SEARCH · PubMed Health

Results for “Introns”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 595 records · Page 33Linked to original sources

PubMed2003

Introns in gene evolution.

Introns are integral elements of eukaryotic genomes that perform various important functions and actively participate in gene evolution. We review six distinct roles of spliceosomal introns: (1) sources of non-coding RNA; (2) carriers of transcription regulatory elements; (3) actors in alternative and trans-splicing; (4) enhancers of meiotic crossing over within coding sequences; (5) substrates for exon shuffling; and (6) signals for mRNA export from the nucleus and nonsense-mediated decay. We consider transposable capacities of introns and the current state of the long-lasting debate on the 'early-or-late' origin of introns. Cumulative data on known types of contemporary exon shuffling and the estimation of the size of the underlying exon universe are also discussed. We argue that the processes central to introns-early (exon shuffling) and introns-late (intron insertion) theories are entirely compatible. Each has provided insight: the latter through elucidating the transposon capabilities of introns, and the former through understanding the importance of introns in genomic recombination leading to gene rearrangements and evolution.

Alternative Splicing↗

PubMed1991

Rat thymosin beta 4 gene. Intron-containing gene and multiple retroposons.

Thymosin beta 4 (T beta 4), a 43-residue peptide of uncertain function, is widely distributed in most tissues of vertebrates. Southern blot analysis demonstrated that the rat genome contains many closely related T beta 4 sequences. Two distinct T beta 4 sequences were isolated by screening a rat genomic DNA library. Analysis of these clones revealed that they represent T beta 4 retroposons; they lack introns and contain stretches of poly(A) sequence at their 3' ends and direct repeats flanking the cDNA-like sequences. In order to isolate a T beta 4 intron-containing gene, DNA fragments that include T beta 4 introns were generated by polymerase chain reaction, using rat genomic DNA as template. Subsequent Southern blot analysis of rat genomic DNA with intron-specific probes demonstrated the presence of a single T beta 4 intron-containing gene. Upon screening the rat genomic DNA library with an intron-specific probe, two overlapping clones of the T beta 4 intron-containing gene were isolated. Further characterization and sequence analysis showed that the rat T beta 4 intron-containing gene has a 2-kilobase pair-long transcription unit containing two introns. The transcription initiation site and putative regulatory elements of the promoter were identified.

Animals↗

PubMedDate not supplied

[Study of the minimum frequency of phase 2 introns].

A study has been made on the distribution of introns of different groups with respect to phases. It has been established that group II introns and nuclear introns have a similar minimum of relative frequency of phase 2 introns. Since the phase of introns is an extremely conservative index, the observed minimum is a trace of relic evolutionary processes. A sample of all known group I introns proved to be insufficient to obtain a valid characteristic of phase distribution. It has been shown that the picture observed in the phase distribution cannot be explained on the basis of the mobile properties of introns only. One of the probable explanations for the intron phase distribution nonuniformity is the process of exon shuffling. An assumption is made that group II introns originated at the early stages of evolution and were involved in the process of exon shuffling.

Animals↗

PubMed1993

Mutation of the conserved first nucleotide of a group II intron from yeast mitochondrial DNA reduces the rate but allows accurate splicing.

Group II introns have a phylogenetically conserved 5'-terminal pentanucleotide, -G1U2G3C4G5-, that resembles the conserved 5' end sequence of nuclear pre-mRNA introns. No functional interaction or catalytic role for the conserved G1 position has been proposed, although a tertiary structure involving -G3C4- has been implicated in splicing in vitro. We have analyzed splicing phenotypes both in vitro and in vivo for all three point mutants affecting guanosine at position 1 (G1) of intron 5 gamma from the COXI gene of yeast mitochondrial DNA. While all of these G1N substitutions slow splicing in vitro, G1C is clearly the most defective. All three mutant transcripts splice as accurately as the wild-type transcript, although the yield of lariat intron is reduced. The branched trinucleotide core includes the mutated position 1 nucleotide linked to the canonical branchpoint adenosine. The mutant lariats vary significantly in their susceptibility to the debranching activity from human cells. After wild-type, G1A was most sensitive, G1U was somewhat resistant, while G1C was highly resistant to debranching. These mutant lariats had normal ribozyme activity for promoting spliced exon reopening. The three mutant introns were transformed into otherwise normal yeast mitochondrial DNA. These mutants grow on nonfermentable carbon sources and splce aI5 gamma to yield excised intron lariat and mRNA. Nonetheless, each mutant splices with reduced efficiency, roughly parallel to their in vitro activity. In vivo, all three mutants accumulate both the pre-mRNA retaining intron 5 gamma and the lariat splicing intermediate containing intron and 3' exon. Clearly, this primary sequence element, shared with nuclear pre-mRNA introns, has a very different functional significance in group II splicing.

Base Sequence↗

PubMed1996

Functional analysis of an intron 3' splice site in Caenorhabditis elegans.

Caenorhabditis elegans introns typically lack both branch point and polypyrimidine tract consensus sequences utilized in other organisms for intron recognition. However, most introns have an unusually long, highly conserved consensus, UUUCAG/R, at the 3' splice site. This site can be recognized even when the -1G is changed to A. To determine how the 3' splice site is defined, we tested mutations in the sequence UUUCAA/A at the 3' splice site of the first intron of a test gene in vivo. Replacement of individual U's with A's or C's compromised splicing. When the sequence UUUCAA/AAG was tested, splicing occurred following both the -1A and the +3G, indicating that both UUUC and the AG contain 3' splice site information. When the sequence UUUCAA/AAA was tested, all splicing occurred following the -1A, suggesting that the UUUC contains sufficient information in the absence of an AG to specify the location of the splice site. In support of this idea, when point mutations were introduced into the UUUC, unspliced RNAs accumulated. Surprisingly, RNAs containing the mutant intron often contained the second, nonmutated intron as well, suggesting that interference with splicing of one intron can interfere with splicing of a second intron in the same pre-mRNA. The majority of these unspliced RNAs were degraded by the system responsible for degradation of transcripts containing nonsense mutations (smg), even though the intron contained no nonsense codon.

Animals↗

PubMed1996

Replacement of two non-adjacent amino acids in the S.cerevisiae bi2 intron-encoded RNA maturase is sufficient to gain a homing-endonuclease activity.

Two homologous group I introns, the second intron of the cyt b gene, from related Saccharomyces species differ in their mobility. The S.capensis intron is mobile and encodes the I-ScaI endonuclease promoting intron homing, whilst the homologous S.cerevisiae intron is not mobile, but functions as an RNA maturase promoting splicing. These two intron-encoded proteins differ by only four amino acid substitutions. Taking advantage of the remarkable similarity of the two intron open reading frames and using biolistic transformation of mitochondria, we show that the replacement of only two non-adjacent residues in the S.cerevisiae maturase carboxy-terminal sequence is sufficient to induce a homing-endonuclease activity without losing the splicing function. Also, we demonstrate that these two activities reside in the S.capensis bi2-encoded protein which functions in both splicing and intron mobility in the wild-type cells. These results provide new insight into our understanding of the activity and the evolution of group I intron-encoded proteins.

Amino Acid Sequence↗

PubMed1996

Exon 10 skipping caused by intron 10 splice donor site mutation in cholesteryl ester transfer protein gene results in abnormal downstream splice site selection.

Cholesteryl ester transfer protein (CETP) deficiency is the most common cause of hyperalphalipoproteinemia in Japan. However, the genetic basis of this disorder has not been fully characterized. We have studied a 49-year-old Japanese male presenting with total cholesterol, HDL-cholesterol, and apolipoprotein A-I levels of 300, 236, and 233 mg/dl, respectively, and total absence of CETP activity and mass in plasma. Sequence analysis of the patient's CETP gene revealed that the splice donor consensus GT was substituted by GG in intron 10 (intron 10 splice defect) and by AT in intron 14 (intron 14 splice defect). Restriction digestion of PCR-amplified DNA using NdeI and MaeIII established that the patient was a compound heterozygote for both gene defects. Sequencing of cDNA amplified by RT-PCR from the patient's monocyte-derived macrophage RNA demonstrated abnormal splicing with deletion of exon 10 as well as alternative splicing at a native AG site located 31 nucleotides 5' of the normal splice acceptor in intron 13. Thus, the intron 10 splice defect results in exon 10 skipping and the insertion of a 31 bp fragment between exon 13 and exon 14, which contains an in frame stop codon. The presence of abnormally spliced mRNA was further confirmed by amplification of patient cDNA using CETP specific primers. Abnormal splicing of exon 14 as a result of the intron 14 splice defect was not detected, indicating potential unstable CETP mRNA derived from that mutation. These findings demonstrate that a novel splice site mutation in intron 10 of the CETP gene results in the skipping of exon 10, as well as disruption of downstream splicing at intron 13 identifying a novel mechanism leading to CETP deficiency.

Base Sequence↗

PubMed1997

Naegleria nucleolar introns contain two group I ribozymes with different functions in RNA splicing and processing.

We have characterized the structural organization and catalytic properties of the large nucleolar group I introns (NaSSU1) of the different Naegleria species N. jamiesoni, N. andersoni, N. italica, and N. gruberi. NaSSU1 consists of three distinct RNA domains: an open reading frame encoding a homing-type endonuclease, and a small group I ribozyme (NaGIR1) inserted into the P6 loop of a second group I ribozyme (NaGIR2). The two ribozymes have different functions in RNA splicing and processing. NaGIR1 is an unusual self-cleaving group I ribozyme responsible for intron processing at two internal sites (IPS1 and IPS2), both close to the 5' end of the open reading frame. This processing is hypothesized to lead to formation of a messenger RNA for the endonuclease. Structurally, NaGIR2 is a typical group IC1 ribozyme, catalyzing intron excision and exon ligation reactions. NaGIR2 is responsible for circularization of the excised intron, a reaction that generates full-length RNA circles of wild-type intron. Although it is only distantly related in primary sequence, NaSSU1 RNA has a predicted organization and function very similar to that of the mobile group I intron DiSSU1 of Didymium, the only other group I intron known to encode two ribozymes. We propose that these twin-ribozyme introns define a distinct category of group I introns with a conserved structural organization and function.

Animals↗

PubMed1998

Characterization of a single group I intron in the 18S rRNA gene of the pathogenic fungus Histoplasma capsulatum.

A 425-bp insertion in Histoplasma capsulatum strain G186B, denoted as Hc.SSU.1, was identified as a group I intron, based on the presence of the conserved sequence elements P, Q, R and S and a predicted secondary structure consistent for group I introns. The Hc. SSU.1 sequence from strain G186B was identical to strain G184B but differed from strain FLs1 by five nucleotides. Hc.SSU.1 was most similar to the group I intron from the black mould Exophiala castellanii. Southern blot analysis suggests that the intron is not dispersed in the genome and that most, if not all 18S rRNA genes harbour the intron. Northern blots demonstrated absence of the intron from mature 18S rRNA. A Hc.SSU.1-specific PCR assay detected the intron in six of 37 isolates of Histoplasma. Hc.SSU.1-containing strains exhibited no significant differences in antimicrobial susceptibilities when compared to isolates not containing Hc.SSU.1. This investigation demonstrates the existence of group I intron sequences in the H. capsulatum genome and its evolutionary relationship among other group I intron sequences.

Base Sequence↗

PubMed1985

Complete sequence of a bovine type I cytokeratin gene: conserved and variable intron positions in genes of polypeptides of the same cytokeratin subfamily.

The complete sequence of a bovine gene encoding an epidermal cytokeratin of mol. wt. 54 500 (No VIb) of the acidic (type I) subfamily is presented, including an extended 5' upstream region. The gene (4377 bp, seven introns) which codes for a representative of the glycine-rich subtype of cytokeratins of this subfamily, is compared with genes coding for: another subtype of type I cytokeratin; a basic (type II) cytokeratin gene; and vimentin, a representative of another intermediate filament (IF) protein class. The positions of the five introns located within the highly homologous alpha-helix-rich rod domain are identical or equivalent, i.e., within the same triplet, in the two cytokeratin I genes. Four of these intron positions are also identical with intron sites in the vimentin gene, and three of these intron positions are identical or similar in the type I and type II cytokeratin subfamilies. On the other hand, the gene organization of both type I cytokeratins differs from that of the type II cytokeratin in the rod region in five intron positions and in the introns located in the carboxy-terminal tail region, with the exception of one position at the rod-tail junction. Remarkably, the two type I cytokeratins also differ from each other in the positions of two introns located at and in the region coding for the hypervariable, carboxy-terminal portion. The introns and the 5' upstream regions of the cytokeratin VIb gene do not display notable sequence homologies with the other IF protein genes, but sequences identical with--or very similar to--certain viral and immunoglobulin enhancers have been identified.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

PubMed1983

The intron of the mitochondrial 21S rRNA gene: distribution in different yeast species and sequence comparison between Kluyveromyces thermotolerans and Saccharomyces cerevisiae.

We have screened numerous different yeast species for the presence of sequences homologous to the intron of the mitochondrial 21S rRNA gene of Saccharomyces cerevisiae (intron r1) and found them in all Kluyveromyces species, some of the Saccharomyces species and none of the other yeasts tested. We have determined the nucleotide sequence of the r1-intron in K. thermotolerans and compared it with that of S. cerevisiae. The two introns are inserted at the same position within the 21S rRNA gene. They contain homologous internal open reading frames (ORFs) initiated at the same AUG codon which can be aligned over their entire length. Several silent multi-substitutions indicate that these intronic ORFs represent selectively conserved functional genes. Other intron segments, on the contrary, reveal short blocks of extensive homology separated by non-homologous stretches and/or additions-deletions. Comparison of our two yeast r1-introns with equivalent introns of N. crassa and A. nidulans mitochondria reveals that introns with very similar RNA secondary structures can accommodate different types of ORFs.

Base Sequence↗

PubMed1984

Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing--a review.

A widespread class of introns is characterized by a particular RNA secondary structure, based upon four conserved nucleotide sequences. Among such "class I" introns are found the majority of introns in fungal mitochondrial genes and the self-splicing intron of the large ribosomal RNA of several species of Tetrahymena. A model of the RNA secondary structure, which must underlie the self-splicing activity, is here evaluated in the light of data on 16 further introns. The main body or "core structure" of the intron always consists of the base-paired regions P3 to P9 with the associated single-stranded loops, with P2 present also in most cases. Two minority sub-classes of core structure occur, one of which is typical of introns in fungal ribosomal RNA. Introns in which the core structure is close to the 5' splice site all have an internal guide sequence (IGS) which can pair with exon sequences adjacent to the 5' and 3' splice sites to align them precisely, as proposed by Davies et al. [Nature 300 (1982) 719-724]. In these cases, the internal guide model allows us to predict correctly the exact location of splice sites. All other introns probably use other mechanisms of alignment. This analysis provides strong support for the RNA splicing model which we have developed.

Base Sequence↗

PubMed2006

Did group II intron proliferation in an endosymbiont-bearing archaeon create eukaryotes?

Martin & Koonin recently proposed that the eukaryote nucleus evolved as a quality control mechanism to prevent ribosome readthrough into introns. In their scenario, the bacterial ancestor of mitochondria was resident in an archaeal cell, and group II introns (carried by the fledgling mitochondrion) inserted into coding regions in the archaeal host genome. They suggest that if transcription and translation were coupled, and because splicing is expected to have been slower than translation, the effect of insertion would have been ribosome readthrough into introns, resulting in production of aberrant proteins. The emergence of the nuclear compartment would thus have served to separate transcription and splicing from translation, thereby alleviating this problem. In this article, I argue that Martin & Koonin's model is not compatible with current knowledge. The model requires that group II introns would spread aggressively through an archaeal genome. It is well known that selfish elements can spread through an outbreeding sexual population despite a substantial fitness cost to the host. The same is not true for asexual lineages however, where both theory and observation argue that such elements will be under pressure to reduce proliferation, and may be lost completely. The recent introduction of group II introns into archaea by horizontal transfer provides a natural test case with which to evaluate Martin & Koonin's model. The distribution and behaviour of these introns fits prior theoretical expectations, not the scenario of aggressive proliferation advocated by Martin & Koonin. I therefore conclude that the mitochondrial seed hypothesis for the origin of eukaryote introns, on which their model is based, better explains the early expansion of introns in eukaryotes. The mitochondrial seed hypothesis has the capacity to separate the origin of eukaryotes from the origin of introns, leaving open the possibility that the cell that engulfed the ancestor of mitochondria was a sexually outcrossing eukaryote cell.

Journal Article↗

PubMed1994

Ancient, highly polymorphic human major histocompatibility complex DQA1 intron sequences.

A 438 basepair intron 1 sequence adjacent to exon 2 in the human major histocompatibility complex DQA1 gene defined 16 allelic variants in 69 individuals from wide ethnic backgrounds. In contrast, the most variable coding region spanned by the 247 basepair exon 2 defined 11 allelic variants. Our phylogenetic human intron 1 tree derived by the Bootstrap algorithm reflects the same relative allelic relationships as the reported DQA1 exon 2 tree [Gyllensten and Erlich, Hum Immunol 36:1-10, 1989]. Thus 3' DQA1 intron 1 and exon 2 have cosegregated since divergence of the human races. Comparison of human alleles to a Rhesus monkey DQA1 first intron sequence found only 10 nucleotide substitutions unique to Rhesus, with the other 428 positions (98%) found in at least one human allele. This high degree of homology reflects the evolutionary stability of intron sequences since these two species diverged over 20 million years ago. Because more intron 1 alleles exist than exon 2 alleles, these polymorphic introns can be used to improve tissue typing for transplantation, paternity testing, and forensics and to derive more complete phylogenetic trees. These results suggest that introns represent a previously underutilized polymorphic resource.

Algorithms↗

PubMed1985

The structure of precursor mRNAs and of excised intron RNAs in chloroplasts of Euglena gracilis.

Partially spliced precursor mRNAs (pre-mRNAs) in the steady-state population of RNA from chloroplasts of Euglena gracilis were found by electron microscopy. The structure and the frequency of the pre-mRNAs of the psbA gene (the gene for the 32-kd protein of photosystem II), which is split by four introns in Euglena chloroplasts was analysed by electron microscopy. A chloroplast DNA (cpDNA) fragment containing the psbA gene from Euglena, was cloned into a pEMBL vector. The single-stranded recombinant phage DNA of the coding strand was prepared and hybridized with cpRNA. The majority of hybrids were formed with mature mRNA, but approximately 8% of the hybrids were formed with pre-mRNAs. The pre-mRNAs were either unspliced or incompletely spliced. A detailed analysis of the structure and the frequency of the pre-mRNAs of the psbA gene showed that the four introns are neither spliced out in a strictly random way, nor in a 5'-3' or 3'-5' direction. Introns 2 and 3 are preferentially spliced out first, intron 1 intermediately and intron 4 is generally spliced out last. However, this sequence is not a strict rule. We conclude that the introns can be spliced independently, each one at a different rate. The coding strand from a fragment of the psbA gene was separated and annealed with low mol. wt. cpRNA, which was isolated from an agarose gel. Small circular hybrids were found at the positions of the four introns, demonstrating for the first time covalently closed circular excised intron RNAs (iRNAs) in chloroplasts.

Animals↗

PubMed1993

Asymmetrical recognition and activity of the I-SceI endonuclease on its site and on intron-exon junctions.

Group I intron-encoded endonucleases represent a new class of double strand cutting endonucleases whose function is to initiate the homing of introns by generating double strand breaks in site-specific sequences. We have studied the mechanism of interaction of the I-SceI endonuclease with different DNA substrates derived from its natural site in the intron-less gene or from intron-exon junctions in the gene with an intron. We show that the enzyme recognizes its asymmetrical site with high affinity binding to the sequence corresponding to the downstream exon followed by binding to the upstream exon and catalysis of phosphodiester bond hydrolysis. Asymmetrical nicking activity is observed as an intermediate of the cleavage reaction. In the intron-containing gene, the enzyme recognizes the downstream intron-exon junction without any cleavage activity. This binding raises the possibility of a specific function of homing endonucleases in either gene expression or intron homing steps subsequent to DNA cleavage.

Base Sequence↗

PubMed1994

Evidence of selection for protein introns in the recAs of pathogenic mycobacteria.

Protein introns are recently discovered genetic elements whose intervening sequences are removed from a precursor protein by an unusual protein splicing reaction. This involves the excision of a central spacer molecule, the protein intron, and the religation of the amino- and carboxy-terminal fragments of the precursor. The recA gene of Mycobacterium tuberculosis contains one such element and we now show that the other major mycobacterial pathogen, Mycobacterium leprae, also possesses a protein intron in its recA, although other mycobacterial recA genes do not. However, these two protein introns are different in size, sequence and location of insertion of their coding sequences into the recAs of M. tuberculosis and M. leprae, indicating that acquisition of the protein introns has occurred independently in the two species, and thus suggesting that there has been selection for splicing in the maturation of RecA in the pathogenic mycobacteria. The M. leprae protein intron provides an example of conditional protein splicing, splicing occurring in M. leprae itself but not when expressed in Escherichia coli, unlike most previously described protein introns. These observations suggest that protein introns may perform a function for their host, rather than being just selfish elements.

Amino Acid Sequence↗

PubMed2000

Restoration of mRNA splicing by a second-site intragenic suppressor in the T4 ribonucleotide reductase (small subunit) self-splicing intron.

The nrdB gene of bacteriophage T4 codes for the small subunit of ribonucleotide reductase and contains a 598-base self-splicing intron which is closely related to other group I introns of T4 and eukaryotes. Thirty-one mutants causing splicing defects in the nrdB intron were isolated. Twenty-three EMS-induced revertants for these 31 primary mutants were isolated by the strategic usage of the white halo plaque phenotype. We mapped these revertants by marker rescue using subclones of the nrdB gene. Some of these second-site mutations mapped to regions currently predicted by the secondary structure model of the nrdB intron. One of these suppressor mutants (nrdB753R) was found to be intragenic by marker rescue with the whole nrdB gene. However, this mutation failed to map within the nrdB intron. Splicing assays showed that this pseudorevertant restored splicing proficiency of the nrdB primary mutation to almost wild-type conditions. This is the first example of a mutation within the exons of a gene containing a self-splicing intron that is capable of restoring a self-splicing defect caused by a primary mutation within the intron. In addition, two other suppressor mutations are of interest (nrdB429R and nrdB399R). These suppressors were able to restore their primary 5' defect but in turn create a 3' splicing defect. Both of these revertants mapped in different regions of the intron with respect to their primary mutations.

Bacteriophage T4↗