Origin and evolution of a new retained intron on the vulcan gene in Drosophila melanogaster subgroup species

Genome ◽  
2014 ◽  
Vol 57 (10) ◽  
pp. 567-572 ◽  
Author(s):  
Leilei Zhan ◽  
Qiaohong Meng ◽  
Ran Chen ◽  
Yuan Yue ◽  
Yongfeng Jin
Keyword(s):  
Drosophila Melanogaster ◽  
Intron Retention ◽  
Coding Region ◽  
Orthologous Genes ◽  
Exon 2 ◽  
Origin And Evolution ◽  
Donor And Acceptor ◽  
Drosophila Melanogaster Subgroup ◽  
The Common ◽  
Exonic Sequence

Although numerous intron gains have been discovered, the mechanisms of intron creation have proven to be elusive. Previous study revealed that the vulcan gene of Drosophila melanogaster contained four exons in its coding region. In the current study, a newly created intron (Intron L) was identified on exon 2 of vulcan in D. melanogaster by comparing expression sequence tags. The RT–PCR experiment revealed that Intron L was associated with intron retention, in which two alternative transcripts of the gene differ by the inclusion or removal of an intron. It was found that Intron L was created by intronization of exonic sequence, and its donor and acceptor splice sites were created by synonymous mutation, leading to the origin of a new vulcan protein that is 22 amino acids shorter than the previously reported vulcan protein. Moreover, to track the origin of Intron L, 36 orthologous genes of species of Drosophila were cloned or annotated, and phylogenetic analysis was carried out. It indicated that the common ancestor of D. melangaster subgroup species created Intron L about 15 million years ago.

scholarly journals Structure and Regulation of the Salivary Gland Secretion Protein Gene Sgs-1 of Drosophila melanogaster

Genetics ◽  
1999 ◽  
Vol 153 (2) ◽  
pp. 753-762
Author(s):  
Günther E Roth ◽  
Sigrid Wattler ◽  
Hartmut Bornschein ◽  
Michael Lehmann ◽  
Günter Korge
Keyword(s):  
Drosophila Melanogaster ◽  
Tandem Repeats ◽  
Transcriptional Start Site ◽  
Regulatory Elements ◽  
Coding Region ◽  
Band Shift ◽  
Salivary Gland Secretion ◽  
Enhancer Binding Protein ◽  
Factor Secretion ◽  
Third Instar Larvae

Abstract The Drosophila melanogaster gene Sgs-1 belongs to the secretion protein genes, which are coordinately expressed in salivary glands of third instar larvae. Earlier analysis had implied that Sgs-1 is located at the 25B2-3 puff. We cloned Sgs-1 from a YAC covering 25B2-3. Despite using a variety of vectors and Escherichia coli strains, subcloning from the YAC led to deletions within the Sgs-1 coding region. Analysis of clonable and unclonable sequences revealed that Sgs-1 mainly consists of 48-bp tandem repeats encoding a threonine-rich protein. The Sgs-1 inserts from single λ clones are heterogeneous in length, indicating that repeats are eliminated. By analyzing the expression of Sgs-1/lacZ fusions in transgenic flies, cis-regulatory elements of Sgs-1 were mapped to lie within 1 kb upstream of the transcriptional start site. Band shift assays revealed binding sites for the transcription factor fork head (FKH) and the factor secretion enhancer binding protein 3 (SEBP3) at positions that are functionally relevant. FKH and SEBP3 have been shown previously to be involved in the regulation of Sgs-3 and Sgs-4. Comparison of the levels of steady state RNA and of the transcription rates for Sgs-1 and Sgs-1/lacZ reporter genes indicates that Sgs-1 RNA is 100-fold more stable than Sgs-1/lacZ RNA. This has implications for the model of how Sgs transcripts accumulate in late third instar larvae.

scholarly journals Contrasting Histories of Three Gene Regions Associated With In(3L)Payne of Drosophila melanogaster

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1565-1575 ◽  
Author(s):  
Esteban Hasson ◽  
Walter F Eanes
Keyword(s):  
Drosophila Melanogaster ◽  
Sequence Variation ◽  
Present Report ◽  
Genetic Exchange ◽  
Nucleotide Variation ◽  
Distal Breakpoint ◽  
Esterase 6 ◽  
The Common ◽  
Neutrality Tests ◽  
Hsp83 Gene

In the present report, we studied nucleotide variation in three gene regions of Drosophila melanogaster, spanning >5 kb and showing different degrees of association with the cosmopolitan inversion In(3-L)Payne. The analysis of sequence variation in the regions surrounding the breakpoints and the heat shock 83 (Hsp83) gene locus, located close to the distal breakpoint, revealed the absence of shared polymorphisms and the presence of a number of fixed differences between arrangements, indicating absence of genetic exchange. In contrast, for the esterase-6 gene region, located in the center of the inversion, we observed the presence of shared polymorphisms between arrangements suggesting genetic exchange. In the regions close to the breakpoints, the common St arrangement is 10 times more polymorphic than inverted chromosomes. We propose that the lack of recombination between arrangements in these regions coupled with genetic hitchhiking is the best explanation for the low heterozygosity observed in inverted lines. Using the data for the breakpoints, we estimate that this inversion polymorphism is around 0.36 million yr old. Although it is widely accepted that inversions are examples of balanced polymorphisms, none of the current neutrality tests including our Monte Carlo simulations showed significant departure from neutral expectations.

Studies on the Toxicity of Aromatic Hydrocarbons on Chorella Vulgaris by 3D-QSAR Using CoMFA and CoMSIA Methods

2012 ◽  
Vol 610-613 ◽  
pp. 3574-3579
Author(s):  
Cui Hua Wang ◽  
Sheng Long Yang ◽  
Chao Lu ◽  
Hong Xia Yu ◽  
Lian Shen Wang ◽  
...  
Keyword(s):  
Benzene Ring ◽  
Aromatic Hydrocarbons ◽  
Common Factor ◽  
3D Qsar ◽  
The Other ◽  
Contour Maps ◽  
Substituent Group ◽  
Donor And Acceptor ◽  
The Common ◽  
Insight Into

By using CoMFA and CoMSIA methods, the new quantitative structures of 25 aromatic hydrocarbons and the 96 hr-EC50 data with C. vulgaris have been investigated to obtain more detailed insight into the relationships between molecular structure and bioactivity. Compared to CoMFA (the average Q2LOO option =0.610), CoMSIA (the average Q2LOO =0.736) has the better results with robustness and stability. CoMSIA analysis using steric, electrostatic, hydrophobic, and H-bond donor and acceptor descriptors show H-bond donor is the common factor for influencing the toxicity, the steric and electrostatic descriptors are next and the hydrophobic descriptor was last. From the contour maps, the number of benzene ring is more crucial for the compound toxicity and the compounds with more benzene ring make toxicity increased. Under the same number of benzene ring, the kind of substituent group and the formed ability of H-bond are the other parameters to influencing the aromatic hydrocarbons toxicity.

scholarly journals Complete Thyroxine-Binding Globulin (TBG) Deficiency Produced by a Mutation in Acceptor Splice Site Causing Frameshift and Early Termination of Translation (TBG-Kankakee)12

1998 ◽  
Vol 83 (10) ◽  
pp. 3604-3608
Author(s):  
Gisah A. Carvalho ◽  
Roy E. Weiss ◽  
Samuel Refetoff
Keyword(s):  
Splice Site ◽  
Messenger Rna ◽  
Restriction Site ◽  
Splice Junction ◽  
Early Termination ◽  
Coding Region ◽  
Acceptor Splice Site ◽  
Exon 2 ◽  
Gene Level ◽  
Exon 1

Fourteen T4-binding globulin (TBG) variants have been identified at the gene level. They are all located in the coding region of the gene and 6 produce complete deficiency of TBG (TBG-CD). We now describe the first mutation in a noncoding region producing TBG-CD. The proband was treated for over 20 yr with L-T4 because of fatigue associated with a low concentration of serum total T4. Fifteen family members were studied showing low total T4 inherited as an X chromosome-linked trait, and affected males had undetectable TBG in serum. Sequencing of the entire coding region and promoter of the TBG gene revealed no abnormality. However, an A to G transition was found in the acceptor splice junction of intron II that produced a new HaeIII restriction site cosegregating with the TBG-CD phenotype. Sequencing exon 1 to exon 3 of TBG complementary DNA reverse transcribed from messenger RNA of skin fibroblasts from an affected male, confirmed a shift in the ag acceptor splice site. This results in the insertion of a G in exon 2 and causes a frameshift and a premature stop at codon 195. This early termination of translation predicts a truncated TBG lacking 201 amino acids.

KIF3B gene silent variant leading to sperm morphology and motility defects and male infertility

2021 ◽  
Author(s):  
Raheleh Heydari ◽  
Mehrshad Seresht-Ahmadi ◽  
Shahab Mirshahvaladi ◽  
Marjan Sabbaghian ◽  
Anahita Mohseni-Meybodi
Keyword(s):  
Male Infertility ◽  
Protein Expression ◽  
Binding Site ◽  
Sperm Count ◽  
Critical Role ◽  
Coiled Coil ◽  
Control Group ◽  
Coding Region ◽  
Exon 2 ◽  
Coiled Coil Domain

Abstract Sperm structural and functional defects are leading causes of male infertility. Patients with immotile sperm disorders suffer from axoneme failure and show a significant reduction in sperm count. The kinesin family member 3B (KIF3B) is one of the genes involved in the proper formation of sperm with a critical role in intraflagellar and intramanchette transport. A part of exon 2 and exons 3–5 of the KIF3B encodes a protein coiled-coil domain that interacts with IFT20 from the IFT protein complex. In the present study, the coding region of KIF3B coiled-coil domain was assessed in 88 oligoasthenoteratozoospermic patients, and the protein expression was evaluated in the mature spermatozoa of the case and control groups using immunocytochemistry and western blotting. According to the results, there was no genetic variation in the exons 3–5 of the KIF3B, but a new A > T variant was identified within the exon 2 in 30 patients, where nothing was detected in the control group. In contrast to healthy individuals, significantly reduced protein expression was observable in oligoasthenoteratozoospermic (OAT) patients carrying variation where protein organization was disarranged, especially in the principal piece and midpiece of the sperm tail. Besides, the protein expression level was lower in the patients’ samples compared to that of the control group. According to the results of the present study the NM_004798.3:c.1032A > T, p.Pro344 = variant; which has been recently submitted to the Clinvar database; although synonymous, causes alterations in the transcription factor binding site, exon skipping, and also exonic splicing enhancer-binding site. Therefore, KIF3B can play an important role in spermatogenesis and the related protein reduction can cause male infertility.

Intronic SMCHD1 variants in FSHD: testing the potential for CRISPR-Cas9 genome editing

2019 ◽  
Vol 56 (12) ◽  
pp. 828-837 ◽  
Author(s):  
Remko Goossens ◽  
Marlinde L van den Boogaard ◽  
Richard J L F Lemmers ◽  
Judit Balog ◽  
Patrick J van der Vliet ◽  
...  
Keyword(s):  
Genome Editing ◽  
Intron Retention ◽  
Wild Type ◽  
Repeat Array ◽  
D4z4 Repeat ◽  
Intronic Mutation ◽  
Whole Exome ◽  
Efficient Suppression ◽  
The Common ◽  
Chromatin Relaxation

BackgroundFacioscapulohumeral dystrophy (FSHD) is associated with partial chromatin relaxation of the DUX4 retrogene containing D4Z4 macrosatellite repeats on chromosome 4, and transcriptional de-repression of DUX4 in skeletal muscle. The common form of FSHD, FSHD1, is caused by a D4Z4 repeat array contraction. The less common form, FSHD2, is generally caused by heterozygous variants in SMCHD1.MethodsWe employed whole exome sequencing combined with Sanger sequencing to screen uncharacterised FSHD2 patients for extra-exonic SMCHD1 mutations. We also used CRISPR-Cas9 genome editing to repair a pathogenic intronic SMCHD1 variant from patient myoblasts.ResultsWe identified intronic SMCHD1 variants in two FSHD families. In the first family, an intronic variant resulted in partial intron retention and inclusion of the distal 14 nucleotides of intron 13 into the transcript. In the second family, a deep intronic variant in intron 34 resulted in exonisation of 53 nucleotides of intron 34. In both families, the aberrant transcripts are predicted to be non-functional. Deleting the pseudo-exon by CRISPR-Cas9 mediated genome editing in primary and immortalised myoblasts from the index case of the second family restored wild-type SMCHD1 expression to a level that resulted in efficient suppression of DUX4.ConclusionsThe estimated intronic mutation frequency of almost 2% in FSHD2, as exemplified by the two novel intronic SMCHD1 variants identified here, emphasises the importance of screening for intronic variants in SMCHD1. Furthermore, the efficient suppression of DUX4 after restoring SMCHD1 levels by genome editing of the mutant allele provides further guidance for therapeutic strategies.

A genetic and molecular analysis of an invectedDominant mutation in Drosophila melanogaster

Genome ◽  
1998 ◽  
Vol 41 (3) ◽  
pp. 381-390 ◽  
Author(s):  
A J Simmonds ◽  
J B Bell
Keyword(s):  
Drosophila Melanogaster ◽  
Imaginal Disc ◽  
Transcriptional Start Site ◽  
Ectopic Expression ◽  
Careful Analysis ◽  
Wing Imaginal Disc ◽  
Coding Region ◽  
Specific Expression ◽  
Additional Lesion ◽  
Normal Expression

The invected gene of Drosophila melanogaster is a homeobox-containing gene that is closely related to engrailed. A dominant gain of function allele, invectedDominant, was derived from mutagenesis of a dominant allele of vestigial, In(2R)vgW. A careful analysis of the phenotype of invectedDominant shows that it is associated with a transformation of the anterior compartment of the wing to a posterior fate. This transformation is normally limited to the wing blade itself and does not involve the remaining tissues derived from the wing imaginal disc, including the wing hinge and dorsal thorax of the fly. The ectopic expression of invected protein associated with invectedDominant correlates spatially with the normal expression pattern of vestigial in the wing imaginal disc, suggesting that control elements of vestigial are driving ectopic invected expression. This was confirmed by sequence analysis that shows that the dominant vestigial activity was eliminated by a deletion that removes the 3' portion of the vestigial coding region. This leaves a gene fusion wherein the vestigial enhancer elements are still juxtaposed immediately 5' to the invected transcriptional start site, but with the vg sequences harboring an additional lesion. Unlike recessive invected alleles, the invectedDominant allele produces an observable phenotype, and as such, should prove useful in determining the role of invected in patterning the wing imaginal disc. Genetic analysis has shown that mutations of polyhomeotic, a gene involved in regulating engrailed expression, cause a reproducible alteration in the invectedDominant phenotype. Finally, the invectedDominant allele should prove valuable for identifying and characterizing genes that are activated within the posterior compartment. A screen using various lacZ lines that are asymmetrically expressed in an anterior-posterior manner in the wing imaginal disc isolated one line that shows posterior-specific expression within the transformed anterior compartment.Key words: Drosophila, development, dominant mutation, ectopic, wings.

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