A structural analysis of P. polycephalum U1 RNA at the RNA and gene levels. Are there differentially expressed U1 RNA genes in P. polycephalum? U1 RNA evolution

SV2A PET imaging in human neurodegenerative diseases

This manuscript presents a thorough review of synaptic vesicle glycoprotein 2A (SV2A) as a biomarker for synaptic integrity using Positron Emission Tomography (PET) in neurodegenerative diseases. Synaptic pathology, characterized by synaptic loss, has been linked to various brain diseases. Therefore, there is a need for a minimally invasive approach to measuring synaptic density in living human patients. Several radiotracers targeting synaptic vesicle protein 2A (SV2A) have been created and effectively adapted for use in human subjects through PET scans. SV2A is an integral glycoprotein found in the membranes of synaptic vesicles in all synaptic terminals and is widely distributed throughout the brain. The review delves into the development of SV2A-specific PET radiotracers, highlighting their advancements and limitations in neurodegenerative diseases. Among these tracers, 11C-UCB-J is the most used so far. We summarize and discuss an increasing body of research that compares measurements of synaptic density using SV2A PET with other established indicators of neurodegenerative diseases, including cognitive performance and radiological findings, thus providing a comprehensive analysis of SV2A's effectiveness and reliability as a diagnostic tool in contrast to traditional markers. Although the literature overall suggests the promise of SV2A as a diagnostic and therapeutic monitoring tool, uncertainties persist regarding the superiority of SV2A as a biomarker compared to other available markers. The review also underscores the paucity of studies characterizing SV2A distribution and loss in human brain tissue from patients with neurodegenerative diseases, emphasizing the need to generate quantitative neuropathological maps of SV2A density in cases with neurodegenerative diseases to fully harness the potential of SV2A PET imaging in clinical settings. We conclude by outlining future research directions, stressing the importance of integrating SV2A PET imaging with other biomarkers and clinical assessments and the need for longitudinal studies to track SV2A changes throughout neurodegenerative disease progression, which could lead to breakthroughs in early diagnosis and the evaluation of new treatments.

Chlamydomonas U2, U4 and U6 snRNAs. An evolutionary conserved putative third interaction between U4 and U6 snRNAs which has a counterpart in the U4atac-U6atac snRNA duplex

The spliceosomal UsnRNAs U2, U4 and U6 from the green alga Chlamydomonas reinhardtii (Cre) were sequenced using a combination of RNA and cDNA sequencing methods and were compared to other sequenced UsnRNAs. The lengths of Cre U6 and Cre U2 RNAs are similar to those of their higher plant equivalents. Cre U4 RNA is shorter (139 nt) than its counterpart from higher plants (150-154 nt), and contains stem IV and loop D which are absent, with the exception of the Tetrahymena U4 RNA, from the U4 RNAs of other unicellular organisms studied to date. Base-pairing interactions between U6 and U4 RNAs and between U6 and U2 RNAs, identical to those described for mammalian and yeast systems, are structurally feasible in the Cre system. In addition, based on comparative analyses of the predicted U4/U6 RNA duplex from various species, an evolutionary conserved third putative U6-U4 interaction was found. Interestingly, it can also be formed with the recently discovered U6atac and U4atac RNAs. This is a strong support in favor of the possible biological significance of this third putative interaction. Based on comparative analysis, an extension of the earlier described U6-U2 interaction patterns is also proposed.

A unique U5-->A substitution in the Physarum polycephalum U1 snRNA: evidence at the RNA and gene levels

The 5' terminal sequence of U1 snRNA that base-pairs with the intron 5' splice site in the course of spliceosome assembly was considered to be universally conserved. A study of the P polycephalum U1 snRNA at both RNA and gene levels shows that there are exceptions to this rule: the P polycephalum U1 snRNA has a U to A substitution at position 5, that is partially compensated by a high frequency of T residue at position +4 of introns. In contrast to the yeast genome, the P polycephalum genome contains several U1 snRNA coding sequences (about 20). They either encode the U1A snRNA expressed in microplasmodia or correspond to the previously cloned U1B coding sequence. Both coding sequences show the U5A substitution. The ratio of U1A versus U1B coding sequences is of about 3. A U1A gene was cloned. The 60 nt region upstream of the coding sequence has the same sequence as in the U1B gene. The U1B gene is probably expressed at another stage of the P polycephalum life cycle.

Phylogenetic conservation of modified nucleotides in the terminal loop 1 of the spliceosomal U5 snRNA

In order to study the phylogenetic conservation of modified nucleotides in the spliceosomal U5 snRNA, we determined the nucleotide sequences of the U5 snRNAs from the slime mold Physarum polycephalum (EMBL data bank accession numbers: X74440 and X74441) and we identified the pseudouridine and 2'-O-methylated residues. From a comparison of all the U5 snRNAs studied at the level of nucleotide modifications, we concluded that the modified nucleotides in U5 snRNA can be divided into three classes according to their degree of conservation: i) the modified nucleotides of the 5' terminal cap structure that display some variations from one species to the other; ii) the modified nucleotides located in the helical part of the stem/loop structure I that vary greatly in number, position and identity from one species to the other; and iii) the modified nucleotides of the terminal loop 1, that are almost identical in all the species studied. Taking into account the recent discovery of a crucial role played by this terminal loop of U5 snRNA in 5' and 3' splice site definition, we postulate that the numerous modified nucleotides it contains, five out of a total of 11, play an important role in spliceosome assembly and function. Their possible role is discussed.

An additional long-range interaction in human U1 snRNA

We present evidence for the existence of an additional long-range interaction in vertebrate U1 snRNAs. By submitting human U1 snRNP, HeLa nuclear extracts, authentic human or X. laevis in vitro transcribed U1 snRNAs to RNase V1, a nuclease specific for double-stranded regions, cleavages occurred in the sequence psi psi ACC (positions 5-9) residing in the 5' terminal region of the RNA. The RNase V1 sensitive region is insensitive to single-stranded probes, something unexpected knowing that it was considered single-stranded in order to base-pair to pre-mRNA 5' splice site. We have identified the sequence GGUAG (positions 132-136) as the only possible 3' partner. Mutants, either abolishing or restoring the interaction between the partners, coupled to an RNase V1 assay, served to substantiate this base-pairing model. The presence of this additional helix, even detected in nuclear extracts under in vitro splicing conditions, implies that a conformational change must occur to release a free U1 snRNA 5' end.

Spliceosomal small nuclear RNAs of Tetrahymena thermophila and some possible snRNA-snRNA base-pairing interactions

We have identified and characterized the full set of spliceosomal small nuclear RNAs (snRNAs; U1, U2, U4, U5 and U6) from the ciliated protozoan Tetrahymena thermophila. With the exception of U4 snRNA, the sizes of the T. thermophila snRNAs are closely similar to their metazoan homologues. The T. thermophila snRNAs all have unique 5' ends, which start with an adenine residue. In contrast, with the exception of U6, their 3' ends show some size heterogeneity. The primary sequences of the T. thermophila snRNAs contain the sequence motifs shown, or proposed, to be of functional importance in other organisms. Furthermore, secondary structures closely similar to phylogenetically proven models can be inferred from the T. thermophila data. Analysis of the snRNA sequences identifies three potential snRNA-snRNA base-pairing interactions, all of which are consistent with available phylogenetic data. Two of these occur between U2 and U6, whereas the third occurs between U1 and U2. The proposed interactions locate the intron 5' splice-site close to the intron branch-site nucleotide as well as to the most highly conserved domain of U6. We envisage that these interactions may facilitate the first step of pre-mRNA splicing.

A phylogenetic study of U4 snRNA reveals the existence of an evolutionarily conserved secondary structure corresponding to 'free' U4 snRNA

The nucleotide sequence of Physarum polycephalum U4 snRNA*** was determined and compared to published U4 snRNA sequences. The primary structure of P polycephalum U4 snRNA is closer to that of plants and animals than to that of fungi. But, both fungi and P polycephalum U4 snRNAs are missing the 3' terminal hairpin and this may be a common feature of lower eucaryote U4 snRNAs. We found that the secondary structure model we previously proposed for 'free' U4 snRNA is compatible with the various U4 snRNA sequences published. The possibility to form this tetrahelix structure is preserved by several compensatory base substitutions and by compensatory nucleotide insertions and deletions. According to this finding, association between U4 and U6 snRNAs implies the disruption of 2 internal helical structures of U4 snRNA. One has a very low free energy, but the other, which represents one-half of the helical region of the 5' hairpin, requires 4 to 5 kcal to be open. The remaining part of the 5' hairpin is maintained in the U4/U6 complex and we observed the conservation, in all U4 snRNAs studied, of a U bulge residue at the limit between the helical region which has to be melted and that which is maintained. The 3' domain of U4 snRNA is less conserved in both size and primary structure than the 5' domain; its structure is also more compact in the RNA in solution. In this domain, only the Sm binding site and the presence of a bulge nucleotide in the hairpin on the 5' side of the Sm site are conserved throughout evolution.

Drosophila melanogaster genes for U1 snRNA variants and their expression during development

We have cloned and characterized a complete set of seven U1-related sequences from Drosophila melanogaster. These sequences are located at the three cytogenetic loci 21D, 82E, and 95C. Three of these sequences have been previously studied: one U1 gene at 21D which encodes the prototype U1 sequence (U1a), one U1 gene at 82E which encodes a U1 variant with a single nucleotide substitution (U1b), and a pseudogene at 82E. The four previously uncharacterized genes are another U1b gene at 82E, two additional U1a genes at 95C, and a U1 gene at 95C which encodes a new variant (U1c) with a distinct single nucleotide change relative to U1a. Three blocks of 5' flanking sequence similarity are common to all six full length genes. Using specific primer extension assays, we have observed that the U1b RNA is expressed in Drosophila Kc cells and is associated with snRNP proteins, suggesting that the U1b-containing snRNP particles are able to participate in the process of pre-mRNA splicing. We have also examined the expression throughout Drosophila development of the two U1 variants relative to the prototype sequence. The U1c variant is undetectable by our methods, while the U1b variant exhibits a primarily embryonic pattern reminiscent of the expression of certain U1 variants in sea urchin, Xenopus, and mouse.

U1 small nuclear RNA from Schizosaccharomyces pombe has unique and conserved features and is encoded by an essential single-copy gene

We have cloned, sequenced, and disrupted the gene encoding U1 small nuclear RNA (snRNA) in the fission yeast Schizosaccharomyces pombe. This RNA is close in size and exhibits a high degree of secondary structure homology to human U1 RNA. There exist two regions of extended primary sequence identity between S. pombe and human U1 RNAs; the first comprises nucleotides involved in hydrogen bonding to 5' splice junctions, and the second is a single-stranded region which, in the human snRNA, forms part of the A protein binding site. S. pombe U1 lacks two nucleotides just following the 5' cap structure which are present in all other U1 homologs examined to date, and the region which corresponds to the binding site for the human 70K protein (molecular weight of 55,000) is more divergent than in other organisms. A putative upstream transcription signal is conserved in sequence and location among all loci encoding spliceosomal snRNAs in S. pombe with the exception of U6. Disruption of the single-copy U1 gene, designated snu1, reveals that this RNA is indispensable for viability.

U1 small nuclear RNA from Schizosaccharomyces pombe has unique and conserved features and is encoded by an essential single-copy gene

We have cloned, sequenced, and disrupted the gene encoding U1 small nuclear RNA (snRNA) in the fission yeast Schizosaccharomyces pombe. This RNA is close in size and exhibits a high degree of secondary structure homology to human U1 RNA. There exist two regions of extended primary sequence identity between S. pombe and human U1 RNAs; the first comprises nucleotides involved in hydrogen bonding to 5' splice junctions, and the second is a single-stranded region which, in the human snRNA, forms part of the A protein binding site. S. pombe U1 lacks two nucleotides just following the 5' cap structure which are present in all other U1 homologs examined to date, and the region which corresponds to the binding site for the human 70K protein (molecular weight of 55,000) is more divergent than in other organisms. A putative upstream transcription signal is conserved in sequence and location among all loci encoding spliceosomal snRNAs in S. pombe with the exception of U6. Disruption of the single-copy U1 gene, designated snu1, reveals that this RNA is indispensable for viability.