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At least 307 records · Page 17Linked to original sources

PubMed2000

The hormone-sensitive lipase gene is transcribed from at least five alternative first exons in mouse adipose tissue.

Hormone-sensitive lipase (HSL) mediates triglyceride hydrolysis in adipocytes, in which its expression varies with physiological stress and is controlled posttranslationally and transcriptionally. We sequenced the mouse HSL gene for 8.2 kb upstream of the translation start codon and studied the steady-state HSL mRNA levels in mouse adipose tissue. In 50 clones derived from primer extension and PCR of mouse adipose cDNA, we found five distinct 5' extremities that correspond to distinct exons in genomic DNA. Exon A is located approximately 7 kb 5' to the HSL translation start site. Exons B. C, and D are clustered 1.5-2 kb upstream, and the previously described exon 1 is immediately upstream and contiguous with the previously described HSL translation start site. Exon A is located -7 kb upstream and contains an in-frame methionine codon that could potentially generate another HSL isoform with 43 additional N-terminal residues. cDNA clones containing the newly described exons suggested that each exon has several transcription start sites but that all splice to an acceptor site located 20 nt upstream of the translation initiation codon in exon 1. HSL transcription in mouse adipose tissue originates from multiple sites in the 7-kb region between exon A and exon 1, with peaks at exon C (50-70% of HSL transcripts), exon 1 (5-30%), and exon A (approximately 10%). There are multiple potential transcription factor-binding elements upstream of each exon, suggesting the possibility of differential transcriptional regulation of HSL in different tissues and under various physiologic conditions.

Adipose Tissue↗

PubMed2001

Developmental regulation of alternative exon usage in the house fly Vssc1 sodium channel gene.

Sequence analysis of cDNA clones amplified by PCR from house fly ( Musca domestica L.) Vssc1 voltage-sensitive sodium channel alpha subunit transcript templates identified 11 putative alternatively spliced exons. Nine of these corresponded to the 7 optional exons (designated a, b, e, f, h, i, and j) and 2 mutually exclusive exons (designated c/d) identified previously in the orthologous para sodium channel alpha subunit genes of Drosophila melanogaster and Drosophila virilis, whereas two segments represented new mutually exclusive exons in Vssc1 (designated k/l) located in a region not previously identified as a site of alternative splicing in para. Diagnostic PCR assays on individual Vssc1 cDNA templates detected the presence or absence of each putative alternative exon in multiple partial cDNAs (42-96 individual clones per cDNA pool) from newly emerged first instar larvae, pupae, day 1 adult heads, and day 1 adult bodies. Exons h and i were present in all cDNA clones from all developmental stages. Exon d was also present in all clones from all developmental stages that encoded full-length amino acid sequences; however, 1 of 42 clones from adult head contained an exon c-like segment in which the coding sequence was terminated by a premature stop codon. In contrast, the frequencies of exons a, b, e, f, j, k, and l differed between developmental stages and adult anatomical regions. Analysis of the Vssc1 region containing alternative exons a, b, c/d, e, f, h, and i as a single amplified cDNA segment identified nine Vssc1 splice variants involving these exons. The splice variant containing exons a, d, h, and i was the most abundant form in all cDNA pools examined, but the observed patterns of splice variant expression were specific to each developmental stage and adult anatomical region. Our results document the strong conservation of alternative exon location and structure between the Vssc1 gene of the house fly and the para gene of D. melanogaster but identify marked differences in exon usage between these species.

Alternative Splicing↗

PubMed1998

The multiple untranslated first exons and promoters system of the oestrogen receptor gene in the brain and peripheral tissues of the rat and monkey and the developing rat cerebral cortex.

Recent studies on the human oestrogen receptor (ER) gene have revealed the complex system with the multiple untranslated first exons and promoters in the ER gene expression. Little information is however available on the system in the ER gene of the rat or nonhuman primate. The rat genomic library was first screened by the rat ER cDNA (0-1) probe. One of the four positive clones (lambda rEgE1) was subcloned and sequenced. The nucleotide sequence was found to contain the exon 0, the intron 0, and the exon 1 with its 3'-ends. The novel untranslated first exons, the exon ON and the exon OS, were further identified. These results indicated the presence of at least four subtypes of the rat ER mRNAs; the messages transcribed from promoter P-0 (ER mRNA (0-1)), putative promoter P-1 (ER mRNA (1-1)), promoter P-ON (ER mRNA (ON-1)) and promoter P-OS (ER mRNA (OS-1)). The P-O- or P-1 driven message (0-1) or (1-1) appeared to be expressed most strongly in major oestrogen central- (anterior pituitary, AP, hypothalamus-preoptic area, HPOA, and amygdala, AMG) and peripheral targets (uterus and ovary). The message (ON-1) was strongly expressed in the liver and kidney, but not in the HPOA, AMG, cerebral cortex, CC, and cerebellum, Ce. The OS-1 message was expressed variably but generally in the tissues examined except for the CC and Ce. Thus, the region- and tissue specific expression of the rat ER gene is likely to be regulated by the multiple untranslated exons and promoters system. Furthermore, when the ER mRNA subtypes were examined in the rat neonatal CC where the ER protein level rose transiently, considered as a model for the development of the ER or progestin receptor A and B isoforms, the expression of the ER mRNAs seemed to be differential postnatally, implicating some stage dependent usage of the promoters in the development. In the monkey, we identified the untranslated first exon OS, the homologue of the rat exon OS. Interestingly, the exon C was found to consist of two different exons, the exon OK and the exon OG. By the alternative usage of the promoters and the alternative splicing, at least six ER mRNA subtypes, that is, ER mRNAs (0-1), (1-1), (OS-1), (OS-OG-1), (OK-1) and (OK-OG-1) were identified in the monkey tissues. These messages were also differentially distributed in the monkey brain and other tissues. It was noteworthy that the P-OK driven messages were expressed almost exclusively in the monkey liver. These results have suggested that the systems of the multiple untranslated first exons and promoters and the alternative splicing are involved in the regulation of the region- and tissue specific expression of the ER gene in the brain and peripheral tissues of the rat and monkey. Stage-related usage of the promoters was also suggested in the ER gene expression in the CC of the postnatal rat in development.

Amino Acid Sequence↗

PubMed2005

Differential expression of CD45 isoforms is controlled by the combined activity of basal and inducible splicing-regulatory elements in each of the variable exons.

The human CD45 gene encodes five isoforms of a transmembrane tyrosine phosphatase that differ in their extracellular domains as a result of alternative splicing of exons 4-6. Expression of the CD45 isoforms is tightly regulated in peripheral T cells such that resting cells predominantly express the larger CD45 isoforms, encoded by mRNAs containing two or three variable exons. In contrast, activated T cells express CD45 isoforms encoded by mRNAs lacking most or all of the variable exons. We have previously identified the sequences within CD45 variable exon 4 that control its level of inclusion into spliced mRNAs. Here we map the splicingregulatory sequences within CD45 variable exons 5 and 6. We show that, like exon 4, exons 5 and 6 each contain an exonic splicing silencer (ESS) and an exonic splicing enhancer (ESE), which together determine the level of exon inclusion in naïve cells. We further demonstrate that the primary activation-responsive silencing motif in exons 5 and 6 is homologous to that in exon 4 and, as in exon 4, binds specifically to the protein heterogeneous nuclear ribonucleoprotein L. Together these studies reveal common themes in the regulation of the CD45 variable exons and provide a mechanistic explanation for the observed physiological expression of CD45 isoforms.

Alternative Splicing↗

PubMed2001

Mouse connexin 45: genomic cloning and exon usage.

Connexin 45 is a gap junction protein that is prominent in early embryos and is widely expressed in many mature cell types. To elucidate its gene structure, expression, and regulation, we isolated mouse Cx45 genomic clones. Alignment of the genomic DNA and cDNA sequences revealed the presence of three exons and two introns. The first two exons contained only 5' untranslated sequences, while exon 3 contained the remaining 5' UTR, the entire coding region, and the 3' UTR. An RT-PCR with exon-specific primers was utilized to examine exon usage in F9 mouse embryonal carcinoma cells and adult mouse tissues. In all samples, PCR products amplified using exon 2/exon 3 or exon 3/exon 3 primer pairs were much more abundant than products produced using exon 1/exon 2 or exon 1/exon 3 primer pairs, suggesting that Cx45 mRNAs containing exon 1 were relatively rare compared with mRNAs containing the other exons. Rapid amplification of cDNA ends (5'-RACE) was performed using antisense primers from within exon 3 and template RNA prepared from F9 cells or from adult mouse kidney. We obtained multiple RACE products from both templates, including products that contained all three exons and were spliced identically to the cDNA. However, clones were also isolated (from kidney) that began within the region previously identified as intron 1 and continued upstream with a sequence identical to the cDNA, including splicing to exon 3. These results show that mouse Cx45 has a gene structure that differs from that of previously studied connexins and allows the production of heterogeneous Cx45 mRNAs with differing 5' UTRs. These differences might contribute to regulation of Cx45 protein levels by modulating mRNA stability or translational efficiency.

3' Untranslated Regions↗

PubMed2003

A frameshifting mutation in CHRNE unmasks skipping of the preceding exon.

A frameshifting 7 bp deletion (epsilon553del7) in exon 7 of CHRNE encoding the acetylcholine receptor epsilon subunit, observed in seven congenital myasthenic syndrome patients, enhances expression of an aberrantly spliced transcript that skips the preceding 101 bp exon 6. To recapitulate the aberrant splicing, we cloned the entire CHRNE spanning 12 exons and 11 introns and expressed it in COS cells. Scanning mutagenesis revealed that epsilon553del7 does not disrupt an exonic splicing enhancer. Inhibition of protein synthesis and of nonsense-mediated mRNA decay (NMD) by anisomycin shows that even wild-type CHRNE produces an exon 6-skipped transcript, and that even epsilon553del7-CHRNE yields a normally spliced transcript. Both transcripts, however, are degraded by NMD due to a premature stop codon. In contrast, the normally spliced transcript from wild-type CHRNE and the exon 6-skipped transcript from epsilon553del7-CHRNE carry no premature stop codon and hence are immune to NMD. Optimization of splicing signals for exon 6 prevents it being skipped even in the presence of anisomycin and/or epsilon553del7, indicating that inherently weak splicing signals for exon 6 account for its skipping. We suggest that a similar mechanism probably operates in other genes in skipping of remote exons. The presence of weak splicing signals for exon 6 also prompted us to search for mutations in exon 6 that disrupt an exonic splicing enhancer. Indeed, we found that epsilonEF157V and epsilonE154X in exon 6, observed in two other patients, caused aberrant splicing of exon 6.

Adolescent↗

PubMed1996

During in vivo maturation of eukaryotic nuclear mRNA, splicing yields excised exon circles.

Circular splicing has already been described on nuclear pre-mRNA for certain splice sites far apart in the multi exonic ETS-1 gene and in the single 1.2 kb exon of the Sry locus. To date, it is unclear how splice site juxtaposition occurs in normal and circular splicing. The splice site selection of an internal exon is likely to involve pairing between splice sites across that exon. Based on this, we predict that, albeit at low frequency, internal exons yield circular RNA by splicing as an error-prone mechanism of exon juxtaposition or, perhaps more interestingly, as a regulated mechanism on alternative exons. To address this question, the circular exon formation was analyzed at three ETS-1 internal exons (one alternative spliced exon and two constitutive), in human cell line and blood cell samples. Here, we show by RT-PCR and sequencing that exon circular splicing occurs at the three individual exons that we examined. RNase protection experiments suggest that there is no correlation between exon circle expression and exon skipping.

Base Sequence↗

PubMed1999

Complete genomic organization of futb encoding a bovine alpha 3-fucosyltransferase: exons in human orthologous genes emerged from ancestral intronic sequences.

The futb gene, which encodes the first bovine alpha 3-fucosyltransferase described, consists of five exons (a, b, c, d, and e), the first four being located upstream of the coding exon e. Together with the four introns (i1, i2, i3, and i4) they span a DNA genomic sequence of about 10 kb. futb is expressed as four tissue-specific transcripts differing by their 5'-untranslated (5'-UT) regions, but only one transcript includes all exons, while the other three begin at internal sites of exon c. A short sequence of the latter is homologous to distinct 5'-UT exons of FUT6 (alpha 3-fucosylation) and FUT3 (alpha 4-fucosylation), two human genes whose coding sequences are homologous to coding exon e of futb. Upstream and downstream, the exon c intronic regions of the bovine gene are homologous to 5'-UT exons of human FUT3 (exon B) and FUT6 (exons A, B, and C). Thus, exon c appears to be the most ancestral 5'-UT exon known among these alpha 3-fucosyltransferase genes. Interestingly, distribution of short interspersed nuclear elements in the i3 intron adjacent to exon c reveals that two repeat sequences are joined to form a reverse-transcriptase-like encoding sequence highly homologous to an open reading frame located at the 3' end of the bovine gamma globin gene. This organization suggests that duplication events that have generated the primate FUT3-FUT5-FUT6 cluster might have occurred through a long-interspersed-nuclear-element-based mechanism of unequal crossing over, as described for the globin cluster. Complete organization of the bovine futb gene reveals that in addition to duplication events, the lineage leading to primate FUT3, FUT5, and FUT6 genes results from rearrangements of intronic sequences which have created for each new gene specific regulatory 5'-UT exonic sequences.

3' Untranslated Regions↗

PubMed1992

Alternative splicing of a human alpha-tropomyosin muscle-specific exon: identification of determining sequences.

The human alpha-tropomyosin gene hTMnm has two mutually exclusive versions of exon 5 (NM and SK), one of which is expressed specifically in skeletal muscle (exon SK). A minigene construct expresses only the nonmuscle (NM) isoform when transfected into COS-1 cells and both forms when transfected into myoblasts. Twenty-four mutants were produced to determine why the SK exon is not expressed in COS cells. The results showed that exons NM and SK are not in competition for splicing to the flanking exons and that there is no intrinsic barrier to splicing between the exons. Instead, exon SK is skipped whenever there are flanking introns. Splicing of exon SK was induced when the branch site sequence 70 nucleotides upstream of the exon was mutated to resemble the consensus and when the extremities of the exon itself were changed to the corresponding NM sequence. Precise swaps of the NM and SK exon sequences showed that the exon sequence effect was dominant to that of intron sequences. The mechanism of regulation appears to be unlike that of other tropomyosin genes. We propose that exclusion of exon SK arises because its 3' splicing signals are weak and are prevented by an exon-specific repressor from competing for splice site recognition.

Base Sequence↗

PubMed1996

Interactions among SR proteins, an exonic splicing enhancer, and a lentivirus Rev protein regulate alternative splicing.

We examine here the roles of cellular splicing factors and virus regulatory proteins in coordinately regulating alternative splicing of the tat/rev mRNA of equine infectious anemia virus (EIAV). This bicistronic mRNA contains four exons; exons 1 and 2 encode Tat, and exons 3 and 4 encode Rev. In the absence of Rev expression, the four-exon mRNA is synthesized exclusively, but when Rev is expressed, exon 3 is skipped to produce an mRNA that contains only exons 1, 2, and 4. We identify a purine-rich exonic splicing enhancer (ESE) in exon 3 that promotes exon inclusion. Similar to other cellular ESEs that have been identified by other laboratories, the EIAV ESE interacted specifically with SR proteins, a group of serine/arginine-rich splicing factors that function in constitutive and alternative mRNA splicing. Substitution of purines with pyrimidines in the ESE resulted in a switch from exon inclusion to exon skipping in vivo and abolished binding of SR proteins in vitro. Exon skipping was also induced by expression of EIAV Rev. We show that Rev binds to exon 3 RNA in vitro, and while the precise determinants have not been mapped, Rev function in vivo and RNA binding in vitro indicate that the RNA element necessary for Rev responsiveness overlaps or is adjacent to the ESE. We suggest that EIAV Rev promotes exon skipping by interfering with SR protein interactions with RNA or with other splicing factors.

Alternative Splicing↗

PubMed1991

Regulation of start site usage in the leader exons of the rat insulin-like growth factor-I gene by development, fasting, and diabetes.

Rat insulin-like growth factor-I (IGF-I) mRNAs with different 5'-untranslated region/prepeptide coding sequences result from transcription initiation in one of two leader exons. While not altering the mature IGF-I coding sequence, these different leaders potentially encode two distinct IGF-I prepeptides, one of 48 amino acids (exon 1) and one of 32 amino acids (exon 2). Within exon 1, transcription initiation is dispersed (i.e. occurs over a approximately 350-basepair region), while within exon 2, it is highly localized. A fourth exon 1 start site, residing only approximately 30 basepairs from its 3' end, is suggested on the basis of RNase protection assays; its use would produce an mRNA encoding a third distinct IGF-I leader peptide of 22 amino acids. We have determined that during postnatal development, and as a result of insulinopenic diabetes and fasting, choice of transcription start sites within exon 1 in the liver is coordinately regulated, i.e. use of all start sites increased during development and decreased in the two catabolic states. Transcription initiation at the single major site within exon 2 was also reduced in diabetes and fasting. Insulin replacement therapy and refeeding restored the levels of all transcripts coordinately. During postnatal development, however, transcripts initiating within exon 2 exhibited a different developmental profile than did exon 1 transcripts, increasing especially at the onset of GH-dependent linear growth. In liver, therefore, negative regulation of exon 1 and exon 2 transcription start site usage occurs in catabolic states, while in development, differential regulation of exon 1 and exon 2 transcription start sites occurs.

Aging↗

PubMed1993

Characterization of the mouse thyrotrophin-releasing hormone receptor gene: an exon corresponds to a deletion in the rat cDNA.

The cloning and characterization of the mouse TRH receptor (TRH-R) gene revealed an untranslated exon (exon 1), a single intron and an upstream dinucleotide repeat sequence (d(TG)16.d(AG)21) in the 5' untranslated region (UTR). The coding region was contained almost entirely on a second exon (exon 2), with the final amino acid and stop codon at the COOH terminus of the gene encoded by a third exon (exon 3) flanked by two introns. The 3' UTR was contained on the remainder of exon 3 and on the final exon (exon 4). Exon 3 (228 bp) corresponds exactly to a 228 bp deletion that exists in the rat TRH-R cDNA, but not in the mouse cDNA. The mouse TRH-R cDNA encodes a protein of 393 amino acids which is 96% homologous to the rat TRH-R protein of 412 amino acids, but is 19 amino acids shorter at its COOH terminus. The coding sequence for these 19 amino acids (plus 1 extra amino acid) does exist in the mouse TRH-R gene, but the sequence is encoded by exon 4, separated from the rest of the coding region by the stop codon and 223 bp of 3' UTR on exon 3. Splicing of exon 3 in the mouse TRH-R gene would remove the last amino acid, the stop codon and the 223 bp of 3' UTR, allowing transcription to continue into the 3' UTR on exon 4, which encodes the 19 extra amino acids found in the rat cDNA.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

PubMed2001

Alu elements in human growth hormone receptor gene 5' untranslated region exons.

The human growth hormone receptor (hGHR) is encoded by exons 2-10 of the hGHR gene on chromosome 5p13.1-p12. There are several different 5' untranslated region (5'UTR) variants of hGHR mRNA (V1-V9) that all encode the same protein. We have recently mapped the V1-V9 5'UTR sequences within 40 kb of the 5' flanking region of the hGHR gene. Seven of the exons are clustered within two small modules, module A (V2-V9-V3) and module B (V7-V1-V4-V8), approximately 38 kb and approximately 18 kb respectively upstream of exon 2 of the coding region; V6 lies midway between the two modules and V5 is adjacent to exon 2. We now report the existence of two subvariant V3 exons, one upstream of module A (exon V3b) and one midway between module B and exon 2 (exon V3a/b). Both have sequences homologous to Alu elements. In addition, we determined the alternative splicing mechanisms that produce three different mRNAs from these exons: V3c (from the V3 exon in module A) or V3a and V3b (from a combination of exon V3 and the Alu-containing V3 subvariant exons). hGHR expression is under developmental- and tissue-specific regulation: module A-derived mRNAs are widely expressed in human tissues, while module B-derived mRNAs are only detectable in postnatal liver. Expression of the variant V3 mRNAs is similar to those from module A, being produced ubiquitously in human fetal and postnatal tissues, with V3c always the major variant detected. The Alu-containing mRNAs (V3a and V3b) are also detectable in baboon and rhesus tissues, in accordance with the finding of Alu elements throughout the primate genome. In summary, we have mapped the relative locations of two new 5'UTR exons within the 5' flanking region of the hGHR gene and described the derivation and expression patterns for two variant hGHR mRNAs from these primate-specific exons. The introduction of Alu elements has contributed to the evolution of the primate GHR gene as a highly complex transcriptional unit.

5' Untranslated Regions↗

PubMed1996

An intron splicing enhancer containing a G-rich repeat facilitates inclusion of a vertebrate micro-exon.

The average length of a vertebrate axon is approximately 130 nt. Decreasing the size of an internal axon to less than 51 nt induces axon skipping, implying a minimal size for exons. A few constitutively included internal exons, however, are extremely small. To investigate if such micro-exons require special mechanisms for their inclusion, we studied the sequences necessary for inclusion of a 6-nt axon from chicken cardiac troponin T (cTNT). In vivo, the cTNT micro-exon was not included in mRNA unless accompanied by a 134-nt sequence located next to the micro-exon in the downstream intron. Increasing the length of the micro-exon alleviated the requirement for the intron element, indicating that the lack of inclusion of the micro-exon in the absence of a facilitating sequence was due to its small size, rather than suboptimal splice sites. The intron element contained six copies of a G-rich 7-nt sequence. Multimers of the repeat supported exon inclusion, indicating that the repeat sequence is an important part of the intron element. The entire intron element activated inclusion of a heterologous 7-nt exon, suggesting that the intron element is a general enhancer for the splicing of micro-exons. In vitro, the intron element and the repeated sequence facilitated splicing of a heterologous exon. Because of the ability of the cTNT intron element to facilitate the splicing of heterologous exons, we have termed the element an intron splicing enhancer (ISE). Interestingly, the ISE demonstrated position independence in that it facilitated inclusion of the heterologous micro-exon when placed either upstream or downstream of the micro-exon. In vitro, the ISE or copies of the ISE G-rich repeat stimulated splicing of an adjacent intron. The ISE thus becomes one of only a few characterized ISEs containing a G-rich repeat and the first to work both upstream and downstream of a target axon.

3T3 Cells↗

PubMed2003

Effects of GC content and mutational pressure on the lengths of exons and coding sequences.

It has been hypothesized that the length of an exon tends to increase with the GC content because stop codons are AT-rich and should occur less frequently in GC-rich exons. This prediction assumes that mutation pressure plays a significant role in the occurrence and distribution of stop codons. However, the prediction is applicable not to all exons, but only to the last coding exon of a gene and to single-exon CDS sequences. We classified exons in multiexon genes in eight eukaryotic species into three groups-the first exon, the internal, and the last exon-and computed the Spearman correlation between the exon length and the percentage GC (%GC) for each of the three groups. In only five of the species studied is the correlation for the last coding exon greater than that for the first or internal exons. For the single-exon CDS sequences, the correlation between CDS length and %GC is mostly negative. Thus, eukaryotic genomes do not support the predicted relationship between exon length and %GC. In prokaryotic genomes, CDS length and %GC are positively correlated in each of the 68 completely sequenced prokaryotic genomes in GenBank with genomic GC contents varying from 25 to 68%, except for the wall-less Mycoplasma genitalium and the syphilis pathogen Treponema pallidum. Moreover, the average CDS length and the genomic GC content are also positively correlated. After correcting for genome size, the partial correlation between the average CDS length and the genomic GC content is 0.3217 ( p < 0.025).

Animals↗

PubMed1996

Tissue-specific splicing of two mutually exclusive exons of the chicken beta-tropomyosin pre-mRNA: positive and negative regulations.

Alternative splicing of premessenger RNA (pre-mRNA) is a widespread process used in higher eucaryotes to regulate gene expression. A single primary transcript can generate multiple proteins with distinct functions in a tissue- and/or developmental-specific manner. A central question in alternative splicing concerns the selection of splice sites in different cell environments. In this review, we present our results on the alternative splicing of the chicken beta-tropomyosin gene which provides an interesting model for understanding mechanisms involved in splice site selection. The beta-tropomyosin gene contains in its central portion a pair of exons (6A and 6B) that are used mutually exclusively in a tissue and developmental stage-specific manner. Exon 6A is present in mRNA of non-muscle and smooth muscle tissues while exon 6B is only present in mRNA of skeletal muscle. Regulation of both exons is necessary to ensure specific expression of beta-tropomyosin gene in non-muscle cells. Several cis-acting elements involved in the repression of exon 6B and activation of exon 6A have been identified. In addition, we show that the tissue-specific choice of exon 6A is mediated through interaction with a specific class of splicing factors, the SR proteins. In the last part of this review we will focus on possible mechanisms needed to switch to exon 6B selection in skeletal muscle tissue. We propose that tissue-specific choice of exon 6B involves down regulation of exon 6A and activation of exon 6B. A G-rich enhancer sequence downstream of exon 6B has been defined that is needed for efficient recognition of the exon 6B 5' splice site. Moreover, we suggest that alteration of the ratio between proteins of the SR family contributes to tissue-specific splice site selection.

Animals↗

PubMed1996

Existence and expression of the untranslated first exon of aromatase mRNA in the rat brain.

Tissue-specific expression of aromatase activity and mRNA occurs by alternative utilization of multiple untranslated first exons and promoters in the human. The major transcript in the human brain contains the brain-specific first exon, "exon I-f". However, few reports on the untranslated first exon of aromatase mRNA in the rat brain have been available so far. In the present study, we investigated the existence and expression of exon I-f in the rat brain to elucidate the mechanism of the tissue-specific expression of the brain aromatase. Total RNA extracted from amygdala (AMY) was subjected to a reverse transcription-polymerase chain reaction (RT-PCR). The nucleotide sequence of the RT-PCR product had 89.4% homology to the corresponding region of exon I-f of the human aromatase cDNA. It was indicated that the major transcript in the rat AMY contained exon I-f by the use of a rapid amplification of cDNA ends (RACE). Furthermore, in order to determine the distribution of the aromatase mRNA with exon I-f, total RNAs from the hypothalamus-preoptic area (HPOA), AMY, testis and ovary were analysed by RT-PCR using the primers specific for the mouse exon I-f and the primers for the rat exon III-V. Significant levels of PCR products were found in all tissues with the highest level being in the ovary, using the primers for exon III-V. On the other hand, using the primers for exon I-f, the levels of signals from HPOA and AMY were higher than those from the testis and ovary. These results suggest that tissue-specific expression of aromatase mRNA occurs by an alternative utilization of multiple promoters in the rat, as in the human. It should be noted that minor transcripts containing exon I-f were observed in the testis and ovary.

Animals↗

PubMed2004

Another face of the Treacher Collins syndrome (TCOF1) gene: identification of additional exons.

Treacher Collins syndrome (TCS) is characterized by an abnormality in craniofacial development during early embryogenesis. TCS is caused by mutations in the gene TCOF1, which encodes the nucleolar phosphoprotein treacle. Genetic and proteomic characterizations of TCS/treacle are based on the previously reported 26 exons of TCOF1. Here, we report the identification of 231-nucleotide (nt) exon 6A (between exons 6 and 7) and 108-nt exon 16A (between exons 16 and 17). Isoforms with exon 6A are up to 3.7-fold more abundant than alternatively spliced variants without exon 6A, but only minor isoforms contain exon 16A. Exon 6A encodes a peptide sequence containing basic and acidic domains similar to 10 other exons of TCOF1. Unlike the other exons, exon 6A encodes a nuclear localization signal (NLS) which does not, however, alter the nucleolar localization of full-length treacle. The discovery of exons 6A and 16A is relevant to mutational analysis of the TCOF1 gene in TCS patients, and to functional analysis of its gene product.

Amino Acid Sequence↗