Genome-wide census and expression profiling of chicken neuropeptide and prohormone convertase genes

Abstract

Neuropeptides regulate cell-cell signaling and influence many biological processes in vertebrates, including development, growth, and reproduction. The complex processing of neuropeptides from prohormone proteins by prohormone convertases, combined with the evolutionary distance between the chicken and mammalian species that have experienced extensive neuropeptide research, has led to the empirical confirmation of only 18 chicken prohormone proteins. To expand our knowledge of the neuropeptide and prohormone convertase gene complement, we performed an exhaustive survey of the chicken genomic, EST, and proteomic databases using a list of 95 neuropeptide and 7 prohormone convertase genes known in other species. Analysis of the EST resources and 22 microarray studies offered a comprehensive portrait of gene expression across multiple conditions. Five neuropeptide genes (apelin, cocaine-and amphetamine-regulated transcript protein, insulin-like 5, neuropeptide S, and neuropeptide B) previously unknown in chicken were identified and 62 genes were confirmed. Although most neuropeptide gene families known in human are present in chicken, there are several gene not present in the chicken. Conversely, several chicken neuropeptide genes are absent from mammalian species, including C-RF amide, c-type natriuretic peptide 1 precursor, and renal natriuretic peptide. The prohormone convertases, with one exception, were found in the chicken genome. Bioinformatic models used to predict prohormone cleavages confirm that the processing of prohormone proteins into neuropeptides is similar between species. Neuropeptide genes are most frequently expressed in the brain and head, followed by the ovary and small intestine. Microarray analyses revealed that the expression of adrenomedullin, chromogranin-A, augurin, neuromedin-U, platelet-derived growth factor A and D, proenkephalin, relaxin-3, prepronociceptin, and insulin-like growth factor I was most susceptible (P-value < 0.001) to changes in developmental stage, gender, and genetic line among other conditions studied. Our complete survey and characterization facilitates understanding of neuropeptides genes in the chicken, an animal of importance to biomedical and agricultural research.

Characterization of the prohormone complement in Amphiprion and related fish species integrating genome and transcriptome assemblies

“…In mammals, PCSK1N participates in the processing of neuropeptides and also acts as a neural chaperon. Consistent with prior studies [30,31,33,107], PCSK1N prohormone was generally not detected in homology searches within Sauropsida and non-Eutherian mammals with genome assemblies. However, a partial Terrapene mexicana triunguis PCSK1N prohormone was identified, indicating that PCSK1N may have been lost when Archosauria diverged from Testudines.…”

“…Neuropeptides are formed by enzymatic cleavage and chemical post-translational modifications of larger, inactive precursor proteins referred to as prohormones. In order to characterize these neuropeptides, the prohormone complement first needs to be revealed using sequence information and a list of known prohormones [28][29][30][31][32][33][34]. Ideally, the sequence information is obtained from the genome sequencing project of the species of interest but next-generation sequencing of the transcriptome can also be used for identification [35].…”

Transcription Factor-MicroRNA-Target Gene Networks Associated with Ovarian Cancer Survival and Recurrence

“…The transcriptome data is available at (https://tcga-data.nci.nih.gov/tcga/dataAccessMatrix.htm). The expression measurements were quantile normalized (probe level), collapsed within the miRNA, TF or gene, and log 2 transformed following the procedures available in Beehive (http://stagbeetle.animal.uiuc.edu/Beehive) [7] and previously described in [8]–[10].…”

Biology of the Gastrointestinal Tract in Poultry

“…Examples of neuropeptides expressed in small intestine include the following: cholecystokinin, chromogranin-A, augurin (oesophageal cancer-related gene 4 protein), endothelin-2, galanin, gastric inhibitory polypeptide, glucagon, neurotensin, neuromedin-U, orexin, plateletderived growth factor alpha polypeptide, secretin, somatostatin, tachykinin, precursor 1, urocortin 3, vascular endothelial growth factor D and vasoactive intestinal peptide (Delfino et al, 2010). Many neuropeptides are not expressed in the small intestine including the following: adrenomedullin, atrial natriuretic factor, C-type natriuretic peptide, C-RF amide peptide, calcitonin/calcitonin gene-related peptide 1, proopiomelanocortin, endothelin-1, endothelin-3, obestatin, gastrin-releasing peptide, islet amyloid polypeptide, insulin-like growth factor 1, insulin-like growth factor 2, insulin, pro-melanin-concentrating hormone, neurophysin-II, neuromedin-B, neuropeptide Y, osteocrin (musclin), pituitary adenylate cyclase-activating polypeptide (but detected by immunocytochemistry see below), platelet-derived growth factor beta polypeptide, platelet derived growth factor D, proenkephalin, prepronociceptin, prokineticin 2, prolactinreleasing peptide, parathyroid hormone-related protein, relaxin-3, secretogranin-1, secretogranin-2, somatoliberin, urotensin II-related peptide and vascular endothelial growth factor C (Delfino et al, 2010). The physiology of many of these neuropeptides in birds remains to be explored.…”