Poikilothermic animals living in high-altitude environments can be greatly affected by the anaerobic metabolism and lactate recycling, which are catalyzed by an enzyme called lactate dehydrogenase(LDH). However, the f...Poikilothermic animals living in high-altitude environments can be greatly affected by the anaerobic metabolism and lactate recycling, which are catalyzed by an enzyme called lactate dehydrogenase(LDH). However, the function and possible regulatory mechanisms of their anaerobic glycolysis remained elusive. We compared the difference in LDH between a native high-altitude(4 353 m) lizard, Phrynocephalus erythrurus, and a closely related species, Phrynocephalus przewalskii that lives in intermediate altitude environment(1 400 m). The activity of LDH, the concentration of lactate, the distribution of isoenzyme, and the mRNA amounts of Ldh-A and Ldh-B were determined. In cardiac muscle, the lactate-forming activity of P. erythrurus in LDH was higher than of P. przewalskii LDH at all three temperatures tested(10 °C, 25 °C and 35 °C), while lactate-oxidation activity of LDH was significantly different between the two species only at 25 °C and 35 °C. In skeletal muscle, both lactate-forming and lactate-oxidation rates of P. erythrurus were lower than that of P. przewalskii. There was a higher proportion of H subunit and a significantly higher expression of Ldh-B, with a concomitant decrease of lactate concentration in P. erythrurus. These results indicate that P. erythrurus may have a strong potential for anaerobic metabolism, which is likely adapted to the hypoxic environment at high altitudes. Furthermore, P. erythrurus is capable of oxidizing more lactate than P. przewalskii. The Ldh-A cDNA of the two species consists of a 999 bp open reading frame(ORF), which encodes 332 amino acids, while Ldh-B cDNA consists of a 1 002 bp ORF encoding 333 amino acids. LDHA has the same amino acid sequence between the two species, but three amino acid substitutions(V12 I, N21S and N318K) were observed in LDHB. Structure analysis of LDH indicated that the substitutions of residues Val12 and Asp21 in P. erythrurus could be responsible for the highaltitude adaptation. The LDH characteristics of LDH in P. erythrurus suggest unique adaptation strategies of anaerobic metabolism in hypoxia and cold environments at high altitudes for poikilothermic animals.展开更多
Sheep were domesticated in the Fertile Crescent and then spread globally,where they have been encountering various environmental conditions.The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau ...Sheep were domesticated in the Fertile Crescent and then spread globally,where they have been encountering various environmental conditions.The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau over the past 3000 years.To explore genomic variants associated with high-altitude adaptation in Tibetan sheep,we analyzed Illumina short-reads of 994 whole genomes representing∼60 sheep breeds/populations at varied altitudes,PacBio High fidelity(HiFi)reads of 13 breeds,and 96 transcriptomes from 12 sheep organs.Association testing between the inhabited altitudes and 34,298,967 variants was conducted to investigate the genetic architecture of altitude adaptation.Highly accurate HiFi reads were used to complement the current ovine reference assembly at the most significantly associatedβ-globin locus and to validate the presence of two haplotypes A and B among 13 sheep breeds.The haplotype A carried two homologous gene clusters:(1)HBE1,HBE2,HBB-like,and HBBC,and(2)HBE1-like,HBE2-like,HBB-like,and HBB;while the haplotype B lacked the first cluster.The high-altitude sheep showed highly frequent or nearly fixed haplotype A,while the low-altitude sheep dominated by haplotype B.We further demonstrated that sheep with haplotype A had an increased hemoglobin–O_(2)affinity compared with those carrying haplotype B.Another highly associated genomic region contained the EGLN1 gene which showed varied expression between high-altitude and low-altitude sheep.Our results provide evidence that the rapid adaptive evolution of advantageous alleles play an important role in facilitating the environmental adaptation of Tibetan sheep.展开更多
Altered three-dimensional architecture of chromatin influences various genomic regulators and subsequent gene expression in human cancer.However,knowledge of the topological rearrangement of genomic hierarchical layer...Altered three-dimensional architecture of chromatin influences various genomic regulators and subsequent gene expression in human cancer.However,knowledge of the topological rearrangement of genomic hierarchical layers in cancer is largely limited.Here,by taking advantage of in situ Hi-C,RNA-sequencing,and chromatin immunoprecipitation sequencing(ChIP-seq),we investigated structural reorganization and functional changes in chromosomal compartments,topologically associated domains(TADs),and CCCTC binding factor(CTCF)-mediated loops in gallbladder cancer(GBC)tissues and cell lines.We observed that the chromosomal compartment A/B switch was correlated with CTCF binding levels and gene expression changes.Increased inter-TAD interactions with weaker TAD boundaries were identified in cancer cell lines relative to normal controls.Furthermore,the chromatin short loops and cancer unique loops associated with chromatin remodeling and epithelial–mesenchymal transition activation were enriched in cancer compared with their control counterparts.Cancer-specific enhancer–promoter loops,which contain multiple transcription factor binding motifs,acted as a central element to regulate aberrant gene expression.Depletion of individual enhancers in each loop anchor that connects with promoters led to the inhibition of their corresponding gene expressions.Collectively,our data offer the landscape of hierarchical layers of cancer genome and functional alterations that contribute to the development of GBC.展开更多
基金supported by the National Natural Science Foundation of China (No. 31501860 to Xiaolong TANG, No. 31272313 and No. 31472005 to Qiang CHEN) Fundamental Research Funds for the Central Universities (lzujbky-2017-150 to Xiaolong TANG)Natural Science Foundation of Gansu Province: 1506RJYA243
文摘Poikilothermic animals living in high-altitude environments can be greatly affected by the anaerobic metabolism and lactate recycling, which are catalyzed by an enzyme called lactate dehydrogenase(LDH). However, the function and possible regulatory mechanisms of their anaerobic glycolysis remained elusive. We compared the difference in LDH between a native high-altitude(4 353 m) lizard, Phrynocephalus erythrurus, and a closely related species, Phrynocephalus przewalskii that lives in intermediate altitude environment(1 400 m). The activity of LDH, the concentration of lactate, the distribution of isoenzyme, and the mRNA amounts of Ldh-A and Ldh-B were determined. In cardiac muscle, the lactate-forming activity of P. erythrurus in LDH was higher than of P. przewalskii LDH at all three temperatures tested(10 °C, 25 °C and 35 °C), while lactate-oxidation activity of LDH was significantly different between the two species only at 25 °C and 35 °C. In skeletal muscle, both lactate-forming and lactate-oxidation rates of P. erythrurus were lower than that of P. przewalskii. There was a higher proportion of H subunit and a significantly higher expression of Ldh-B, with a concomitant decrease of lactate concentration in P. erythrurus. These results indicate that P. erythrurus may have a strong potential for anaerobic metabolism, which is likely adapted to the hypoxic environment at high altitudes. Furthermore, P. erythrurus is capable of oxidizing more lactate than P. przewalskii. The Ldh-A cDNA of the two species consists of a 999 bp open reading frame(ORF), which encodes 332 amino acids, while Ldh-B cDNA consists of a 1 002 bp ORF encoding 333 amino acids. LDHA has the same amino acid sequence between the two species, but three amino acid substitutions(V12 I, N21S and N318K) were observed in LDHB. Structure analysis of LDH indicated that the substitutions of residues Val12 and Asp21 in P. erythrurus could be responsible for the highaltitude adaptation. The LDH characteristics of LDH in P. erythrurus suggest unique adaptation strategies of anaerobic metabolism in hypoxia and cold environments at high altitudes for poikilothermic animals.
基金supported by the Tibetan R&D Program,China(Grant No.XZ202101ZD0001N)the China Agriculture Research System(Grant No.CARS-39)the National Natural Science Foundation of China(Grant Nos.31900313,32161143010,and 31972526).
文摘Sheep were domesticated in the Fertile Crescent and then spread globally,where they have been encountering various environmental conditions.The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau over the past 3000 years.To explore genomic variants associated with high-altitude adaptation in Tibetan sheep,we analyzed Illumina short-reads of 994 whole genomes representing∼60 sheep breeds/populations at varied altitudes,PacBio High fidelity(HiFi)reads of 13 breeds,and 96 transcriptomes from 12 sheep organs.Association testing between the inhabited altitudes and 34,298,967 variants was conducted to investigate the genetic architecture of altitude adaptation.Highly accurate HiFi reads were used to complement the current ovine reference assembly at the most significantly associatedβ-globin locus and to validate the presence of two haplotypes A and B among 13 sheep breeds.The haplotype A carried two homologous gene clusters:(1)HBE1,HBE2,HBB-like,and HBBC,and(2)HBE1-like,HBE2-like,HBB-like,and HBB;while the haplotype B lacked the first cluster.The high-altitude sheep showed highly frequent or nearly fixed haplotype A,while the low-altitude sheep dominated by haplotype B.We further demonstrated that sheep with haplotype A had an increased hemoglobin–O_(2)affinity compared with those carrying haplotype B.Another highly associated genomic region contained the EGLN1 gene which showed varied expression between high-altitude and low-altitude sheep.Our results provide evidence that the rapid adaptive evolution of advantageous alleles play an important role in facilitating the environmental adaptation of Tibetan sheep.
基金supported by the National Natural Science Foundation of China(Nos.81874181,81902361,3213000192,and 91940305)the National Science and Technology Major Projects for“Major New Drug Innovation and Development”(No.2019ZX09301-158)+1 种基金the Shanghai Sailing Program(No.19YF1433000)the Open Project Program of State Key Laboratory of Oncogenes and Related Genes(No.KF2120).
文摘Altered three-dimensional architecture of chromatin influences various genomic regulators and subsequent gene expression in human cancer.However,knowledge of the topological rearrangement of genomic hierarchical layers in cancer is largely limited.Here,by taking advantage of in situ Hi-C,RNA-sequencing,and chromatin immunoprecipitation sequencing(ChIP-seq),we investigated structural reorganization and functional changes in chromosomal compartments,topologically associated domains(TADs),and CCCTC binding factor(CTCF)-mediated loops in gallbladder cancer(GBC)tissues and cell lines.We observed that the chromosomal compartment A/B switch was correlated with CTCF binding levels and gene expression changes.Increased inter-TAD interactions with weaker TAD boundaries were identified in cancer cell lines relative to normal controls.Furthermore,the chromatin short loops and cancer unique loops associated with chromatin remodeling and epithelial–mesenchymal transition activation were enriched in cancer compared with their control counterparts.Cancer-specific enhancer–promoter loops,which contain multiple transcription factor binding motifs,acted as a central element to regulate aberrant gene expression.Depletion of individual enhancers in each loop anchor that connects with promoters led to the inhibition of their corresponding gene expressions.Collectively,our data offer the landscape of hierarchical layers of cancer genome and functional alterations that contribute to the development of GBC.
