HNF-1 regulates the liver-specific transcription of the chipmunk HP-20 gene

A Unique Energy-Saving Strategy during Hibernation Revealed by Multi-Omics Analysis in the Chinese Alligator

Many ectotherms hibernate in face of the harsh winter conditions to improve their survival rate. However, the molecular mechanism underlying this process remains unclear. Here, we explored the hibernation mechanism of Chinese alligator using integrative multi-omics analysis. We revealed that (1) the thyroid hormone biosynthesis, nutrition absorption and metabolism, muscle contraction, urinary excretion and immunity function pathways are overall downregulated during hibernation; (2) the fat catabolism is completely suppressed, contrasting with the upregulation of hepatic fatty-acid-transporter CPT1A, suggesting a unique energy-saving strategy that differs from that in hibernating mammals; (3) the hibernation-related genes are not only directly regulated by DNA methylation but also controlled by methylation-dependent transcription networks. In addition, we identified and compared tissue-specific, species-specific, and conserved season-biased miRNAs, demonstrating complex post-transcriptional regulation during hibernation. Our study revealed the genetic and epigenetic mechanisms underlying hibernation in the Chinese alligator and provided molecular insights into the evolution of hibernation regulation.

Epigenetic regulation of hibernation-associated HP-20 and HP-27 gene transcription in chipmunk liver

The chipmunk hibernation-related proteins (HPs) HP-20 and HP-27 are components of a 140-kDa complex that dramatically decreases in the blood during hibernation. The HP-20 and HP-27 genes are expressed specifically in the liver and are downregulated in hibernating chipmunks. Hibernation-associated physiological changes are assumed to be under genetic control. Therefore, to elucidate the molecular mechanisms of hibernation, here we examined the mechanisms behind the altered HP-20 and HP-27 gene expression in nonhibernating versus hibernating chipmunks. Chromatin immunoprecipitation (ChIP) analyses revealed that histone H3 on the HP-20 and HP-27 gene promoters was highly acetylated at lysine (K) 9 and K14 and highly trimethylated at K4 in the liver of nonhibernating chipmunks, while these active histone modifications were nearly absent in hibernating chipmunks. Furthermore, histone acetyltransferases and a histone methyltransferase were associated with the HP-20 and HP-27 gene promoters primarily in nonhibernating chipmunks. Consistent with a previous finding that HNF-1 and USF can activate HP-20 and HP-27 gene transcription by binding to the proximal promoter region, ChIP-quantitative PCR (qPCR) analyses revealed that significantly less HNF-1 and USF were bound to these gene promoters in hibernating than in nonhibernating chipmunks. These findings collectively indicated that the hibernation-associated HP-20 and HP-27 gene expression is epigenetically regulated at the transcriptional level by the binding of HNF-1 and USF to their proximal promoters, and that histone modification has a key role in hibernation-associated transcriptional regulation.

Seasonal oscillation of liver-derived hibernation protein complex in the central nervous system of non-hibernating mammals

Mammalian hibernation elicits profound changes in whole-body physiology. The liver-derived hibernation protein (HP) complex, consisting of HP-20, HP-25 and HP-27, was shown to oscillate circannually, and this oscillation in the central nervous system (CNS) was suggested to play a role in hibernation. The HP complex has been found in hibernating chipmunks but not in related non-hibernating tree squirrels, leading to the suggestion that hibernation-specific genes may underlie the origin of hibernation. Here, we show that non-hibernating mammals express and regulate the conserved homologous HP complex in a seasonal manner, independent of hibernation. Comparative analyses of cow and chipmunk HPs revealed extensive biochemical and structural conservations. These include liver-specific expression, assembly of distinct heteromeric complexes that circulate in the blood and cerebrospinal fluid, and the striking seasonal oscillation of the HP levels in the blood and CNS. Central administration of recombinant HPs affected food intake in mice, without altering body temperature, physical activity levels or energy expenditure. Our results demonstrate that HP complex is not unique to the hibernators and suggest that the HP-regulated liver-brain circuit may couple seasonal changes in the environment to alterations in physiology.

Identification of bovine hibernation-specific protein complex and evidence of its regulation in fasting and aging

Hibernation-specific protein (HP) is a plasma protein that regulates hibernation in chipmunks. The HP complex (HP20c) consists of three homologous proteins, HP20, HP25 and HP27, all produced by liver and belonging to the C1q family. To date, HP20c has not been identified in any mammalian species except chipmunk and ground squirrel hibernators. Here, we report a bovine HP20 gene isolated from liver tissue and aortic endothelial cells. Total homology between bovine and chipmunk variants was 63% at the amino acid level. Gene expression was highest in the liver. Western blot revealed HP20 protein in foetal, newborn, calf and adult serum, with highest concentrations in the adult. Similar proteins were detected in sera of other ruminants but not in humans, bears, mice or rats. Bovine HP20 protein was found mainly in ovaries, stomach, heart, kidneys, lungs, testes and prostate, but not in the skeletal muscle. Native HP20 was purified from bovine adult serum as a complex containing 25 and 27 kDa proteins. Mass spectrometry revealed that these proteins are orthologues of chipmunk HP25 and HP27, respectively. Interestingly, bovine HP20 was highly expressed in cattle serum after fasting. Native bovine HP20c may be a useful tool for investigating HP function.

CpG methylation at the USF-binding site is important for the liver-specific transcription of the chipmunk HP-27 gene

The chipmunk hibernation-specific HP-27 gene is expressed specifically in the liver and has a CpG-poor promoter. To reveal how the liver-specific transcription of the HP-27 gene is regulated, we performed yeast one-hybrid screening of a chipmunk liver cDNA library. A 5'-flanking sequence of the HP-27 gene, extending from -170 to -140 and containing an E-box (5'-CACGTG-3'), is essential for the liver-specific transcription of HP-27. We used this sequence as bait and found that a ubiquitously expressed transcription factor, USF (upstream stimulatory factor), bound to the E-box. In COS-7 cells, USF activated transcription from the HP-27 gene promoter. We then used bisulphite genomic sequencing to analyse the methylation status of the four CpG dinucleotides that lie in the 5'-flanking sequence of the HP-27 gene up to -450, to investigate how the ubiquitously expressed USF activates transcription of the HP-27 gene only in the liver, while its transcription is repressed elsewhere. The only difference in methylation in the tissues tested was in the CpG dinucleotide in the USF-binding site, which was hypomethylated in the liver, but highly methylated in the kidney and heart. The specific methylation of the CpG dinucleotide at the USF-binding site impeded both the binding of USF and its transcriptional activation of the HP-27 gene. Chromatin immunoprecipitation using anti-USF antibodies revealed that USF bound to the HP-27 gene promoter in the liver, but not in the kidney or heart. Thus CpG methylation at the USF-binding site functions in establishing and maintaining tissue-specific transcription from the CpG-poor HP-27 gene promoter.

HNF-1 regulates the promoter activity of the HP-27 gene

The hibernation-specific HP-27 gene is expressed specifically in the liver of the chipmunk, a hibernating species of the squirrel family, and exists as a pseudogene in the tree squirrel, a nonhibernating species. In the promoter region, the chipmunk gene has a potential HNF-1 binding site, and the tree squirrel gene has two base substitutions in the corresponding sequence. In this paper, we investigated the role of HNF-1 in the HP-27 gene promoter activity. Gel retardation assays with in vitro-translated HNF-1 and super-shift assays using HepG2 nuclear extracts and an anti-HNF-1 antibody revealed that HNF-1 bound to the chipmunk gene sequence. HNF-1 also bound to the tree squirrel sequence, but with much lower affinity. In HepG2 cells, HNF-1 activated transcription from the chipmunk HP-27 gene, but not from the tree squirrel gene. In addition, the tree squirrel-type base substitutions in the HNF-1 binding site greatly reduced the promoter activity of the chipmunk HP-27 gene. These results indicate that HNF-1 is required for the promoter activity of the chipmunk HP-27 gene, and that the base substitutions in the HNF-1 binding site are involved in the lack of HP-27 gene expression in the tree squirrel.

Mammalian hibernation: cellular and molecular responses to depressed metabolism and low temperature

Mammalian hibernators undergo a remarkable phenotypic switch that involves profound changes in physiology, morphology, and behavior in response to periods of unfavorable environmental conditions. The ability to hibernate is found throughout the class Mammalia and appears to involve differential expression of genes common to all mammals, rather than the induction of novel gene products unique to the hibernating state. The hibernation season is characterized by extended bouts of torpor, during which minimal body temperature (Tb) can fall as low as -2.9 degrees C and metabolism can be reduced to 1% of euthermic rates. Many global biochemical and physiological processes exploit low temperatures to lower reaction rates but retain the ability to resume full activity upon rewarming. Other critical functions must continue at physiologically relevant levels during torpor and be precisely regulated even at Tb values near 0 degrees C. Research using new tools of molecular and cellular biology is beginning to reveal how hibernators survive repeated cycles of torpor and arousal during the hibernation season. Comprehensive approaches that exploit advances in genomic and proteomic technologies are needed to further define the differentially expressed genes that distinguish the summer euthermic from winter hibernating states. Detailed understanding of hibernation from the molecular to organismal levels should enable the translation of this information to the development of a variety of hypothermic and hypometabolic strategies to improve outcomes for human and animal health.

Differential expression of Akt, PPARγ, and PGC-1 during hibernation in bats

The effects of hibernation on the expression of Akt (protein kinase B), the peroxisome proliferator-activated receptor gamma isoform (PPARγ), and the PPARγ coactivator PGC-1 were assessed in seven tissues of the little brown bat, Myotis lucifugus. Western blotting revealed that the levels of active phosphorylated Akt were strongly reduced in brain, kidney, liver, and white adipose during torpor as compared with aroused animals and that total Akt protein was also reduced in white adipose during torpor. By contrast, both total and phospho-Akt were elevated in brown adipose tissue, the thermogenic organ. PPARγ and PGC-1 levels showed parallel changes in all organs. Both were strongly suppressed in brain, but levels increased significantly in all other organs during hibernation (except for PGC-1 in heart). Reduced Akt activity is consistent with a probable reduced insulin response during torpor that facilitates the mobilization of lipid reserves for fuel supply and is further supported by increased gene expression of enzymes and proteins involved in lipid catabolism under the stimulation of enhanced PPARγ and PGC-1 levels.Key words: Myotis lucifugus, mammalian hibernation, lipid metabolism in torpor, protein kinase B, peroxisome proliferator-activated receptor gamma, PPARγ coactivator.

Comparative study of HP-27 gene promoter activities between the chipmunk and tree squirrel

The chipmunk hibernation-specific protein HP-27 is a component of the 140-kDa complex that decreases in the blood during hibernation. Although the HP-27 gene is detected in both the chipmunk, a hibernating species of the squirrel family, and the tree squirrel, a nonhibernating species, it is expressed only in the chipmunk, in a liver-specific manner. To understand the difference in HP-27 gene expression between the chipmunk and tree squirrel, we isolated chipmunk and tree squirrel HP-27 genomic clones, and compared their promoter activities. Transient transfection studies in HepG2 cells revealed that the 170 bp 5'-flanking sequence of the chipmunk HP-27 gene was sufficient for liver-specific promoter activity and that deletion of the sequence from -170 to -140 reduced the promoter activity by 90%. Although the corresponding 170 bp 5'-flanking sequence of the tree squirrel HP-27 gene had 89% nucleotide sequence homology to that of the chipmunk, it showed almost no promoter activity in HepG2 cells. In a gel retardation assay using HepG2 or chipmunk liver nuclear extracts, the 5'-flanking sequence of the chipmunk HP-27 gene from -170 to -140 showed a shifted band, but the corresponding tree squirrel sequence did not. Taken together, these data indicate that a transcription factor that binds to this 5'-flanking sequence of the chipmunk HP-27 gene plays an important role in HP-27 gene expression, and the failure of this factor to bind in the case of the tree squirrel HP-27 gene could be responsible for this animal's lack of HP-27 gene expression.