Alternative Splicing within and between Drosophila Species, Sexes, Tissues, and Developmental Stages

Samples of Drosophila species were collected from some selected sites (viz., Dohar Upazila of Dhaka Division, Hironpoint of the Sundarbans, Satchori of Sylhet Division) of Bangladesh and these were cultured in the laboratory to study developmental stages, external morphological traits and sex comb. They were identified as D. melanogaster, D. ananassae and D. bipectinata. The sex comb teeth number and arrangement were distinct for all three species. D. melanogaster had one row of 10 - 11 teeth in the sex comb. D. ananassae had eight rows of teeth in the sex comb possessing 32 - 33 teeth in total. D. bipectinata had 2 - 3 rows of teeth in the sex comb and total teeth number varied from 11 to 15. Among three species, sex comb teeth number of D. bipectinata varied most. Eleven different patterns (n=20) in sex comb were observed in D. bipectinata indicating significant diversity within species. Variation in pupation sites among three species was also observed in the laboratory condition. D. bipectinata pupated on the food medium, whereas other two species pupated on the vial wall. Thus, diversity among these three species of Drosophila was documented which could be utilized as bioindicator in future. Dhaka Univ. J. Biol. Sci. 28(2): 167-176, 2019 (July)

Download Full-text

Alternative RNA splicing that is spatially regulated: generation of transcripts from the Antennapedia gene of Drosophila melanogaster with different protein-coding regions

Molecular and Cellular Biology ◽

10.1128/mcb.8.10.4143-4154.1988 ◽

1988 ◽

Vol 8 (10) ◽

pp. 4143-4154

Author(s):

V L Stroeher ◽

J C Gaiser ◽

R L Garber

Keyword(s):

Alternative Splicing ◽

Rna Splicing ◽

Developmental Stages ◽

Molecular Evidence ◽

Rnase Protection ◽

Protein Coding ◽

Spatial Regulation ◽

Coding Regions ◽

Imaginal Disks ◽

Isolated Tissues

We have shown previously that transcription of the Drosophila homeotic gene Antennapedia results in four major RNA species which differ in long 5'- and 3'-untranslated sequences. The protein-coding portion of these transcripts, however, is located in exons common to all. Using RNase protection assays and further cDNA clone isolation, we have now detected two alternative splicing events between exons of this region. These result in four RNA variations which, if translated, would encode a family of Antennapedia proteins. By analyzing transcripts from various developmental stages and isolated tissues, we show that alternative splicing is under strict temporal and spatial regulation. For example, while similar patterns of splicing were found for all wild-type thoracic imaginal disks examined, these differed distinctly from the patterns observed in neural tissues. Our results suggest that individual RNAs may be associated with different biological roles, and provide molecular evidence that the Antennapedia gene is involved in multiple functions.

Download Full-text

A moveable 5' splice site in adenine phosphoribosyltransferase genes of Drosophila species.

Molecular and Cellular Biology ◽

10.1128/mcb.9.5.2220 ◽

1989 ◽

Vol 9 (5) ◽

pp. 2220-2223 ◽

Cited By ~ 6

Author(s):

D Johnson ◽

S Henikoff

Keyword(s):

Gene Expression ◽

Alternative Splicing ◽

Splice Site ◽

Gene Evolution ◽

Drosophila Species ◽

Splice Sites ◽

Adenine Phosphoribosyltransferase ◽

Splice Junctions ◽

Encoding Genes ◽

Normal Feature

In two distantly related Drosophila species, the use of alternate 5' splice sites to process an intron in pre-mRNA from homologous adenine phosphoribosyltransferase (APRT)-encoding genes led to RNAs encoding nonfunctional peptides in addition to APRT. The production of aberrantly spliced transcripts as a normal feature of gene expression supports a general model of eucaryotic gene evolution through alternative splicing and moveable splice junctions.

Download Full-text

An alternative splicing event in the Pax-3 paired domain identifies the linker region as a key determinant of paired domain DNA-binding activity.

Molecular and Cellular Biology ◽

10.1128/mcb.16.12.6677 ◽

1996 ◽

Vol 16 (12) ◽

pp. 6677-6686 ◽

Cited By ~ 66

Author(s):

K J Vogan ◽

D A Underhill ◽

P Gros

Keyword(s):

Alternative Splicing ◽

Dna Binding ◽

Developmental Stages ◽

Paired Domain ◽

Binding Studies ◽

Recognition Sequence ◽

Linker Region ◽

Glutamine Residue ◽

Dna Binding Studies

We have identified alternatively spliced isoforms of murine Pax-3 and Pax-7 which differ by the presence or absence of a single glutamine residue in a linker region which separates two distinct DNA-binding subdomains within the paired domain. By reverse transcription-PCR, these isoforms of Pax-3 and Pax-7 (Q+ and Q-) were detected at similar levels through multiple developmental stages in the early mouse embryo. DNA-binding studies using the Q+ and Q- isoforms of Pax-3 revealed that this alternative splicing event had no major effect on the ability of these isoforms to bind to an oligonucleotide specific for the Pax-3 homeodomain (P2) or to a paired domain recognition sequence (e5) that interacts primarily with the N-terminal subdomain of the paired domain. However, DNA-binding studies with sequences (P6CON and CD19-2/A) containing consensus elements for both the N-terminal and C-terminal subdomains revealed that the Q- isoform binds to these sequences with a two- to fivefold-higher affinity; further mutation of the GTCAC core N-terminal subdomain recognition motif of CD19-2/A generated binding sites with a high degree of specificity for the Q- isoform. These differences in DNA binding in vitro were also reflected in the enhanced ability of the Q- isoform to stimulate transcription of a reporter containing multiple copies of CD19-2/A upstream of the thymidine kinase basal promoter. In support of the observations made with these naturally occurring Pax-3 isoforms, introducing a glutamine residue at the analogous position in PAX6 caused a fivefold reduction in binding to P6CON and a complete loss of binding to CD19-2/A and to the C-terminal subdomain-specific probe 5aCON. These studies therefore provide direct evidence for a role for the paired-domain linker region in DNA target site selection, and they identify novel isoforms of Pax-3 and Pax-7 that have the potential to mediate distinct functions in the developing embryo.

Download Full-text

The Variable Transmembrane Domain of Drosophila N-Cadherin Regulates Adhesive Activity

Molecular and Cellular Biology ◽

10.1128/mcb.00241-06 ◽

2006 ◽

Vol 26 (17) ◽

pp. 6598-6608 ◽

Cited By ~ 19

Author(s):

Shinichi Yonekura ◽

Chun-Yuan Ting ◽

Guilherme Neves ◽

Kimberly Hung ◽

Shu-ning Hsu ◽

...

Keyword(s):

Alternative Splicing ◽

Fluorescent Protein ◽

Developmental Stages ◽

Transmembrane Domain ◽

Cell Aggregation ◽

Transmembrane Domains ◽

Molecular Architecture ◽

Cell Type Specific ◽

Green Fluorescent

ABSTRACT Drosophila N-cadherin (CadN) is an evolutionarily conserved classic cadherin which has a large, complex extracellular domain and a catenin-binding cytoplasmic domain. The CadN locus contains three modules of alternative exons (7a/b, 13a/b, and 18a/b) and undergoes alternative splicing to generate multiple isoforms. Using quantitative transcript analyses and green fluorescent protein-based cell sorting, we found that during development CadN alternative splicing is regulated in a temporal but not cell-type-specific fashion. In particular, exon 18b is predominantly expressed during early developmental stages, while exon 18a is prevalent at the late developmental and adult stages. All CadN isoforms share the same molecular architecture but have different sequences in their extracellular and transmembrane domains, suggesting functional diversity. In vitro quantitative cell aggregation assays revealed that all CadN isoforms mediate homophilic interactions, but the isoforms encoded by exon 18b have a higher adhesive activity than those by its alternative, 18a. Domain-swapping experiments further revealed that the different sequences in the transmembrane domains of isoforms are responsible for their differential adhesive activities. CadN alternative splicing might provide a novel mechanism to fine-tune its adhesive activity at different developmental stages or to restrict the use of high-affinity 18b-type isoforms at the adult stage.

Download Full-text

Transcriptome profiling of developing testes and spermatogenesis in the Mongolian horse

10.21203/rs.2.16493/v3 ◽

2020 ◽

Author(s):

Bei LI ◽

Xiaolong He ◽

Yiping Zhao ◽

Dongyi Bai ◽

Ming Du ◽

...

Keyword(s):

Alternative Splicing ◽

Developmental Stages ◽

Male Gamete ◽

Transcriptome Profiling ◽

Differentially Expressed ◽

Testicular Development ◽

Testis Development ◽

Oocyte Meiosis ◽

Alternative Splicing Events ◽

Mongolian Horse

Abstract Background: Horse testis development and spermatogenesis are complex physiological processes. Methods: To study these processes, three immature and three mature testes were collected from the Mongolian horse, and six libraries were established using high-throughput RNA sequencing technology (RNA-Seq) to screen for genes related to testis development and spermatogenesis. Results: A total of 16,237 upregulated genes and 8,641 downregulated genes were detected in the testis of the Mongolian horse. These genes play important roles in different developmental stages of spermatogenesis and testicular development. Five genes with alternative splicing events that may influence spermatogenesis and development of the testis were detected. GO (Gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses were performed for functional annotation of the differentially expressed genes. Pathways related to “spermatogenesis,” male gamete generation,” “spermatid development” and “oocyte meiosis” were significantly involved in different stages of testis development and spermatogenesis. Conclusion: Genes, pathways and alternative splicing events were identified with inferred functions in the process of spermatogenesis in the Mongolian horse. The identification of these differentially expressed genetic signatures improves our understanding of horse testis development and spermatogenesis.

Download Full-text

Transcriptome profiling of developing testes and spermatogenesis in the Mongolian horse

10.21203/rs.2.16493/v4 ◽

2020 ◽

Author(s):

Bei LI ◽

Xiaolong He ◽

Yiping Zhao ◽

Dongyi Bai ◽

Ming Du ◽

...

Keyword(s):

Alternative Splicing ◽

Developmental Stages ◽

Male Gamete ◽

Transcriptome Profiling ◽

Differentially Expressed ◽

Testicular Development ◽

Testis Development ◽

Oocyte Meiosis ◽

Alternative Splicing Events ◽

Mongolian Horse

Abstract Background: Horse testis development and spermatogenesis are complex physiological processes. Methods: To study these processes, three immature and three mature testes were collected from the Mongolian horse, and six libraries were established using high-throughput RNA sequencing technology (RNA-Seq) to screen for genes related to testis development and spermatogenesis. Results: A total of 16,237 upregulated genes and 8,641 downregulated genes were detected in the testis of the Mongolian horse. These genes play important roles in different developmental stages of spermatogenesis and testicular development. Five genes with alternative splicing events that may influence spermatogenesis and development of the testis were detected. GO (Gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses were performed for functional annotation of the differentially expressed genes. Pathways related to “spermatogenesis,” male gamete generation,” “spermatid development” and “oocyte meiosis” were significantly involved in different stages of testis development and spermatogenesis. Conclusion: Genes, pathways and alternative splicing events were identified with inferred functions in the process of spermatogenesis in the Mongolian horse. The identification of these differentially expressed genetic signatures improves our understanding of horse testis development and spermatogenesis.

Download Full-text

Genome-wide transcriptome analysis of the early developmental stages of Echinococcus granulosus protoscoleces reveals extensive alternative splicing events in the spliceosome pathway

Parasites & Vectors ◽

10.1186/s13071-021-05067-9 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Mohammad Ali Mohammadi ◽

Majid Fasihi Harandi ◽

Donald P. McManus ◽

Mehdi Mansouri

Keyword(s):

Alternative Splicing ◽

Echinococcus Granulosus ◽

Developmental Stages ◽

Biological Effects ◽

Complex Life Cycle ◽

Sequencing Data ◽

Cellular Functions ◽

Related Factors ◽

Whole Transcriptome Sequencing ◽

Biphasic Medium

Abstract Background The complex life cycle of Echinococcus granulosus involves numerous environmental conditions within different intermediate and definitive hosts. This requires adaptation at different levels of transcript regulation. Alternative splicing (AS) and the related cellular functions as one of the major fields of post-genomics has been poorly studied in tapeworms. In the present study, we investigated AS events and their potential biological effects in E. granulosus. Methods Whole transcriptome sequencing data of four groups of protoscoleces were prepared for RNA-seq library construction. Fresh protoscoleces were either used as non-induced controls (NT group) or incubated for 15 min with pepsin (PEP group) and cultivated in a biphasic medium for 12 and 24 h (12 and 24 h groups). The frequency and different types of AS events were identified using rMATS software. Functional annotations and gene ontology of differential AS (DAS) genes were performed using Blast2GO software. AS events were experimentally validated by PCR on the protoscolex cDNAs using specific primers for each gene. Results At least one AS event was found in 38.1% of the genes (3904 out of 10,245) in the protoscoleces during early strobilar development. The genes were associated primarily with cellular and metabolic processes and binding and catalytic activity. KEGG pathway analysis of DAS events revealed a number of genes belonging to different components of the spliceosome complex. These genes tended to belong to common SR proteins, U1-related factors, U2-related factors, complex A-specific factors and other splicing-related proteins. Conclusions The high number of AS events in the transcriptome regulatory mechanisms indicates the essential rapid molecular processes required by the parasite for adaptation in different environments. Graphical Abstract

Download Full-text

A moveable 5' splice site in adenine phosphoribosyltransferase genes of Drosophila species

Molecular and Cellular Biology ◽

10.1128/mcb.9.5.2220-2223.1989 ◽

1989 ◽

Vol 9 (5) ◽

pp. 2220-2223

Author(s):

D Johnson ◽

S Henikoff

Keyword(s):

Gene Expression ◽

Alternative Splicing ◽

Splice Site ◽

Gene Evolution ◽

Drosophila Species ◽

Splice Sites ◽

Adenine Phosphoribosyltransferase ◽

Splice Junctions ◽

Encoding Genes ◽

Normal Feature

In two distantly related Drosophila species, the use of alternate 5' splice sites to process an intron in pre-mRNA from homologous adenine phosphoribosyltransferase (APRT)-encoding genes led to RNAs encoding nonfunctional peptides in addition to APRT. The production of aberrantly spliced transcripts as a normal feature of gene expression supports a general model of eucaryotic gene evolution through alternative splicing and moveable splice junctions.

Download Full-text

Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed

Plants ◽

10.3390/plants9080977 ◽

2020 ◽

Vol 9 (8) ◽

pp. 977

Author(s):

Ai Lin ◽

Jinqi Ma ◽

Fei Xu ◽

Wen Xu ◽

Huanhuan Jiang ◽

...

Keyword(s):

Alternative Splicing ◽

Seed Coat ◽

Rna Binding ◽

Developmental Stages ◽

Coat Color ◽

Intron Retention ◽

Seed Color ◽

Seed Coat Color ◽

Flavonoid Pathway ◽

Transcriptional Regulatory

Yellow seed coat color is a desirable characteristic in rapeseed (Brassica napus), as it is associated with higher oil content and higher quality of meal. Alternative splicing (AS) is a vital post-transcriptional regulatory process contributing to plant cell differentiation and organ development. To identify novel transcripts and differences at the isoform level that are associated with seed color in B. napus, we compared 31 RNA-seq libraries of yellow- and black-seeded B. napus at five different developmental stages. AS events in the different samples were highly similar, and intron retention accounted for a large proportion of the observed AS pattern. AS mainly occurred in the early and middle stage of seed development. Weighted gene co-expression network analysis (WGCNA) identified 23 co-expression modules composed of differentially spliced genes, and we picked out two of the modules whose functions were highly associated with seed color. In the two modules, we found candidate DAS (differentially alternative splicing) genes related to the flavonoid pathway, such as TT8 (BnaC09g24870D), TT5 (BnaA09g34840D and BnaC08g26020D), TT12 (BnaC06g17050D and BnaA07g18120D), AHA10 (BnaA08g23220D and BnaC08g17280D), CHI (BnaC09g50050D), BAN (BnaA03g60670D) and DFR (BnaC09g17150D). Gene BnaC03g23650D, encoding RNA-binding family protein, was also identified. The splicing of the candidate genes identified in this study might be used to develop stable, yellow-seeded B. napus. This study provides insight into the formation of seed coat color in B. napus.

Download Full-text