Molecular characterization and SNP identification in HSPB1 gene in Murrah buffalo

2015 ◽  
Author(s):  
Ashwani Arya ◽  
Archana Verma ◽  
I. D. Gupta ◽  
Shahid A. Shergojry ◽  
Ankit Magotra ◽  
...  
Keyword(s):  
Heat Shock ◽  
Marker Assisted Selection ◽  
Bos Taurus ◽  
Nucleotide Position ◽  
Coding Region ◽  
Murrah Buffalo ◽  
Future Improvement ◽  
Pcr Products ◽  
Exon 1 ◽  
Heat Shock Protein Genes

Present study was conducted on 100 lactating Murrah buffaloes maintained at LRC, NDRI Karnal (Haryana) to characterize and to identify genetic polymorphisms in HSPB1 gene. Two sets of primers specific to coding sequence of HSPB1 gene were designed using Primer3 software and PCR products of 631 bp and 670 bp were obtained. Amplicons were custom sequenced and subjected to ClustalW analysis which revealed 8 nucleotide changes, 7 in non coding region and one in coding region in Murrah buffalo sequence as compared to Bos taurus. Only one SNP at nucleotide position G225A in exon 1 of HSPB1 gene was observed in Murrah buffalo, which resulted in two genotypes GG and AG with respective frequency of 0.84 and 0.16 indicating the existence of variability in the sampled population. The study has opened the possibility of identifying and using genetic variations in major heat shock protein genes, for the future improvement of livestock through marker assisted selection.

Nucleosomal instability and induction of new upstream protein-DNA associations accompany activation of four small heat shock protein genes in Drosophila melanogaster

1986 ◽  
Vol 6 (3) ◽  
pp. 779-791
Author(s):  
I L Cartwright ◽  
S C Elgin
Keyword(s):  
Heat Shock ◽  
Heat Shock Protein ◽  
Structural Changes ◽  
Consensus Sequence ◽  
Small Heat Shock Protein ◽  
Specific Protein ◽  
Dnase I ◽  
Coding Region ◽  
Protein Factor ◽  
Heat Shock Protein Genes

We investigated in detail the structural changes that occur in nuclear chromatin upon activation of the four small heat shock protein genes in D. melanogaster. Both the chemical cleavage reagent methidiumpropyl-EDTA X iron(II) [MPE X Fe(II)] and the nuclease DNase I revealed a complex pattern of four or five hypersensitive sites upstream of each gene before activation. In addition, MPE X Fe(II) detected a short positioned array of nucleosomes located on each coding region. Upon heat shock activation a number of changes in the patterns occurred. For each gene, at least one of the upstream hypersensitive regions was eliminated or substantially shifted in position. Regions were established which became highly refractile to digestion by either MPE X Fe(II) or DNase I and, as such, appeared as small "footprints" in the pattern. The location of these refractile regions relative to the cap site varied for each gene examined. The coding regions themselves became highly accessible to DNase I. The nucleosomal arrays detected by MPE X Fe(II) were characterized by a considerable loss of detail and significantly enhanced accessibility, the extent of which probably reflected the relative transcription rate of each gene. Careful mapping of the location and extent of each upstream footprint and comparison with the DNA sequence revealed the presence at each location of two (or more) contiguous or overlapping segments that bear high homology to the heat shock consensus sequence C-T-N-G-A-A-N-N-T-T-C-N-A-G. A specific protein factor (or factors) is most likely bound at or near these sequence in heat-shocked Drosophila cells.

Sequence characterization and SNP identification of TNP1 gene in Indian cattle breeds

2017 ◽  
Author(s):  
Ashish Ranjan ◽  
K. Raja ◽  
Ranjana Sinha ◽  
I. Ganguly ◽  
I. Gupta ◽  
...  
Keyword(s):  
Promoter Region ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Coding Region ◽  
Sequence Characterization ◽  
Holstein Breed ◽  
Cattle Breeds ◽  
Pcr Rflp ◽  
Pcr Products ◽  
Indian Cattle

Present study was conducted on 50 bulls and 40 male calves of Sahiwal, Tharparkar and Karan Fries cattle maintained at ABRC and LRC, NDRI Karnal (Haryana) to characterize and identify genetic polymorphisms in TNP1 gene. A total of 1568 bp region of TNP-1 gene includes 490 bp of promoter region and two exon and one intron was sequenced and characterized in Bos indicus cattle breeds which are widely distributed in Indian sub-continent. Four sets of primers for TNP1 gene on the basis of Bos Taurus sequence (Acc. No- BK_006511) were designed using Primer3 software and PCR products of 487, 450, 455 and 250 bp were obtained. Amplicons were custom sequenced and subjected to Clustal W analysis which showed no nucleotide changes in coding region and non coding region in Indian cattle breeds as compared to Bos taurus. The 490 bp of promoter region was subjected to transcription factor binding site. Three TATA boxes and two CAAT boxes were identified in the studied fragment. Analysis of SNP was performed using restriction fragment length polymorphism (PCR-RFLP), to detect nucleotide changes in the sequence as reported (g.528G>A, SS1388116558) in Chinese Holstein breed. No polymorphisms were found for tested SNP. Only one genotype GG indicates the absence of variability in the sampled population.

scholarly journals Gonadotropine Releasing Hormone (GnRH) Receptor Profile from Cow’s Hypothalamus

2020 ◽  
Vol 38 (2) ◽  
pp. 188
Author(s):  
Irma Dian Nurani
Keyword(s):  
Bos Taurus ◽  
Gnrh Receptor ◽  
Genomic Variation ◽  
Coding Region ◽  
Government Programs ◽  
Single Nucleotide ◽  
Releasing Hormone ◽  
Pcr Product ◽  
Receptor Profile ◽  
Exon 1

Gonadotropine Releasing Hormone (GnRH) is one of the recommended hormones to overcome ovulation problems and it can increase pregnancy rate so that it is used in government programs to increase cattle population in Indonesia, although the results are not yet optimal. The purpose of this study is to compare the composition of bovine GnRH receptor nucleotides with the GenBank reference so that the level of genetic diversity of bovine receptors in Indonesia is known. PCR product sequencing using Promoter F and Exon 1 R primers were further aligned with the reference sequences of Bos Taurus GnRHR mRNA GenBank using the MEGA X program. The results of the analysis found the presence of Single Nucleotide Polymorphism (SNP) in the coding region  of 1st cow  position 38(A> T), 261(C > T), 342(C >T), 411(C >T) and 495(C > T) and 2nd cow positions 261(C >T). Changes in amino acids were also detected in 1st cow position 13 (H> L). The presence of SNP was found to indicate genomic variation between individuals at cattle receptors in Indonesia.

scholarly journals Nucleosomal instability and induction of new upstream protein-DNA associations accompany activation of four small heat shock protein genes in Drosophila melanogaster.

1986 ◽  
Vol 6 (3) ◽  
pp. 779-791 ◽  
Author(s):  
I L Cartwright ◽  
S C Elgin
Keyword(s):  
Heat Shock ◽  
Heat Shock Protein ◽  
Structural Changes ◽  
Consensus Sequence ◽  
Small Heat Shock Protein ◽  
Specific Protein ◽  
Dnase I ◽  
Coding Region ◽  
Protein Factor ◽  
Heat Shock Protein Genes

We investigated in detail the structural changes that occur in nuclear chromatin upon activation of the four small heat shock protein genes in D. melanogaster. Both the chemical cleavage reagent methidiumpropyl-EDTA X iron(II) [MPE X Fe(II)] and the nuclease DNase I revealed a complex pattern of four or five hypersensitive sites upstream of each gene before activation. In addition, MPE X Fe(II) detected a short positioned array of nucleosomes located on each coding region. Upon heat shock activation a number of changes in the patterns occurred. For each gene, at least one of the upstream hypersensitive regions was eliminated or substantially shifted in position. Regions were established which became highly refractile to digestion by either MPE X Fe(II) or DNase I and, as such, appeared as small "footprints" in the pattern. The location of these refractile regions relative to the cap site varied for each gene examined. The coding regions themselves became highly accessible to DNase I. The nucleosomal arrays detected by MPE X Fe(II) were characterized by a considerable loss of detail and significantly enhanced accessibility, the extent of which probably reflected the relative transcription rate of each gene. Careful mapping of the location and extent of each upstream footprint and comparison with the DNA sequence revealed the presence at each location of two (or more) contiguous or overlapping segments that bear high homology to the heat shock consensus sequence C-T-N-G-A-A-N-N-T-T-C-N-A-G. A specific protein factor (or factors) is most likely bound at or near these sequence in heat-shocked Drosophila cells.

scholarly journals Evolution of tissue and developmental specificity of transcription start sites in Bos taurus indicus

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Mehrnush Forutan ◽  
Elizabeth Ross ◽  
Amanda J. Chamberlain ◽  
Loan Nguyen ◽  
Brett Mason ◽  
...  
Keyword(s):  
Heat Shock ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
Genome Wide ◽  
Bos Taurus Indicus ◽  
Heat Shock Protein Genes ◽  
Tropical Adaptation ◽  
Transcriptional Start Sites

AbstractTo further the understanding of the evolution of transcriptional regulation, we profiled genome-wide transcriptional start sites (TSSs) in two sub-species, Bos taurus taurus and Bos taurus indicus, that diverged approximately 500,000 years ago. Evolutionary and developmental-stage differences in TSSs were detected across the sub-species, including translocation of dominant TSS and changes in TSS distribution. The 16% of all SNPs located in significant differentially used TSS clusters across sub-species had significant shifts in allele frequency (472 SNPs), indicating they may have been subject to selection. In spleen and muscle, a higher relative TSS expression was observed in Bos indicus than Bos taurus for all heat shock protein genes, which may be responsible for the tropical adaptation of Bos indicus.

scholarly journals The TRACE-Seq method tracks recombination alleles and identifies clonal reconstitution dynamics of gene targeted human hematopoietic stem cells

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Rajiv Sharma ◽  
Daniel P. Dever ◽  
Ciaran M. Lee ◽  
Armon Azizi ◽  
Yidan Pan ◽  
...  
Keyword(s):  
Genetic Diseases ◽  
Basic Research ◽  
Gene Correction ◽  
Coding Region ◽  
Hematopoietic Stem ◽  
Hematopoietic Reconstitution ◽  
Exon 1 ◽  
Template Library ◽  
Donor Template

AbstractTargeted DNA correction of disease-causing mutations in hematopoietic stem and progenitor cells (HSPCs) may enable the treatment of genetic diseases of the blood and immune system. It is now possible to correct mutations at high frequencies in HSPCs by combining CRISPR/Cas9 with homologous DNA donors. Because of the precision of gene correction, these approaches preclude clonal tracking of gene-targeted HSPCs. Here, we describe Tracking Recombination Alleles in Clonal Engraftment using sequencing (TRACE-Seq), a methodology that utilizes barcoded AAV6 donor template libraries, carrying in-frame silent mutations or semi-randomized nucleotides outside the coding region, to track the in vivo lineage contribution of gene-targeted HSPC clones. By targeting the HBB gene with an AAV6 donor template library consisting of ~20,000 possible unique exon 1 in-frame silent mutations, we track the hematopoietic reconstitution of HBB targeted myeloid-skewed, lymphoid-skewed, and balanced multi-lineage repopulating human HSPC clones in mice. We anticipate this methodology could potentially be used for HSPC clonal tracking of Cas9 RNP and AAV6-mediated gene targeting outcomes in translational and basic research settings.

scholarly journals Perturbation of chromatin architecture on ecdysterone induction of Drosophila melanogaster small heat shock protein genes.

1989 ◽  
Vol 9 (1) ◽  
pp. 332-335 ◽  
Author(s):  
S E Kelly ◽  
I L Cartwright
Keyword(s):  
Drosophila Melanogaster ◽  
Heat Shock ◽  
Heat Shock Protein ◽  
Intergenic Region ◽  
Small Heat Shock Protein ◽  
Dnase I ◽  
Developmentally Regulated ◽  
Regulatory Interactions ◽  
Chromatin Architecture ◽  
Heat Shock Protein Genes

Alterations in the pattern of DNase I hypersensitivity were observed on ecdysterone-stimulated transcription of Drosophila melanogaster small heat shock protein genes. Perturbations were induced near hsp27 and hsp22, coupled with an extensive domain of chromatin unfolding in the intergenic region between hsp23 and the developmentally regulated gene 1. These regions represent candidates for ecdysterone regulatory interactions.

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.

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