysis of protist phylogeny using rapid partial sequencing of 28S rRNA. Data from 12 protistan phyla are now available and have been used to construct a tentative dendrogram based on a distance matrix method. The tree is robust and has considerable internal consistency. The following salient points are observed: a number of flagellate groups (particularly Euglenozoa) emerge very early among eukaryotes, whereas ciliates and dinoflagellates emerge late, suggesting that some characteristics that had been considered as primitive may in fact be derived. Both chlorophytic and chromophytic photosynthetic protists emerge very late in the tree, close to the Metazoa-Metaphyta-Fungi radiation, suggesting relatively late occurrence of the photosynthetic symbiosis. Taxonomic and phylogenetic information is also obtained within a phylum where rRNA of enough species are sequenced. A deep trichotomy is thus observed within the ciliates. The data are discussed with respect to classical protist phylogenies.

A U3 RNA pseudogene in mouse: sequence and organization in genomic DNA

A mouse U3 RNA pseudogene has been identified; it corresponds to a U3B full length coding sequence with a 3'-oligo(A) tail, precisely flanked at both ends by a pair of 15 bp direct repeats. These structural features suggest that it has arisen through an RNA-mediated mechanism involving an insertion at staggered nicks in the genome. Sequence data indicate that this mouse specimen has been generated by a different event as compared to the recently described rat pseudogenes. It represents the first reported case, for a pseudogene of this class, to be present at more than one copy per genome.

Phylogeny of helminths determined by rRNA sequence comparison

The nucleotide sequence of the 5' ends of the 28S-like rRNA molecules of five species of helminths was determined directly, using a variation on the dideoxynucleotide chain-termination method which requires only 10 micrograms of total cellular RNA for analysis. Nucleotide sequence comparisons over 208 bases allowed the phylogeny of these organisms to be determined. The data show that the rRNA sequence of Nematospiroides dubius, a nematode, is as divergent from that of two platyhelminths, Hymenolepis diminuta and Schistosoma mansoni, as it is from the rRNA sequence of the two nematodes Onchocerca gibsoni and Brugia pahangi. The latter two appear to be very closely related, whereas the two platyhelminths are more distant from each other. The study demonstrates the usefulness and generality of rRNA sequencing for the systematic phylogenetic classification of parasitic organisms whose tissues are only available in relatively small amounts.