Expression profiling analysis of hypoxic pulmonary disease

Zhou, Ling; Wang, L.M.; Song, Haoming; Yi, Siyan; Xu, Wenjuan; Xu, Jiaming; Liu, Y.; Yan, Wan-Hui; Jiang, Jinlan

doi:10.4238/2013.october.7.2

Cited by 14 publications

(16 citation statements)

References 37 publications

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“…Previously, it has been shown in B16 murine melanoma cells that KCTD12 is up-regulated in hypoxic conditions[59], and thus it may play a role in the hypoxic responses. This gene is predominantly expressed in fetal organs, suggesting a potentially important role in early development, but dramatically lower levels in adult tissue including brain and lung[60].…”

Section: Discussionmentioning

confidence: 99%

“…This gene is predominantly expressed in fetal organs, suggesting a potentially important role in early development, but dramatically lower levels in adult tissue including brain and lung[60]. KCTD12 is differentially expressed in human pulmonary endothelial cells upon 48 hours of hypoxia exposure[59] and noted as one of 40 CpG sites with the greatest difference in methylation levels between highland and lowland Oromo Ethiopians[61]. …”

Section: Discussionmentioning

confidence: 99%

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Evolutionary history of Tibetans inferred from whole-genome sequencing

Petousi

Glusman

et al. 2017

PLoS Genet

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The indigenous people of the Tibetan Plateau have been the subject of much recent interest because of their unique genetic adaptations to high altitude. Recent studies have demonstrated that the Tibetan EPAS1 haplotype is involved in high altitude-adaptation and originated in an archaic Denisovan-related population. We sequenced the whole-genomes of 27 Tibetans and conducted analyses to infer a detailed history of demography and natural selection of this population. We detected evidence of population structure between the ancestral Han and Tibetan subpopulations as early as 44 to 58 thousand years ago, but with high rates of gene flow until approximately 9 thousand years ago. The CMS test ranked EPAS1 and EGLN1 as the top two positive selection candidates, and in addition identified PTGIS, VDR, and KCTD12 as new candidate genes. The advantageous Tibetan EPAS1 haplotype shared many variants with the Denisovan genome, with an ancient gene tree divergence between the Tibetan and Denisovan haplotypes of about 1 million years ago. With the exception of EPAS1, we observed no evidence of positive selection on Denisovan-like haplotypes.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Evolutionary history of Tibetans inferred from whole-genome sequencing

Petousi

Glusman

et al. 2017

PLoS Genet

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“…There are four genes that show strong GxE interactions that also have SNVs within the proximal promoter: Apold1 (Apolipoprotein L domain containing 1), Leo1 (Paf1/RNA Polymerase II Complex Component ), Psme4 (Proteasome Activator Subunit 4) and Snord38a (Small nucleolar RNA, C/D box 38A) (Table 2). Apold1 is thought to be involved in angiogenesis in the brain vasculature (Diez-Roux et al, 2011; Zhou et al, 2013); Leo1 , which important in chromatin remodeling, is involved in neural crest development (Wertz and Herrmann, 2000); Psme4 is a component of the proteasome that specifically targets histones for degradation following DNA damage (Ustrell et al, 2002; Qian et al, 2013); and Snord38a is a C/D box small nucleolar RNA that is important for 2′O-ribose methylation of rRNAs (Nicoloso et al, 1996). …”

Section: Resultsmentioning

confidence: 99%

Implications of genomic signatures in the differential vulnerability to fetal alcohol exposure in C57BL/6 and DBA/2 mice

Lossie

Muir

et al. 2014

Front. Genet.

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Maternal alcohol consumption inflicts a multitude of phenotypic consequences that range from undetectable changes to severe dysmorphology. Using tightly controlled murine studies that deliver precise amounts of alcohol at discrete developmental stages, our group and other labs demonstrated in prior studies that the C57BL/6 and DBA/2 inbred mouse strains display differential susceptibility to the teratogenic effects of alcohol. Since the phenotypic diversity extends beyond the amount, dosage and timing of alcohol exposure, it is likely that an individual's genetic background contributes to the phenotypic spectrum. To identify the genomic signatures associated with these observed differences in alcohol-induced dysmorphology, we conducted a microarray-based transcriptome study that also interrogated the genomic signatures between these two lines based on genetic background and alcohol exposure. This approach is called a gene x environment (GxE) analysis; one example of a GxE interaction would be a gene whose expression level increases in C57BL/6, but decreases in DBA/2 embryos, following alcohol exposure. We identified 35 candidate genes exhibiting GxE interactions. To identify cis-acting factors that mediated these interactions, we interrogated the proximal promoters of these 35 candidates and found 241 single nucleotide variants (SNVs) in 16 promoters. Further investigation indicated that 186 SNVs (15 promoters) are predicted to alter transcription factor binding. In addition, 62 SNVs created, removed or altered the placement of a CpG dinucleotide in 13 of the proximal promoters, 53 of which overlapped putative transcription factor binding sites. These 53 SNVs are also our top candidates for future studies aimed at examining the effects of alcohol on epigenetic gene regulation.

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“…TMCO5A is related to spermatogenesis and testis development processes with signi cant glycolysis and pyruvate metabolism [42,43,44]. KCTD12 is a component of the G-protein-coupled receptors for Y-aminobutyric acid receptor and using B16 murine melanoma cells it has been shown that it may play a role in hypoxic responses [45,46]. Several studies have implicated mutations in ADAMTS20 in skin pigmentation [47,48].…”

Section: Discussionmentioning

confidence: 99%

Genomic signatures of divergent selection for production and adaptation in domestic goats (Capra hircus)

Mwacharo¹,

Kim²,

Elbeltagy³

et al. 2019

Preprint

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Background : Goats are distributed worldwide and include many breeds with marked phenotypic variation. Both natural and human driven processes have shaped their genomes. Here, 52K genome-wide SNP genotypes were used to investigate signatures of divergent selection between indigenous goats from an arid hot environment in Egypt and breeds developed under temperate environments in Europe. Three selection signature approaches were used, the di derivative of F ST , iHS and Rsb. Results: Out of a total of 36 candidate regions that were detected to be under selection by the three approaches, the analysis detected nine regions with the strongest selection signatures spanning 134 genes of which 68 were the most significantly functionally enriched. In addition to well-known genes affecting dairy traits ( LAP3 , ABCG2 , MEPE , IBSP , MED28 ) and body weight and stature ( LCORL , NCAPG , CCSER1 , DCAF16 ) in several mammalian species, we found evidence for selection in regions spanning genes implicated in the regulation of fatty acid synthesis and metabolic pathways ( PI4K2B and PPARGC1A ), inflammatory gene expression and autoimmune response pathways ( CXCL8 , HERC5 , RGS18 , TROVE2 ) and spermatogenesis ( SPATA18 , LAP3 ). Other genes not reported before in goats included SLIT2 , PACRGL , GRP125 , DHX15 , SOD3 and KCNIP4 which have been associated with thermal nociception in mice. We also detected a paralog of TBC1D12 , namely TBC1D14 , in one of the candidate regions. TBC1D12 has been linked to environmental adaptation in sheep. Gene ontology analysis revealed the 68 candidate genes were highly enriched in two biological processes viz regulation of G protein-coupled receptor signaling pathway (GO:0045744) and cellular response to stress (GO:0033554). Conclusions: Our results provide evidence that goat genomes have evolved, in part, via diverse positive selection directed at breed formation, at past and recent genetic improvement and adaptation to environments. Based on their uniqueness, these breed-group specific signatures of selection can be considered to be footprints of divergence which may be useful in characterizing genome architecture and diversity in domestic animals and for targeted genetic improvement.

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Expression profiling analysis of hypoxic pulmonary disease

Cited by 14 publications

References 37 publications

Evolutionary history of Tibetans inferred from whole-genome sequencing

Evolutionary history of Tibetans inferred from whole-genome sequencing

Implications of genomic signatures in the differential vulnerability to fetal alcohol exposure in C57BL/6 and DBA/2 mice

Genomic signatures of divergent selection for production and adaptation in domestic goats (Capra hircus)

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