scholarly journals Trans-acting Factors Required for Inclusion of Regulated Exons in the Ultrabithorax mRNAs of Drosophila melanogaster

Genetics ◽  
1999 ◽  
Vol 151 (4) ◽  
pp. 1517-1529 ◽  
Author(s):  
James M Burnette ◽  
Allyson R Hatton ◽  
A Javier Lopez
Keyword(s):  
Drosophila Melanogaster ◽  
Alternative Splicing ◽  
P Element ◽  
Splicing Factors ◽  
Loss Of Function ◽  
Large Collection ◽  
Splicing Pattern ◽  
Alternatively Spliced ◽  
Hypomorphic Alleles

Abstract Alternatively spliced Ultrabithorax mRNAs differ by the presence of internal exons mI and mII. Two approaches were used to identify trans-acting factors required for inclusion of these cassette exons. First, mutations in a set of genes implicated in the control of other alternative splicing decisions were tested for dominant effects on the Ubx alternative splicing pattern. To identify additional genes involved in regulation of Ubx splicing, a large collection of deficiencies was tested first for dominant enhancement of the haploinsufficient Ubx haltere phenotype and second for effects on the splicing pattern. Inclusion of the cassette exons in Ubx mRNAs was reduced strongly in heterozygotes for hypomorphic alleles of hrp48, which encodes a member of the hnRNP A/B family and is implicated in control of P-element splicing. Significant reductions of mI and mII inclusion were also observed in heterozygotes for loss-of-function alleles of virilizer, fl(2)d, and crooked neck. The products of virilizer and fl(2)d are also required for Sxl autoregulation at the level of splicing; crooked neck encodes a protein with structural similarities to yeast-splicing factors Prp39p and Prp42p. Deletion of at least five other loci caused significant reductions in the inclusion of mI and/or mII. Possible roles of identified factors are discussed in the context of the resplicing strategy for generation of alternative Ubx mRNAs.

scholarly journals Cytoplasmic dynein (ddlc1) mutations cause morphogenetic defects and apoptotic cell death in Drosophila melanogaster.

1996 ◽  
Vol 16 (5) ◽  
pp. 1966-1977 ◽  
Author(s):  
T Dick ◽  
K Ray ◽  
H K Salz ◽  
W Chia
Keyword(s):  
Drosophila Melanogaster ◽  
Light Chain ◽  
Blot Analysis ◽  
Cytoplasmic Dynein ◽  
P Element ◽  
Female Sterility ◽  
Dynein Light Chain ◽  
Loss Of Function ◽  
Light Chain Gene

We report the molecular and genetic characterization of the cytoplasmic dynein light-chain gene, ddlc1, from Drosophila melanogaster. ddlc1 encodes the first cytoplasmic dynein light chain identified, and its genetic analysis represents the first in vivo characterization of cytoplasmic dynein function in higher eucaryotes. The ddlc1 gene maps to 4E1-2 and encodes an 89-amino-acid polypeptide with a high similarity to the axonemal 8-kDa outer-arm dynein light chain from Chlamydomonas flagella. Developmental Northern (RNA) blot analysis and ovary and embryo RNA in situ hybridizations indicate that the ddlc1 gene is expressed ubiquitously. Anti-DDLC1 antibody analyses show that the DDLC1 protein is localized in the cytoplasm. P-element-induced partial-loss-of-function mutations cause pleiotropic morphogenetic defects in bristle and wing development, as well as in oogenesis, and hence result in female sterility. The morphological abnormalities found in the ovaries are always associated with a loss of cellular shape and structure, as visualized by a disorganization of the actin cytoskeleton. Total-loss-of-function mutations cause lethality. A large proportion of mutant animals degenerate during embryogenesis, and the dying cells show morphological changes characteristic of apoptosis, namely, cell and nuclear condensation and fragmentation, as well as DNA degradation. Cloning of the human homolog of the ddlc1 gene, hdlc1, demonstrates that the dynein light-chain 1 is highly conserved in flies and humans. Northern blot analysis and epitope tagging show that the hdlc1 gene is ubiquitously expressed and that the human dynein light chain 1 is localized in the cytoplasm. hdlc1 maps to 14q24.

Multiple variants and a differential splicing pattern of kinectin in human hepatocellular carcinoma

2004 ◽  
Vol 82 (2) ◽  
pp. 321-327 ◽  
Author(s):  
Hong-Cheng Wang ◽  
Yan-Rong Su ◽  
Ke-Jun Han ◽  
Xue-Wen Pang ◽  
Ji-Run Peng ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Alternative Splicing ◽  
Tissue Sample ◽  
Cdna Expression Library ◽  
Serological Analysis ◽  
Expression Library ◽  
Humoral Immune ◽  
Cdna Expression ◽  
Splicing Pattern ◽  
Alternatively Spliced

To extend the search for hepatocellular carcinoma (HCC) associated antigens with immunogenicity for clinical applications, we constructed a cDNA expression library using resected human HCC tissue sample and screened it by serological analysis of recombinant cDNA expression library (SEREX) with autologous and allogeneic sera. A total of 24 distinct antigens were isolated and kinectin was the antigen most frequently identified. We found that kinectin was alternatively spliced at four sites and obtained all eight theoretical forms of variant, six by SEREX and two by RT-PCR, from the different splicing combinations of the last three sites. In addition, the splicing patterns of four sites were analyzed. Variant containing D2 was overexpressed in cancerous tissues and this alteration may be tumor associated. The four splicing sites, the variants generated by alternative splicing, and the humoral immune response in HCC patients, may help to analyze the role of kinectin in human HCC cell biology.Key words: alternative splicing, antibody response, hepatocellular carcinoma, kinectin, serological analysis of recombinant cDNA expression library (SEREX).

scholarly journals Aurora-A phosphorylates splicing factors and regulates alternative splicing

2020 ◽  
Author(s):  
Arun Prasath Damodaran ◽  
Olivia Gavard ◽  
Jean-Philippe Gagné ◽  
Malgorzata Ewa Rogalska ◽  
Estefania Mancini ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Direct Interaction ◽  
Splicing Factors ◽  
Sequencing Analysis ◽  
Aurora A Kinase ◽  
Aurora A ◽  
Nuclear Speckles ◽  
Rrm Domain ◽  
Alternatively Spliced

ABSTRACTAurora-A kinase is well known to regulate progression through mitosis. However, the kinase also performs additional functions that could explain the failure of its inhibitors to be effective in cancer treatments. To identify these functions, we applied a proteomics approach to search for interactors of Aurora-A. We found a large number of proteins involved in pre-mRNA splicing, strongly suggesting an important role for Aurora-A in this biological process. Consistently, we first report the subcellular localization of Aurora-A in nuclear speckles, the storehouse of splicing proteins. We also demonstrate direct interaction of Aurora-A with RRM domain-containing splicing factors such as hnRNP and SR proteins and their phosphorylation in vitro. Further, RNA-sequencing analysis following pharmacological inhibition of Aurora-A resulted in alternative splicing changes corresponding to 505 genes, including genes with functions regulated by Aurora-A kinase. Finally, we report enrichment of RNA motifs within the alternatively spliced regions affected by Aurora-A kinase inhibition which are bound by Aurora-A interacting splicing factors, suggesting that Aurora-A regulates alternative splicing by modulating the activity of these interacting splicing factors. Overall our work identified Aurora-A as a novel splicing kinase and for the first time, describes a broad role of Aurora-A in regulating alternative splicing.

scholarly journals The unusual spectrum of mutations induced by hybrid dysgenesis at the Triplo-lethal locus of Drosophila melanogaster.

Genetics ◽  
1990 ◽  
Vol 125 (4) ◽  
pp. 795-801 ◽  
Author(s):  
D R Dorer ◽  
A C Christensen
Keyword(s):  
Drosophila Melanogaster ◽  
Chromosomal Region ◽  
Hybrid Dysgenesis ◽  
P Element ◽  
Relative Ease ◽  
Rare Class ◽  
Complex Locus ◽  
Hypomorphic Alleles ◽  
Redundant Functions ◽  
New Mutations

Abstract The Triplo-lethal locus (Tpl) is unique in its dosage sensitivity; no other locus in Drosophila has been identified that is lethal when present in three doses. Tpl is also haplo-lethal, and its function is still a mystery. Previous workers have found it nearly impossible to mutationally inactive Tpl other than by completely deleting the chromosomal region in which Tpl resides (83DE). We have utilized P-M hybrid dysgenesis in an effort to obtain new mutations of Tpl. We recovered 19 new duplications of Tpl, 15 hypomorphic mutations of Tpl (a previously rare class of mutation), and no null mutations. Surprisingly, 14 of the 15 hypomorphic alleles have no detectable P element sequences at the locus. The difficulty in recovering null mutations in Tpl suggests that it may be a complex locus, perhaps consisting of several genes with redundant functions. The relative ease with which we recovered hypomorphic alleles is in sharp contrast to previous attempts by others to mutagenize Tpl. A higher mutation rate with hybrid dysgenesis than with radiation or chemicals also suggests a peculiar genetic organization for the locus.

scholarly journals Origin, Splicing, and Expression of Rodent Amelogenin Exon 8

2006 ◽  
Vol 85 (10) ◽  
pp. 894-899 ◽  
Author(s):  
J.D. Bartlett ◽  
R. L. Ball ◽  
T. Kawai ◽  
C.E. Tye ◽  
M. Tsuchiya ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Splice Site ◽  
Site Selection ◽  
Proteolytic Processing ◽  
Rt Pcr ◽  
Splice Site Selection ◽  
Rna Transcripts ◽  
Splicing Pattern ◽  
Alternatively Spliced ◽  
Gene Structures

Amelogenin RNA transcripts undergo extensive alternative splicing, and MMP-20 processes the isoforms following their secretion. Since amelogenins have been ascribed cell-signaling activities, we asked if a lack of proteolytic processing by MMP-20 affects amelogenin signaling and consequently alters amelogenin splice site selection. RT-PCR analyses of amelogenin mRNA between control and Mmp20− /−mice revealed no differences in the splicing pattern. We characterized 3 previously unidentified amelogenin alternatively spliced transcripts and demonstrated that exon-8-encoded amelogenin isoforms are processed by MMP-20. Transcripts with exon 8 were expressed approximately five-fold less than those with exon 7. Analyses of the mouse and rat amelogenin gene structures confirmed that exon 8 arose in a duplication of exons 4 through 5, with translocation of the copy downstream of exon 7. No downstream genomic sequences homologous to exons 4–5 were present in the bovine or human amelogenin genes, suggesting that this translocation occurred only in rodents.

Genetic and molecular analysis of the X chromosomal region 14B17-14C4 in Drosophila melanogaster: loss of function in NONA, a nuclear protein common to many cell types, results in specific physiological and behavioral defects.

Genetics ◽  
1993 ◽  
Vol 135 (2) ◽  
pp. 419-442
Author(s):  
R Stanewsky ◽  
K G Rendahl ◽  
M Dill ◽  
H Saumweber
Keyword(s):  
Drosophila Melanogaster ◽  
Nuclear Protein ◽  
Rna Binding ◽  
Sequence Data ◽  
Polytene Chromosomes ◽  
Cell Types ◽  
Nucleic Acid Binding ◽  
Loss Of Function ◽  
Nucleic Acid Binding Proteins ◽  
Hypomorphic Alleles

Abstract We have performed a genetic analysis of the 14C region of the X chromosome of Drosophila melanogaster to isolate loss of function alleles of no-on-transient A (nonA; 14C1-2; 1-52.3). NONA is a nuclear protein common to many cell types, which is present in many puffs on polytene chromosomes. Sequence data suggest that the protein contains a pair of RNA binding motifs (RRM) found in many single-strand nucleic acid binding proteins. Hypomorphic alleles of this gene, which lead to aberrant visual and courtship song behavior, still contain normally distributed nonA RNA and NONA protein in embryos, and in all available alleles NONA protein is present in puffs of third instar larval polytene chromosomes. We find that complete loss of this general nuclear protein is semilethal in hemizygous males and homozygous cell lethal in the female germline. Surviving males show more extreme defects in nervous system function than have been described for the hypomorphic alleles. Five other essential genes that reside within this region have been partially characterized.

scholarly journals cis-regulatory sequences responsible for alternative splicing of the Drosophila dopa decarboxylase gene.

1994 ◽  
Vol 14 (11) ◽  
pp. 7385-7393 ◽  
Author(s):  
J Shen ◽  
J Hirsh
Keyword(s):  
Alternative Splicing ◽  
Germ Line ◽  
Fusion Gene ◽  
P Element ◽  
Dopa Decarboxylase ◽  
Regulatory Sequences ◽  
Exon 1 ◽  
Alternatively Spliced ◽  
The Central Nervous System ◽  
Germ Line Transformation

The Drosophila dopa decarboxylase gene, Ddc, is expressed in the hypoderm and in specific sets of cells in the central nervous system (CNS). The unique Ddc primary transcript is alternatively spliced in these two tissues. The Ddc CNS mRNA contains all four exons (A through D), whereas the hypodermal mRNA contains only three exons (A, C, and D). To localize cis-regulatory sequences responsible for Ddc alternative splicing, a Ddc minigene and several fusion genes containing various amounts of Ddc sequences fused to fushi tarazu (ftz) exon 1 were constructed and introduced into flies by P-element-mediated germ line transformation. We find that Ddc intron ab and exon B are sufficient to regulate Ddc alternative splicing, since transcripts of a minimal fusion gene containing most of Ddc intron ab and exon B are spliced to exon B in the CNS but not in the hypoderm. These results indicate that Ddc alternative splicing is regulated by either a negative mechanism preventing splicing to exon B in the hypoderm or a positive mechanism activating splicing to exon B in the CNS. Our previous data suggest that Ddc hypodermal splicing is the actively regulated splicing pathway (J. Shen, C. J. Beall, and J. Hirsh, Mol. Cell. Biol. 13:4549-4555, 1993). Here we show that deletion of Ddc intron ab sequences selectively disrupts hypodermal splicing specificity. These results support a model in which Ddc alternative splicing is negatively regulated by a blockage mechanism preventing splicing to exon B in the hypoderm.

scholarly journals Functional Differences in Ionic Regulation between Alternatively Spliced Isoforms of the Na+-Ca2+ Exchanger from Drosophila melanogaster

1998 ◽  
Vol 111 (5) ◽  
pp. 691-702 ◽  
Author(s):  
Alexander Omelchenko ◽  
Christopher Dyck ◽  
Mark Hnatowich ◽  
John Buchko ◽  
Debora A. Nicoll ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Alternative Splicing ◽  
Xenopus Laevis Oocytes ◽  
Patch Clamp Technique ◽  
Inactive State ◽  
Functional Differences ◽  
Dependent Inactivation ◽  
Current Voltage ◽  
Alternatively Spliced ◽  
Regulatory Properties

Ion transport and regulation were studied in two, alternatively spliced isoforms of the Na+-Ca2+ exchanger from Drosophila melanogaster. These exchangers, designated CALX1.1 and CALX1.2, differ by five amino acids in a region where alternative splicing also occurs in the mammalian Na+-Ca2+ exchanger, NCX1. The CALX isoforms were expressed in Xenopus laevis oocytes and characterized electrophysiologically using the giant, excised patch clamp technique. Outward Na+-Ca2+ exchange currents, where pipette Ca2+o exchanges for bath Na+i, were examined in all cases. Although the isoforms exhibited similar transport properties with respect to their Na+i affinities and current–voltage relationships, significant differences were observed in their Na+i- and Ca2+i-dependent regulatory properties. Both isoforms underwent Na+i-dependent inactivation, apparent as a time-dependent decrease in outward exchange current upon Na+i application. We observed a two- to threefold difference in recovery rates from this inactive state and the extent of Na+i-dependent inactivation was approximately twofold greater for CALX1.2 as compared with CALX1.1. Both isoforms showed regulation of Na+-Ca2+ exchange activity by Ca2+i, but their responses to regulatory Ca2+i differed markedly. For both isoforms, the application of cytoplasmic Ca2+i led to a decrease in outward exchange currents. This negative regulation by Ca2+i is unique to Na+-Ca2+ exchangers from Drosophila, and contrasts to the positive regulation produced by cytoplasmic Ca2+ for all other characterized Na+-Ca2+ exchangers. For CALX1.1, Ca2+i inhibited peak and steady state currents almost equally, with the extent of inhibition being ≈80%. In comparison, the effects of regulatory Ca2+i occurred with much higher affinity for CALX1.2, but the extent of these effects was greatly reduced (≈20–40% inhibition). For both exchangers, the effects of regulatory Ca2+i occurred by a direct mechanism and indirectly through effects on Na+i-induced inactivation. Our results show that regulatory Ca2+i decreases Na+i-induced inactivation of CALX1.2, whereas it stabilizes the Na+i-induced inactive state of CALX1.1. These effects of Ca2+i produce striking differences in regulation between CALX isoforms. Our findings indicate that alternative splicing may play a significant role in tailoring the regulatory profile of CALX isoforms and, possibly, other Na+-Ca2+ exchange proteins.

scholarly journals Sequence and Evolutionary Features for the Alternatively Spliced Exons of Eukaryotic Genes

2019 ◽  
Vol 20 (15) ◽  
pp. 3834 ◽  
Author(s):  
Shi-Yi Chen ◽  
Cao Li ◽  
Xianbo Jia ◽  
Song-Jia Lai
Keyword(s):  
Alternative Splicing ◽  
High Throughput Sequencing ◽  
Point Of View ◽  
Sequencing Technologies ◽  
Eukaryotic Genes ◽  
Splicing Pattern ◽  
Evolutionary Features ◽  
Alternatively Spliced ◽  
Alternative Splicing Events ◽  
Alternatively Spliced Exons

Alternative splicing of pre-mRNAs is a crucial mechanism for maintaining protein diversity in eukaryotes without requiring a considerable increase of genes in the number. Due to rapid advances in high-throughput sequencing technologies and computational algorithms, it is anticipated that alternative splicing events will be more intensively studied to address different kinds of biological questions. The occurrences of alternative splicing mean that all exons could be classified to be either constitutively or alternatively spliced depending on whether they are virtually included into all mature mRNAs. From an evolutionary point of view, therefore, the alternatively spliced exons would have been associated with distinctive biological characteristics in comparison with constitutively spliced exons. In this paper, we first outline the representative types of alternative splicing events and exon classification, and then review sequence and evolutionary features for the alternatively spliced exons. The main purpose is to facilitate understanding of the biological implications of alternative splicing in eukaryotes. This knowledge is also helpful to establish computational approaches for predicting the splicing pattern of exons.

scholarly journals Optimization of a Weak 3′ Splice Site Counteracts the Function of a Bovine Papillomavirus Type 1 Exonic Splicing Suppressor In Vitro and In Vivo

2000 ◽  
Vol 74 (13) ◽  
pp. 5902-5910 ◽  
Author(s):  
Zhi-Ming Zheng ◽  
Jesse Quintero ◽  
Eric S. Reid ◽  
Christian Gocke ◽  
Carl C. Baker
Keyword(s):  
Alternative Splicing ◽  
Splice Site ◽  
Splicing Factors ◽  
Bovine Papillomavirus ◽  
Splicing Pattern ◽  
In Vitro Splicing

ABSTRACT Alternative splicing is a critical component of the early to late switch in papillomavirus gene expression. In bovine papillomavirus type 1 (BPV-1), a switch in 3′ splice site utilization from an early 3′ splice site at nucleotide (nt) 3225 to a late-specific 3′ splice site at nt 3605 is essential for expression of the major capsid (L1) mRNA. Three viral splicing elements have recently been identified between the two alternative 3′ splice sites and have been shown to play an important role in this regulation. A bipartite element lies approximately 30 nt downstream of the nt 3225 3′ splice site and consists of an exonic splicing enhancer (ESE), SE1, followed immediately by a pyrimidine-rich exonic splicing suppressor (ESS). A second ESE (SE2) is located approximately 125 nt downstream of the ESS. We have previously demonstrated that the ESS inhibits use of the suboptimal nt 3225 3′ splice site in vitro through binding of cellular splicing factors. However, these in vitro studies did not address the role of the ESS in the regulation of alternative splicing. In the present study, we have analyzed the role of the ESS in the alternative splicing of a BPV-1 late pre-mRNA in vivo. Mutation or deletion of just the ESS did not significantly change the normal splicing pattern where the nt 3225 3′ splice site is already used predominantly. However, a pre-mRNA containing mutations in SE2 is spliced predominantly using the nt 3605 3′ splice site. In this context, mutation of the ESS restored preferential use of the nt 3225 3′ splice site, indicating that the ESS also functions as a splicing suppressor in vivo. Moreover, optimization of the suboptimal nt 3225 3′ splice site counteracted the in vivo function of the ESS and led to preferential selection of the nt 3225 3′ splice site even in pre-mRNAs with SE2 mutations. In vitro splicing assays also showed that the ESS is unable to suppress splicing of a pre-mRNA with an optimized nt 3225 3′ splice site. These data confirm that the function of the ESS requires a suboptimal upstream 3′ splice site. A surprising finding of our study is the observation that SE1 can stimulate both the first and the second steps of splicing.

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