scholarly journals Identification of the Ovine Keratin-Associated Protein 21-1 Gene and Its Association with Variation in Wool Traits

Animals ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. 450 ◽  
Author(s):  
Li ◽  
Zhou ◽  
Gong ◽  
Zhao ◽  
Wang ◽  
...  
Keyword(s):  
Coding Region ◽  
Gene Encoding ◽  
Coding Sequence ◽  
Sequence Variations ◽  
Associated Proteins ◽  
Wool Yield ◽  
Fleece Weight

Keratin-associated proteins (KAPs) are key constituents of wool and hair fibers. In this study, an ovine KAP gene encoding a HGT-KAP protein was identified. The gene was different from all of the HGT-KAP genes identified in sheep, but was closely related to the human KAP21-1 gene, suggesting that it represented the unidentified ovine KRTAP21-1. Four variants (named A to D) of ovine KRTAP21-1 were found in 360 Merino × Southdown-cross lambs from four sire lines. Three sequence variations were detected among these variants. Two of the sequence variations were located upstream of the coding region and the remaining one was a synonymous variation in the coding sequence. Six genotypes were found in the Merino-cross lambs, with only two of the genotypes (AA and AC) occurring at a frequency of over 5%. Wool from sheep of genotype AA had a higher yield than that from AC sheep (p = 0.014), but tended to have a lower greasy fleece weight (GFW) than that of genotype AC (P = 0.078). This suggests that variation in KRTAP21-1 affects wool yield and the gene may have potential for use as a genetic maker for improving wool yield.

Variation in the ovine keratin-associated protein 15-1 gene affects wool yield

2018 ◽  
Vol 156 (7) ◽  
pp. 922-928 ◽  
Author(s):  
W. Li ◽  
H. Gong ◽  
H. Zhou ◽  
J. Wang ◽  
X. Liu ◽  
...  
Keyword(s):  
Fibre Diameter ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Chain Reaction ◽  
Single Nucleotide ◽  
Banding Patterns ◽  
Single Stranded Conformational Polymorphism ◽  
Associated Proteins ◽  
Polymerase Chain ◽  
Wool Yield

AbstractKeratin-associated proteins (KAPs) are constituents of wool and hair fibres and are believed to play an important role in determining the characteristics of the fibres. In the current study, a polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) approach was used to screen for variation in the ovine KAP15-1 gene (KRTAP15-1). Four PCR-SSCP banding patterns, representing four different variants (named A to D), were detected. Four single nucleotide polymorphisms were found within the coding region and three of these were non-synonymous. The effect of this genetic variation on wool traits was investigated in 396 Merino × Southdown-cross sheep. Of the three variants found in these sheep (A, B and C), the presence of B was found to be associated with decreased wool yield, while C was associated with increased wool yield and decreased fibre diameter standard deviation. Sheep of genotype AC had a higher wool yield than those of genotype AA or AB.

scholarly journals Is Esterase-P Encoded by a Cryptic Pseudogene In Drosophila melanogaster?

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1511-1518
Author(s):  
Evgeniy S Balakirev ◽  
Francisco J Ayala
Keyword(s):  
Drosophila Melanogaster ◽  
Premature Termination ◽  
Indirect Evidence ◽  
Drosophila Species ◽  
Coding Region ◽  
Gene Encoding ◽  
Coding Sequence ◽  
Stop Codons ◽  
Premature Termination Codons

We have amplified and sequenced the gene encoding Esterase-P (Est-P) in 10 strains of Drosophila melanogaster. Three premature termination codons occur in the coding region of the gene in two strains. This observation, together with other indirect evidence, leads us to propose that Est-P may he a pseudogene in D. melanogaster. Est-P would he a “cryptic” pseudogene, in the sense that it retains intact the coding sequence (without stop codons and other alterations usually observed in pseudogenes) in most D. melanogaster strains. We conjecture that the β-esterase cluster may consist in other Drosophila species of functional and nonfunctional genes. We also conjecture that the rarity of detected pseudogenes in Drosophila may he due to the difficulty of discovering them, because most of them are cryptic.

scholarly journals Influence of the Leader protein coding region of foot-and-mouth disease virus on virus replication

2013 ◽  
Vol 94 (7) ◽  
pp. 1486-1495 ◽  
Author(s):  
Graham J. Belsham
Keyword(s):  
Disease Virus ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Initiation Codon ◽  
Coding Region ◽  
Protein Coding ◽  
Coding Sequence ◽  
Bhk Cells ◽  
Leader Protein ◽  
Mouth Disease Virus

The foot-and-mouth disease virus (FMDV) Leader (L) protein is produced in two forms, Lab and Lb, differing only at their amino-termini, due to the use of separate initiation codons, usually 84 nt apart. It has been shown previously, and confirmed here, that precise deletion of the Lab coding sequence is lethal for the virus, whereas loss of the Lb coding sequence results in a virus that is viable in BHK cells. In addition, it is now shown that deletion of the ‘spacer’ region between these two initiation codons can be tolerated. Growth of the virus precisely lacking just the Lb coding sequence resulted in a previously undetected accumulation of frameshift mutations within the ‘spacer’ region. These mutations block the inappropriate fusion of amino acid sequences to the amino-terminus of the capsid protein precursor. Modification, by site-directed mutagenesis, of the Lab initiation codon, in the context of the virus lacking the Lb coding region, was also tolerated by the virus within BHK cells. However, precise loss of the Lb coding sequence alone blocked FMDV replication in primary bovine thyroid cells. Thus, the requirement for the Leader protein coding sequences is highly dependent on the nature and extent of the residual Leader protein sequences and on the host cell system used. FMDVs precisely lacking Lb and with the Lab initiation codon modified may represent safer seed viruses for vaccine production.

Forebrain and midbrain regions are deleted in Otx2−/− mutants due to a defective anterior neuroectoderm specification during gastrulation

Development ◽  
1995 ◽  
Vol 121 (10) ◽  
pp. 3279-3290 ◽  
Author(s):  
D. Acampora ◽  
S. Mazan ◽  
Y. Lallemand ◽  
V. Avantaggiato ◽  
M. Maury ◽  
...  
Keyword(s):  
Transcriptional Repression ◽  
Null Allele ◽  
External Layer ◽  
Coding Region ◽  
Coding Sequence ◽  
E Coli ◽  
Homozygous Mutant

We have replaced part of the mouse homeogene Otx2 coding region with the E. coli lacZ coding sequence, thus creating a null allele of Otx2. By 9.5 dpc, homozygous mutant embryos are characterized by the absence of forebrain and midbrain regions. From the early to midstreak stages, endomesodermal cells expressing lacZ fail to be properly localized anteriorly. In the ectodermal layer, lacZ transcription is progressively extinguished, being barely detectable by the late streak stage. These data suggest that Otx2 expression in endomesoderm and ectoderm is required for anterior neuroectoderm specification. In gastrulating heterozygous embryos, a post-transcriptional repression acts on lacZ transcripts in the ectoderm, but not in the external layer, suggesting that different post-transcriptional mechanisms control Otx2 expression in both layers.

scholarly journals Hereditary Variation in Platelet Integrin α2β1 Density Is Associated With Two Silent Polymorphisms in the α2 Gene Coding Sequence

Blood ◽  
1997 ◽  
Vol 89 (6) ◽  
pp. 1939-1943 ◽  
Author(s):  
Thomas J. Kunicki ◽  
Marcie Kritzik ◽  
Douglas S. Annis ◽  
Diane J. Nugent
Keyword(s):  
Blood Platelets ◽  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Type I ◽  
Receptor Density ◽  
Coding Region ◽  
Gene Frequencies ◽  
Coding Sequence ◽  
Hereditary Variation ◽  
Donor Population

Abstract The integrin α2β1 is a receptor for collagen that plays a fundamental role in the adhesion of blood platelets to the extracellular matrix. We previously reported that platelet α2β1 levels among randomly selected individuals can vary up to 10-fold and that this correlates with differences in adhesiveness to type-I or type-III collagens. We have now found two linked, allelic polymorphisms within the coding sequence of the α2 gene that correlate with receptor density, TTT/TTC at codon Phe224 and ACA/ACG at codon Thr246. By Southern blot hybridization of specific antisense DNA probes to segments of genomic DNA that encompass each coding region, we have determined the gene frequencies of each allele in a random donor population (n = 65) to be 0.585 (TTC ... ACG) and 0.415 (TTT ... ACA). There is a statistically significant correlation between the alleles TTT ... ACA (codons 224…246) and high receptor density (n = 30; P < .002), whereas the complimentary alleles TTC ... ACG are associated with low receptor density. Heterozygous individuals express intermediate levels of this receptor, and familial studies confirm that these allelic polymorphisms are inherited characteristics. These findings prove that the level of platelet α2β1 is an inherited trait. The molecular basis for receptor density remains to be determined, but our findings establish that these silent alleles within the coding sequence of the α2 gene are linked to the genetic basis for variation in receptor density.

scholarly journals Biochemical and Genetic Studies of the Initiation of Human Rhinovirus 2 RNA Replication: Identification of a cis-Replicating Element in the Coding Sequence of 2Apro

2001 ◽  
Vol 75 (22) ◽  
pp. 10979-10990 ◽  
Author(s):  
Kinga Gerber ◽  
Eckard Wimmer ◽  
Aniko V. Paul
Keyword(s):  
Rna Replication ◽  
Human Rhinovirus ◽  
Viral Sequence ◽  
Coding Region ◽  
Terminal Protein ◽  
Genetic Studies ◽  
Poliovirus Type ◽  
Coding Sequence

ABSTRACT We have previously shown that the RNA polymerase 3Dpolof human rhinovirus 2 (HRV2) catalyzes the covalent linkage of UMP to the terminal protein (VPg) using poly(A) as a template (K. Gerber, E. Wimmer, and A. V. Paul, J. Virol. 75:10969–10978, 2001). The products of this in vitro reaction are VPgpU, VPgpUpU, and VPg-poly(U), the 5′ end of minus-strand RNA. In the present study we used an assay system developed for poliovirus 3Dpol (A. V. Paul, E. Rieder, D. W. Kim, J. H. van Boom, and E. Wimmer, J. Virol. 74: 10359–10370, 2000) to search for a viral sequence or structure in HRV2 RNA that would provide specificity to this reaction. We now show that a small hairpin in HRV2 RNA [cre(2A)], located in the coding sequence of 2Apro, serves as the primary template for HRV2 3Dpol in the uridylylation of HRV2 VPg, yielding VPgpU and VPgpUpU. The in vitro reaction is strongly stimulated by the addition of purified HRV2 3CDpro. Our analyses suggest that HRV2 3Dpol uses a “slide-back” mechanism during synthesis of the VPg-linked precursors. The corresponding cis- replicating RNA elements in the 2CATPase coding region of poliovirus type 1 Mahoney (I. Goodfellow, Y. Chaudhry, A. Richardson, J. Meredith, J. W. Almond, W. Barclay, and D. J. Evans, J. Virol. 74:4590–4600, 2000) and VP1 of HRV14 (K. L. McKnight and S. M. Lemon, RNA 4:1569–1584, 1998) can be functionally exchanged in the assay with cre(2A) of HRV2. Mutations of either the first or the second A in the conserved A1A2A3CA sequence in the loop of HRV2 cre(2A) abolished both viral growth and the RNA's ability to serve as a template in the in vitro VPg uridylylation reaction.

Studies on Western Australian Merino sheep. 1. Stud, strain and environmental effects on hogget performance

1992 ◽  
Vol 43 (6) ◽  
pp. 1381 ◽  
Author(s):  
RP Lewer ◽  
RR Woolaston ◽  
RR Howe
Keyword(s):  
Fibre Diameter ◽  
Strain Differences ◽  
Average Fibre Diameter ◽  
Weaning Age ◽  
Average Fibre ◽  
Males And Females ◽  
Wool Yield ◽  
Fleece Weight ◽  
Western Australian ◽  
Australian Merino

A 6 year study is reported of Merino studs and strains (Peppin, Collinsville and Bungaree) in Western Australia. Wool and body traits of males and females were measured, with additional subjective traits assessed on females. The effects of strain, stud (within strain), birth year, dam age, birth rearing rank, weaning age and their interactions were estimated using least squares procedures. When tested against studs, strain differences were significant for fibre diameter (both sexes), clean wool yield and about half of the subjective traits (females) but for none of the liveweights. Stud and year effects were significant for all traits, as was their interaction for most traits. Some studs were more stable between years than others in both clean fleece weight and average fibre diameter. Of the remaining effects, birth rearing rank influenced the greatest number of traits, while dam age only affected yield in ewes and some early liveweights. Peppins produced wool 2.0-2.3 microns finer than Bungarees, but not significantly different from Collinsvilles. Peppins also had the best subjective wool scores, but had the highest wrinkle scores and scored poorly on other subjective body traits. Twin-born hoggets produced 0.05-0.15 kg less clean wool than their single-born contemporaries, and their fleeces were about 0.4 microns coarser with poorer subjective qualities. Twins were also lighter from birth (by 23%) up to 17 months (by 5%) in females. Late-born lambs had higher birth weights, but lower subsequent weights, persisting until 12 months in females.

New computational model for miRNA-mediated repression reveals novel regulatory roles of miRNA bindings inside the coding region

2020 ◽  
Author(s):  
Shaked Bergman ◽  
Alon Diament ◽  
Tamir Tuller
Keyword(s):  
Binding Sites ◽  
Supplementary Information ◽  
Coding Region ◽  
Reading Frame ◽  
Coding Sequence ◽  
Elastic Net Regularization ◽  
Physiological Processes ◽  
Ribosome Density ◽  
Weak Binding ◽  
Non Coding Rnas

Abstract Motivation MicroRNAs (miRNAs) are short (∼24nt), non-coding RNAs, which downregulate gene expression in many species and physiological processes. Many details regarding the mechanism which governs miRNA-mediated repression continue to elude researchers. Results We elucidate the interplay between the coding sequence and the 3′UTR, by using elastic net regularization and incorporating translation-related features to predict miRNA-mediated repression. We find that miRNA binding sites at the end of the coding sequence contribute to repression, and that weak binding sites are linked to effective de-repression, possibly as a result of competing with stronger binding sites. Furthermore, we propose a recycling model for miRNAs dissociated from the open reading frame (ORF) by traversing ribosomes, explaining the observed link between increased ribosome density/traversal speed and increased repression. We uncover a novel layer of interaction between the coding sequence and the 3′UTR (untranslated region) and suggest the ORF has a larger role than previously thought in the mechanism of miRNA-mediated repression. Availability and implementation The code is freely available at https://github.com/aescrdni/miRNA_model. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Characterization of RPR1, an essential gene encoding the RNA component of Saccharomyces cerevisiae nuclear RNase P.

1991 ◽  
Vol 11 (2) ◽  
pp. 721-730 ◽  
Author(s):  
J Y Lee ◽  
C E Rohlman ◽  
L A Molony ◽  
D R Engelke
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Essential Gene ◽  
Rnase P ◽  
Single Copy ◽  
Temperature Sensitive ◽  
Coding Region ◽  
Gene Encoding ◽  
Processing Steps ◽  
Potential Precursor

RNA components have been identified in preparations of RNase P from a number of eucaryotic sources, but final proof that these RNAs are true RNase P subunits has been elusive because the eucaryotic RNAs, unlike the procaryotic RNase P ribozymes, have not been shown to have catalytic activity in the absence of protein. We previously identified such an RNA component in Saccharomyces cerevisiae nuclear RNase P preparations and have now characterized the corresponding, chromosomal gene, called RPR1 (RNase P ribonucleoprotein 1). Gene disruption experiments showed RPR1 to be single copy and essential. Characterization of the gene region located RPR1 600 bp downstream of the URA3 coding region on chromosome V. We have sequenced 400 bp upstream and 550 bp downstream of the region encoding the major 369-nucleotide RPR1 RNA. The presence of less abundant, potential precursor RNAs with an extra 84 nucleotides of 5' leader and up to 30 nucleotides of 3' trailing sequences suggests that the primary RPR1 transcript is subjected to multiple processing steps to obtain the 369-nucleotide form. Complementation of RPR1-disrupted haploids with one variant of RPR1 gave a slow-growth and temperature-sensitive phenotype. This strain accumulates tRNA precursors that lack the 5' end maturation performed by RNase P, providing direct evidence that RPR1 RNA is an essential component of this enzyme.

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