Molecular characterization of the ACSS2 gene involved in adaptation to hypoxia in high-altitude cattle breeds

2020 ◽  
Vol 71 (1) ◽  
pp. 49-66
Author(s):  
Han Zhao ◽  
Yaping Gao ◽  
Qiang Jiang ◽  
Jinpeng Wang ◽  
Wenhao Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Altitude ◽  
Bos Taurus ◽  
Luciferase Activity ◽  
Core Promoter ◽  
Acetyl Coa ◽  
Altitude Hypoxia ◽  
The Core ◽  
Cattle Breeds ◽  
Bos Taurus Indicus

Abstract Under extreme environmental conditions such as hypoxia, insufficient nutrition, and glucose deficiency, the acetyl-CoA synthetase 2 (ACSS2)-mediated acetyl-CoA synthesis pathway plays an alternative role to ensure the normal operation of metabolic activities. To investigate the potential effect of the ACSS2 gene on hypoxic adaptation and its regulatory mechanism of gene expression in high-altitude cattle breeds, we analyzed the genetic variations of the ACSS2 gene in five Bos taurus taurus, Bos taurus indicus, hybrid Bos taurus taurus × Bos taurus indicus Chinese cattle breeds, and two Bos grunniens (yak) breeds distributed at different altitudes (95-3850 m). A total of 58 SNPs was detected in seven populations, and abundant genetic variation was found in high-altitude breeds. We identified the bovine ACSS2 core promoter region between g.-682 and g.-264 by using the luciferase assay in FFB and HepG2 cells. We also identified that the high-altitude hypoxia-specific haplotype (CAGTCT) was composed of six highly linked SNPs. The tagSNP g.-473 T>C (rs23) is located in the core promoter of ACSS2 in the Bos taurus taurus and yak breeds. The recombinant plasmid containing rs23 and analyses of luciferase activity of different genotypes showed that the activity of ACSS2 promoter increased significantly when T was mutated to C. We also found a yak-specific SNP rs20 that consists of 12 base insertions (g.-562 ins GAAAGGACCCTA) in the promoter of yak breeds. Luciferase activity analysis showed that the insertion mutant significantly decreased the promoter activity of ACSS2. Hence, ACSS2 may play an important role in the adaptation to high-altitude hypoxia by generating adaptive alleles to influence gene transcription in cattle. These results signify that different genetic variants and haplotypes affect the activity of the core promoter to regulate ACSS2 gene expression and subsequently overcome and adapt to a high-altitude environment within different cattle breeds. Our findings may have important implications for understanding the mechanism of adaptation to high altitude and for application of molecular breeding in Bos species.

scholarly journals The Core Promoter Is a Regulatory Hub for Developmental Gene Expression

2021 ◽  
Vol 9 ◽  
Author(s):  
Anna Sloutskin ◽  
Hila Shir-Shapira ◽  
Richard N. Freiman ◽  
Tamar Juven-Gershon
Keyword(s):  
Gene Expression ◽  
Transcriptional Activation ◽  
Transcription Initiation ◽  
Promoter Region ◽  
Core Promoter ◽  
Developmental Gene ◽  
Core Promoter Region ◽  
Developmental Gene Expression ◽  
The Core ◽  
Regulatory Module

The development of multicellular organisms and the uniqueness of each cell are achieved by distinct transcriptional programs. Multiple processes that regulate gene expression converge at the core promoter region, an 80 bp region that directs accurate transcription initiation by RNA polymerase II (Pol II). In recent years, it has become apparent that the core promoter region is not a passive DNA component, but rather an active regulatory module of transcriptional programs. Distinct core promoter compositions were demonstrated to result in different transcriptional outputs. In this mini-review, we focus on the role of the core promoter, particularly its downstream region, as the regulatory hub for developmental genes. The downstream core promoter element (DPE) was implicated in the control of evolutionarily conserved developmental gene regulatory networks (GRNs) governing body plan in both the anterior-posterior and dorsal-ventral axes. Notably, the composition of the basal transcription machinery is not universal, but rather promoter-dependent, highlighting the importance of specialized transcription complexes and their core promoter target sequences as key hubs that drive embryonic development, differentiation and morphogenesis across metazoan species. The extent of transcriptional activation by a specific enhancer is dependent on its compatibility with the relevant core promoter. The core promoter content also regulates transcription burst size. Overall, while for many years it was thought that the specificity of gene expression is primarily determined by enhancers, it is now clear that the core promoter region comprises an important regulatory module in the intricate networks of developmental gene expression.

Endothelial-cell-specific regulation of von Willebrand factor gene expression

1994 ◽  
Vol 14 (2) ◽  
pp. 999-1008
Author(s):  
N Jahroudi ◽  
D C Lynch
Keyword(s):  
Gene Expression ◽  
Endothelial Cell ◽  
Core Promoter ◽  
Regulatory Element ◽  
Regulatory Region ◽  
Specific Gene ◽  
Cell Type ◽  
The Core ◽  
Cell Type Specific ◽  
Von Willebrand

In both tissue sections and cell culture, the endothelial nature of a cell is most commonly determined by demonstration of its expression of von Willebrand factor (vWf) protein and/or mRNA. Thus, the mechanism of cell-type-specific transcriptional regulation of the vWf gene is central to studying the basis of endothelial-cell-specific gene expression. In this study, deletion analyses were carried out to identify the region of the vWf gene which regulates its endothelial-cell-specific expression. A 734-bp fragment which spans the sequence from -487 to +247 relative to the transcription start site was identified as the cell-type-specific promoter. It consists of a minimal core promoter located between -90 and +22, a strong negative regulatory element located upstream of the core promoter (ca. -500 to -300), and a positive regulatory region located downstream of the core promoter in the first exon. The activity of the core promoter is not cell type specific, and the negative regulatory region is required to inhibit its activity in all cell types. The positive regulatory region relieves this inhibition only in endothelial cells and results in endothelial-cell-specific gene expression. The positive regulatory region contains sequences predicting possible SP1, GATA, and octamer binding sites. Mutations in either the SP1 or octamer sequence have no effect on transcriptional activity, while mutation in the GATA binding element totally abolishes the promoter activity. Evidence that a GATA factor is involved in this interaction is presented. Thus, the positive regulatory region with an intact GATA binding site is required to overcome the inhibitory effect of the negative regulatory element and activate vWf gene expression in an endothelial-cell-specific manner.

scholarly journals Highly diversified core promoters in the human genome and their effects on gene expression and disease predisposition

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Hemant Gupta ◽  
Khyati Chandratre ◽  
Siddharth Sinha ◽  
Teng Huang ◽  
Xiaobing Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Genome ◽  
Transcription Initiation ◽  
Gene Expression Regulation ◽  
Core Promoter ◽  
Genome Project ◽  
Human Populations ◽  
Core Promoters ◽  
The Core ◽  
Disease Predisposition

Abstract Background Core promoter controls transcription initiation. However, little is known for core promoter diversity in the human genome and its relationship with diseases. We hypothesized that as a functional important component in the genome, the core promoter in the human genome could be under evolutionary selection, as reflected by its highly diversification in order to adjust gene expression for better adaptation to the different environment. Results Applying the “Exome-based Variant Detection in Core-promoters” method, we analyzed human core-promoter diversity by using the 2682 exome data sets of 25 worldwide human populations sequenced by the 1000 Genome Project. Collectively, we identified 31,996 variants in the core promoter region (− 100 to + 100) of 12,509 human genes (https://dbhcpd.fhs.um.edu.mo). Analyzing the rich variation data identified highly ethnic-specific patterns of core promoter variation between different ethnic populations, the genes with highly variable core promoters, the motifs affected by the variants, and their involved functional pathways. eQTL test revealed that 12% of core promoter variants can significantly alter gene expression level. Comparison with GWAS data we located 163 variants as the GWAS identified traits associated with multiple diseases, half of these variants can alter gene expression. Conclusion Data from our study reals the highly diversified nature of core promoter in the human genome, and highlights that core promoter variation could play important roles not only in gene expression regulation but also in disease predisposition.

scholarly journals Gene expression profile in zebu dairy cows (Bos taurus indicus) with mastitis caused by Streptococcus agalactiae

2015 ◽  
Vol 180 ◽  
pp. 47-57 ◽  
Author(s):  
I. Fonseca ◽  
F.F. Cardoso ◽  
R.H. Higa ◽  
P.F. Giachetto ◽  
H.M. Brandão ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dairy Cows ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Streptococcus Agalactiae ◽  
Bos Taurus ◽  
Bos Taurus Indicus

The core promoter: At the heart of gene expression

2015 ◽  
Vol 1849 (8) ◽  
pp. 1116-1131 ◽  
Author(s):  
Yehuda M. Danino ◽  
Dan Even ◽  
Diana Ideses ◽  
Tamar Juven-Gershon
Keyword(s):  
Gene Expression ◽  
Core Promoter ◽  
The Core

scholarly journals Distinctive Gene Expression Patterns and Imprinting Signatures Revealed in Reciprocal Crosses Between Cattle Sub-Species.

2020 ◽  
Author(s):  
Ruijie Liu ◽  
Rick Tearle ◽  
Wai Yee Low ◽  
Tong Chen ◽  
Dana Thomsen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fetal Development ◽  
Bos Taurus ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Reciprocal Crosses ◽  
Phenotypic Differences ◽  
Bos Taurus Indicus

Abstract Background There are two genetically distinct subspecies of cattle, Bos taurus taurus and Bos taurus indicus, which arose from independent domestication events. The two types of cattle show substantial phenotypic differences, some of which emerge during fetal development and are reflected in birth outcomes, including birth weight. We explored gene expression profiles in the placenta and four fetal tissues at mid-gestation from one taurine (Bos taurus taurus; Angus) and one indicine (Bos taurus indicus; Brahman) breed and their reciprocal crosses.Results A total of 6,456 differentially expressed genes (DEGs) were identified between the two purebreds in at least one fetal tissue of which 110 genes were differentially expressed in all five tissues examined. DEGs shared across tissues were enriched for pathways related to immune and stress response functions. Only the liver had a substantial number of DEGs when reciprocal crossed were compared among which 310 DEGs were found to be in common with DEGs identified between purebred livers; these DEGs were significantly enriched for metabolic process GO terms. Analysis of DEGs across purebred and crossbred tissues suggested an additive expression pattern for most genes, where both paternal and maternal alleles contributed to variation in gene expression levels. However, expression of 5% of DEGs in each tissue was consistent with parent of origin effects, with both paternal and maternal dominance effects identified.Conclusions These data identify candidate genes potentially driving the tissue-specific breed differences and provide biological insight into parental genome effects underlying phenotypic differences in bovine fetal development.

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