scholarly journals Conservation of gene architecture and domains amidst sequence divergence in thehsrωlncRNA gene across theDrosophilagenus: Anin silicoanalysis

2019 ◽  
Author(s):  
Ranjan Kumar Sahu ◽  
Eshita Mutt ◽  
Subhash Chandra Lakhotia
Keyword(s):  
Drosophila Melanogaster ◽  
Tandem Repeat ◽  
Tandem Repeats ◽  
Sequence Divergence ◽  
Splice Junction ◽  
Proximal Part ◽  
Order Structure ◽  
Repeat Region ◽  
Functional Conservation ◽  
Splice Junctions

AbstractThe developmentally active and cell-stress responsivehsrω locus inDrosophila melanogastercarries two exons, oneomegaintron, one short translatable open reading frame ORFω, long stretch of unique tandem repeats and an overlappingmir-4951near its 3’ end. It produces multiple lncRNAs using two transcription start and four termination sites. Earlier studies revealed functional conservation in severalDrosophilaspecies but with little sequence conservation, in three experimentally examined species, of ORFω, tandem repeat and other regions but ultra-conservation of 16nt at 5’ and 60nt at 3’ splice-junctions of theomegaintron. Present bioinformatic study, using the splice-junction landmarks inDrosophila melanogaster hsrω, identified orthologues in publicly available 34Drosophilaspecies genomes. Each orthologue carries the short ORFω, ultra-conserved splice junctions ofomegaintron, repeat region, conserved 3’-end locatedmir-4951, and syntenic neighbours. Multiple copies of conserved nonamer motifs are seen in the tandem repeat region, despite a high variability in repeat sequences. Intriguingly, only the intron sequences in different species show evolutionary relationships matching the general phylogenetic history in the genus. Search in other known insect genomes did not reveal sequence homology although a locus with similar functional properties is suggested inChironomusandCeratitisspecies. Amidst the high sequence divergence, the conserved organization of exons, ORFω andomegaintron in this gene’s proximal part and tandem repeats in distal part across theDrosophilagenus is remarkable and possibly reflects functional importance of higher order structure ofhsrω lncRNAs and the small Omega peptide.

The 93D heat shock locus of Drosophila melanogaster: modulation by genetic and developmental factors

Genome ◽  
1989 ◽  
Vol 31 (2) ◽  
pp. 677-683 ◽  
Author(s):  
S. C. Lakhotia
Keyword(s):  
Drosophila Melanogaster ◽  
Heat Shock ◽  
Developmental Regulation ◽  
Sequence Divergence ◽  
Unique Region ◽  
Reading Frame ◽  
Beta Alanine ◽  
Functional Conservation ◽  
Duplicate Loci ◽  
93D Locus

The 93D locus in Drosophila melanogaster and the 93D-like loci in other species of Drosophila, collectively termed hsr ω (heat shock RNA omega) locus, display several unique and intriguing features: (i) developmental regulation and selective induction by several agents like benzamide, colchicine, thiamphenicol, vit-B6; (ii) functional conservation in the genus but a very rapid DNA base sequence divergence; (iii) in spite of the rapid DNA sequence divergence, a strong conservation of organization (a 5′ unique region and a 3′ long tandem repeat region) and the pattern of multiple ω transcripts in the genus; (iv) a general nontranslatability of all the three major species of ω transcripts (an ~ 10-kb ω1, a 2.0-kb ω2, and a 1.2-kb ω3 species) although some recent evidence favours translatability of a small open reading frame (~ 23 – 27 amino acid long) in the ω3 transcript; (v) dispensability of the hsr ω locus for heat shock protein synthesis but indispensability for viability of flies. The heat shock inducibility of the 93D locus of D. melanogaster is selectively repressed by (i) combination of heat shock with another inducer of 93D; (ii) rearing of larvae at 10 °C; (iii) heterozygous deficiency for the 93D region; and (iv) conditions that alter levels of beta-alanine. In all cases of repression of the 93D locus during heat shock, the 87A and 87C loci (the two duplicate loci harbouring multiple copies for hsp70 and the alpha–beta repeat sequences (at 87C)) develop unequal puffs. The hsr ω locus appears to be under a complex system of regulation involving autoregulation as well as regulation by other factors in the cell which possibly operate through different control elements on the locus.Key words: benzamide, colchicine, beta-alanine, hsr ω, heat shock puffs, Drosophila.

Molecular characterization and distribution of a 145-bp tandem repeat family in the genus Populus

Genome ◽  
1999 ◽  
Vol 42 (5) ◽  
pp. 909-918 ◽  
Author(s):  
J Rajagopal ◽  
S Das ◽  
D K Khurana ◽  
P S Srivastava ◽  
M Lakshmikumaran
Keyword(s):  
Molecular Characterization ◽  
Tandem Repeat ◽  
Tandem Repeats ◽  
Populus Deltoides ◽  
Point Mutations ◽  
Sequence Divergence ◽  
Methylation Pattern ◽  
Dot Blot ◽  
Repeat Family ◽  
Sequence Comparisons

This report aims to describe the identification and molecular characterization of a 145-bp tandem repeat family that accounts for nearly 1.5% of the Populus genome. Three members of this repeat family were cloned and sequenced from Populus deltoides and P. ciliata. The dimers of the repeat were sequenced in order to confirm the head-to-tail organization of the repeat. Hybridization-based analysis using the 145-bp tandem repeat as a probe on genomic DNA gave rise to ladder patterns which were identified to be a result of methylation and (or) sequence heterogeneity. Analysis of the methylation pattern of the repeat family using methylation-sensitive isoschizomers revealed variable methylation of the C residues and lack of methylation of the A residues. Sequence comparisons between the monomers revealed a high degree of sequence divergence that ranged between 6% and 11% in P. deltoides and between 4.2% and 8.3% in P. ciliata. This indicated the presence of sub-families within the 145-bp tandem family of repeats. Divergence was mainly due to the accumulation of point mutations and was concentrated in the central region of the repeat. The 145-bp tandem repeat family did not show significant homology to known tandem repeats from plants. A short stretch of 36 bp was found to show homology of 66.7% to a centromeric repeat from Chironomus plumosus. Dot-blot analysis and Southern hybridization data revealed the presence of the repeat family in 13 of the 14 Populus species examined. The absence of the 145-bp repeat from P. euphratica suggested that this species is relatively distant from other members of the genus, which correlates with taxonomic classifications. The widespread occurrence of the tandem family in the genus indicated that this family may be of ancient origin.Key words: Satellite DNA, centromeric DNA, genome organization, phylogeny.

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 OC125, M11 and OV197 Epitopes Are Not Uniformly Distributed in the Tandem-Repeat Region of CA125 and Require the Entire SEA Domain

2013 ◽  
Vol 34 (4) ◽  
pp. 257-267 ◽  
Author(s):  
Alessandro Bressan ◽  
Francesca Bozzo ◽  
Carlo Alberto Maggi ◽  
Monica Binaschi
Keyword(s):  
Ovarian Cancer ◽  
Monoclonal Antibodies ◽  
Western Blot ◽  
Tandem Repeat ◽  
Blot Analysis ◽  
Western Blot Analysis ◽  
Human Cancer ◽  
Ovarian Cancer Cells ◽  
Repeat Region ◽  
Tandem Repeat Region

The human cancer antigen 125 (CA125) is over-expressed in epithelial ovarian cancer cells and it plays a role in the pathogenesis of ovarian cancer. This protein presents a repeat region containing up to sixty tandem repeat units. The anti-CA125 monoclonal antibodies have been previously classified into three groups: two major families, the OC125-like antibodies and M11-like antibodies, and a third group, the OV197-like antibodies. A model in which a single repeat unit contains all the epitopes for these antibodies has been also proposed, even if their exact position is still undetermined. In the present work, the affinities of the monoclonal antibodies, representative of the three families, have been investigated for different CA125-recombinant repeats through Western blot analysis. Different patterns of antibody recognition for the recombinant repeats show that CA125 epitopes are not uniformly distributed in the tandem repeat region of the protein. The minimal region for the recognition of these antibodies has been also individuated in the SEA domain through the subcloning of deleted sequences of the highly recognized repeat-25 (R-25), their expression as recombinant fragments inE. coliand Western blot analysis. Obtained data have been further confirmed by ELISA using the entire R-25 as coating antigen.

scholarly journals Slipped-Strand Mispairing at Noncontiguous Repeats in Poecilia reticulata: A Model for Minisatellite Birth

Genetics ◽  
2000 ◽  
Vol 155 (3) ◽  
pp. 1313-1320 ◽  
Author(s):  
John S Taylor ◽  
Felix Breden
Keyword(s):  
Tandem Repeat ◽  
Poecilia Reticulata ◽  
Tandem Repeats ◽  
Phylogenetic Reconstruction ◽  
Variable Number ◽  
Repeat Motif ◽  
Raw Material ◽  
Direct Repeats ◽  
Mt Dna ◽  
Variable Number Tandem Repeats

Abstract The standard slipped-strand mispairing (SSM) model for the formation of variable number tandem repeats (VNTRs) proposes that a few tandem repeats, produced by chance mutations, provide the “raw material” for VNTR expansion. However, this model is unlikely to explain the formation of VNTRs with long motifs (e.g., minisatellites), because the likelihood of a tandem repeat forming by chance decreases rapidly as the length of the repeat motif increases. Phylogenetic reconstruction of the birth of a mitochondrial (mt) DNA minisatellite in guppies suggests that VNTRs with long motifs can form as a consequence of SSM at noncontiguous repeats. VNTRs formed in this manner have motifs longer than the noncontiguous repeat originally formed by chance and are flanked by one unit of the original, noncontiguous repeat. SSM at noncontiguous repeats can therefore explain the birth of VNTRs with long motifs and the “imperfect” or “short direct” repeats frequently observed adjacent to both mtDNA and nuclear VNTRs.

scholarly journals Accurate measurement of microsatellite length by disrupting its tandem repeat structure

2021 ◽  
Author(s):  
Dan Levy ◽  
Zihua Wang ◽  
Andrea Moffitt ◽  
Michael H. Wigler
Keyword(s):  
Tandem Repeat ◽  
Error Rate ◽  
Tandem Repeats ◽  
Clinical Applications ◽  
Error Rates ◽  
Sequence Motifs ◽  
High Error Rate ◽  
Repeat Structure ◽  
Flanking Regions ◽  
Simple Sequence

Replication of tandem repeats of simple sequence motifs, also known as microsatellites, is error prone and variable lengths frequently occur during population expansions. Therefore, microsatellite length variations could serve as markers for cancer. However, accurate error-free quantitation of microsatellite lengths is difficult with current methods because of a high error rate during amplification and sequencing. We have solved this problem by using partial mutagenesis to disrupt enough of the repeat structure so that it can replicate faithfully, yet not so much that the flanking regions cannot be reliably identified. In this work we use bisulfite mutagenesis to convert a C to a U, later read as T. Compared to untreated templates, we achieve three orders of magnitude reduction in the error rate per round of replication. By requiring two independent first copies of an initial template, we reach error rates below one in a million. We discuss potential clinical applications of this method.

scholarly journals Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing

2021 ◽  
Author(s):  
Igor Stevanovski ◽  
Sanjog R. Chintalaphani ◽  
Hasindu Gamaarachchi ◽  
James M. Ferguson ◽  
Sandy S. Pineda ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Tandem Repeats ◽  
Fragile X ◽  
Genetic Diagnosis ◽  
Neuromuscular Diseases ◽  
Nanopore Sequencing ◽  
Molecular Tests ◽  
Genetic Landscape ◽  
Long Read ◽  
Short Tandem

ABSTRACTShort-tandem repeat (STR) expansions are an important class of pathogenic genetic variants. Over forty neurological and neuromuscular diseases are caused by STR expansions, with 37 different genes implicated to date. Here we describe the use of programmable targeted long-read sequencing with Oxford Nanopore’s ReadUntil function for parallel genotyping of all known neuropathogenic STRs in a single, simple assay. Our approach enables accurate, haplotype-resolved assembly and DNA methylation profiling of expanded and non-expanded STR sites. In doing so, the assay correctly diagnoses all individuals in a cohort of patients (n = 27) with various neurogenetic diseases, including Huntington’s disease, fragile X syndrome and cerebellar ataxia (CANVAS) and others. Targeted long-read sequencing solves large and complex STR expansions that confound established molecular tests and short-read sequencing, and identifies non-canonical STR motif conformations and internal sequence interruptions. Even in our relatively small cohort, we observe a wide diversity of STR alleles of known and unknown pathogenicity, suggesting that long-read sequencing will redefine the genetic landscape of STR expansion disorders. Finally, we show how the flexible inclusion of pharmacogenomics (PGx) genes as secondary ReadUntil targets can identify clinically actionable PGx genotypes to further inform patient care, at no extra cost. Our study addresses the need for improved techniques for genetic diagnosis of STR expansion disorders and illustrates the broad utility of programmable long-read sequencing for clinical genomics.One sentence summaryThis study describes the development and validation of a programmable targeted nanopore sequencing assay for parallel genetic diagnosis of all known pathogenic short-tandem repeats (STRs) in a single, simple test.

Production of Novel Recombinant Single-Domain Antibodies against Tandem Repeat Region of MUC1 Mucin

2004 ◽  
Vol 23 (3) ◽  
pp. 151-159 ◽  
Author(s):  
F. Rahbarizadeh ◽  
M.J. Rasaee ◽  
M. Forouzandeh Moghadam ◽  
A.A. Allameh ◽  
E. Sadroddiny
Keyword(s):  
Tandem Repeat ◽  
Single Domain ◽  
Repeat Region ◽  
Muc1 Mucin ◽  
Tandem Repeat Region ◽  
Single Domain Antibodies

The Short antennae gene of Tribolium is required for limb development and encodes the orthologue of the Drosophila Distal-less protein

Development ◽  
2001 ◽  
Vol 128 (2) ◽  
pp. 287-297 ◽  
Author(s):  
A. Beermann ◽  
D.G. Jay ◽  
R.W. Beeman ◽  
M. Hulskamp ◽  
D. Tautz ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Drosophila Melanogaster ◽  
Genetic Mapping ◽  
Tribolium Castaneum ◽  
Limb Development ◽  
Distal Region ◽  
Distal Limb ◽  
Functional Conservation ◽  
Young Embryo ◽  
Evolutionary Changes

Insects bear a stereotyped set of limbs, or ventral body appendages. In the highly derived dipteran Drosophila melanogaster, the homeodomain transcription factor encoded by the Distal-less (Dll) gene plays a major role in establishing distal limb structures. We have isolated the Dll orthologue (TcDll) from the beetle Tribolium castaneum, which, unlike Drosophila, develops well-formed limbs during embryogenesis. TcDll is initially expressed at the sites of limb primordia formation in the young embryo and subsequently in the distal region of developing legs, antennae and mouthparts except the mandibles. Mutations in the Short antennae (Sa) gene of Tribolium delete distal limb structures, closely resembling the Dll phenotype in Drosophila. TcDll expression is severely reduced or absent in strong Sa alleles. Genetic mapping and molecular analysis of Sa alleles also support the conclusion that TcDll corresponds to the Sa gene. Our data indicate functional conservation of the Dll gene in evolutionarily distant insect species. Implications for evolutionary changes in limb development are discussed.

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