Domestic animals are excellent models for genetic studies of phenotypic evolution. They have evolved genetic adaptations to a new environment, the farm, and have been subjected to strong human-driven selection leading to remarkable phenotypic changes in morphology, physiology and behaviour. Identifying the genetic changes underlying these developments provides new insight into general mechanisms by which genetic variation shapes phenotypic diversity. Here we describe the use of massively parallel sequencing to identify selective sweeps of favourable alleles and candidate mutations that have had a prominent role in the domestication of chickens (Gallus gallus domesticus) and their subsequent specialization into broiler (meat-producing) and layer (egg-producing) chickens. We have generated 44.5-fold coverage of the chicken genome using pools of genomic DNA representing eight different populations of domestic chickens as well as red jungle fowl (Gallus gallus), the major wild ancestor. We report more than 7,000,000 single nucleotide polymorphisms, almost 1,300 deletions and a number of putative selective sweeps. One of the most striking selective sweeps found in all domestic chickens occurred at the locus for thyroid stimulating hormone receptor (TSHR), which has a pivotal role in metabolic regulation and photoperiod control of reproduction in vertebrates. Several of the selective sweeps detected in broilers overlapped genes associated with growth, appetite and metabolic regulation. We found little evidence that selection for loss-of-function mutations had a prominent role in chicken domestication, but we detected two deletions in coding sequences that we suggest are functionally important. This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research.

This study identifies a previously uncharacterized protein, encoded by a domesticated DNA transposon, called ZBED6 that regulates the expression of the insulin-like growth factor 2 (IGF2) gene, and possibly numerous others, in all placental mammals including human.

Major urinary protein (MUP) 1 is a lipocalin family member abundantly secreted into the circulation by the liver. MUP1 binds to lipophilic pheromones and is excreted in urine. Urinary MUP1/pheromone complexes mediate chemical communication in rodents. However, it is unclear whether circulatory MUP1 has additional physiological functions. Here we show that MUP1 regulates glucose and lipid metabolism. MUP1 expression was markedly reduced in both genetic and dietary fat-induced obesity and diabetes. Mice were infected with MUP1 adenoviruses via tail vein injection, and recombinant MUP1 was overexpressed in the liver and secreted into the bloodstream. Recombinant MUP1 markedly attenuated hyperglycemia and glucose intolerance in genetic (db/db) and dietary fat-induced type 2 diabetic mice as well as in streptozotocininduced type 1 diabetic mice. MUP1 inhibited the expression of both gluconeogenic genes and lipogenic genes in the liver. Moreover, recombinant MUP1 directly decreased glucose production in primary hepatocyte cultures by inhibiting the expression of gluconeogenic genes. These data suggest that MUP1 regulates systemic glucose and/or lipid metabolism through the paracrine/autocrine regulation of the hepatic gluconeogenic and/or lipogenic programs, respectively.Circulatory glucose is maintained within a narrow range by a sophisticated regulatory system to provide a constant fuel supply for cell metabolism. The liver plays a key role in the maintenance of systemic glucose homeostasis. In the absorptive state, ingested glucose is taken up by hepatocytes and converted to glycogen and lipids. In the postabsorptive state, hepatocytes produce glucose, which is secreted into the circulation. Insulin and counter-regulatory hormones (e.g. glucagon and glucocorticoids) regulate hepatic glucose production mainly by regulating the hepatic gluconeogenic program. Insulin decreases hepatic glucose production by suppressing the expression of key gluconeogenic genes, including phosphoenolpyruvate carboxykinase (PEPCK) 2 and glucose-6-phosphatase (G6Pase);conversely, counter-regulatory hormones increase hepatic glucose production by stimulating the transcription of these genes. The hepatic gluconeogenic program is activated at abnormally high levels in diabetic subjects, contributing to hyperglycemia (1). Hyperglycemia initiates pathological changes in multiple tissues, contributing to neuropathy, nephropathy, and cardiovascular disorders in both type 1 and type 2 diabetes. The liver secretes a variety of proteins, including insulin likegrowth factor-1 (IGF-1), insulin-like growth factor-binding proteins, fibroblast growth factor-21 (FGF-21) and major urinary proteins (MUPs) (2-6). Insulin-like growth factor-binding proteins and FGF-21 have been well documented to regulate multiple aspects of glucose and lipid metabolism in animals (2, 3, 7). Interestingly, resveratrol treatments markedly increase MUP1 expression (8). Resveratrol also reduces hyperglycemia and improves insulin sensitivity in high fat diet (HFD)-fed mice (8). ...

Ruminants are the only extant mammalian group possessing bony (osseous) headgear. We obtained 221 transcriptomes from bovids and cervids and sequenced three genomes representing the only two pecoran lineages that convergently lack headgear. Comparative analyses reveal that bovid horns and cervid antlers share similar gene expression profiles and a common cellular basis developed from neural crest stem cells. The rapid regenerative properties of antler tissue involve exploitation of oncogenetic pathways, and at the same time some tumor suppressor genes are under strong selection in deer. These results provide insights into the evolutionary origin of ruminant headgear as well as mammalian organ regeneration and oncogenesis.

Damaged, necrotic, or apoptotic hepatocytes release damage-associated molecular patterns that initiate sterile inflammation, and liver inflammation drives liver injury and fibrosis. Here we identified hepatic NF-κB-inducing kinase (NIK), a Ser/Thr kinase, as a novel trigger of fatal liver inflammation. NIK is activated by a broad spectrum of stimuli. It was upregulated in injured livers in both mice and humans. In primary mouse hepatocytes, NIK overexpression stimulated, independently of cell injury and death, release of numerous chemokines and cytokines that activated bone marrow-derived macrophages (BMDMs). BMDMs in turn secreted pro-apoptotic molecules that stimulated hepatocyte apoptosis. Hepatocyte-specific expression of the NIK transgene triggered massive liver inflammation, oxidative stress, hepatocyte apoptosis, and liver fibrosis, leading to weight loss, hypoglycemia, and death. Depletion of Kupffer cells/macrophages reversed NIK-induced liver destruction and death. Conclusion the hepatocyte NIK-liver immune cell axis promotes liver inflammation, injury and fibrosis, thus driving liver disease progression.

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The canonical IKKβ/NF-κB1 pathway has been well documented to promote insulin resistance; however, the noncanonical NIK/NF-κB2 pathway is poorly understood in obesity. Additionally, the contribution of counterregulatory hormones, particularly glucagon, to hyperglycemia in obesity remains unclear. Here we show that NIK promotes glucagon responses in obesity. Hepatic NIK was abnormally-activated in mice with dietary or genetic obesity. Systemic deletion of NIK decreased glucagon responses and hepatic glucose production (HGP). Obesity is associated with increased glucagon responses, and liver-specific inhibition of NIK decreased glucagon responses and HGP and protected against hyperglycemia and glucose intolerance. Conversely, hepatocyte-specific overexpression of NIK increased glucagon responses and HGP. In isolated livers and primary hepatocytes, NIK also promoted glucagon action and glucose production, at least in part by increasing CREB stability. Therefore, overactivation of liver NIK in obesity promotes hyperglycemia and glucose intolerance by increasing the hyperglycemic response to glucagon and other factors that activate CREB.

Thermogenesis is an important contributor to whole body energy expenditure and metabolic homeostasis. Although circulating factors that promote energy expenditure are known, endocrine molecules that suppress energy expenditure have remained largely elusive. Here we show that Tsukushi (TSK) is a liver-enriched secreted factor that is highly inducible in response to increased energy expenditure. Hepatic Tsk expression and plasma TSK levels are elevated in obesity. TSK deficiency increases sympathetic innervation and norepinephrine release in adipose tissue, leading to enhanced adrenergic signaling and thermogenesis, attenuation of brown fat whitening and protection from diet-induced obesity in mice. Our work reveals TSK as part of a negative feedback mechanism that gates thermogenic energy expenditure and highlights TSK as a potential target for therapeutic intervention in metabolic disease.