Kehoemack9979

Being the center of the hypothalamus-pituitary-ovary (HPO) axis, the pituitary plays a key role in the onset of puberty. Recent studies show that circular RNAs (circRNAs) can perform as miRNA sponges to regulate development in animals. However, the function of pituitary-derived circRNAs in first estrus remains unclear in pigs. In this study, we performed a genome-wide identification and characterization of circRNAs using pituitaries from Landrace × Yorkshire crossbred pigs at three stages pre-, in-, and post-puberty, to describe such pituitary-derived circRNAs in pigs. A total of 5148 circRNAs were found in the gilts' pituitaries, averaging 18 682 bp in genomic distance, which consisted of approximately 91% exonic, 6% intergenic, and 3% intronic circRNAs. Furthermore, 158 novel circRNAs were identified for the first time and classified as putative pituitary-specific circRNAs. Their expression levels during the onset of puberty, significantly exceeded those of the other circRNAs, and the parental genes of these putative pituitary-specific circRNAs were enriched in "ssc04917 prolactin signaling pathway," "ssc04080 neuroactive ligand-receptor interaction," and "ssc04728 dopaminergic synapse" pathways, all of which were consistent with pituitary functioning. Additionally, 17 differentially regulated circRNAs were found and investigated for their potential interaction with miRNAs, along with genes, by constructing a circRNA-targeted miRNA-gene network. Taken together, these results provide new insight into the circRNA-mediated timing of puberty in gilts at the pituitary level. Copyright © 2020 Chen, Pan, Kong, Jiang, Zhong, Zhang, Zhang, Yuan and Li.Tie2, coded by the TEK gene, is a tyrosine kinase receptor and plays a central role in vascular stability. It was suggested that variations in the TEK gene might influence the susceptibility to asthma and allergic conjunctivitis. The aim of this study was to further investigate these suggestions, involving different populations and to study the Tie2 related pathway on a mouse model of asthma. The discovery, stage I cohort involved 306 patients with moderate and severe allergic rhinitis, the stage II study consisted of four cohorts, namely, adult and pediatric asthmatics and corresponding controls. Altogether, there were 1,258 unrelated individuals in these cohorts, out of which 63.9% were children and 36.1% were adults. In stage I, 112 SNPs were screened in the TEK gene of the patients in order to search for associations with asthma and allergic conjunctivitis. The top associated SNPs were selected for association studies on the replication cohorts. The rs3824410 SNP was nominally associated with a reduced rine and its variations might have a role in asthma and allergic conjunctivitis. The gene and its associated pathways can be potential therapeutic targets in both diseases. Copyright © 2020 Gál, Gézsi, Molnár, Nagy, Kiss, Sultész, Csoma, Tamási, Gálffy, Bálint, Póliska and Szalai.The Montana Tropical® Composite is a recently developed beef cattle population that is rapidly expanding in Brazil and other tropical countries. This is mainly due to its improved meat quality and adaptation to tropical climate conditions compared to Zebu and Taurine cattle breeds, respectively. This study aimed to investigate the genetic architecture of ultrasound-based carcass and meat quality traits in Montana Tropical® Composite beef cattle. Therefore, we estimated variance components and genetic parameters and performed genome-wide association studies using the weighted single-step Genomic Best Linear Unbiased Prediction (GBLUP) approach. A pedigree dataset containing 28,480 animals was used, in which 1,436 were genotyped using a moderate-density Single Nucleotide Polymorphism panel (30K; 30,105 SNPs). A total of 9,358, 5,768, 7,996, and 1,972 phenotypic records for the traits Longissimus muscle area (LMA), backfat thickness (BFT), rump fat thickness (RFT), and for marbling score (MARB), respectively, weknown genomic regions related to these traits were identified, which contribute to a better understanding of the underlying genetic background of LMA, BFT, RFT, and MARB in the Montana Tropical Composite population. Copyright © 2020 Grigoletto, Ferraz, Oliveira, Eler, Bussiman, Abreu Silva, Baldi and Brito.The development of integrative methods is one of the main challenges in bioinformatics. Network-based methods for the analysis of multiple gene-centered datasets take into account known and/or inferred relations between genes. In the last decades, the mathematical machinery of network diffusion-also referred to as network propagation-has been exploited in several network-based pipelines, thanks to its ability of amplifying association between genes that lie in network proximity. Indeed, network diffusion provides a quantitative estimation of network proximity between genes associated with one or more different data types, from simple binary vectors to real vectors. Therefore, this powerful data transformation method has also been increasingly used in integrative analyses of multiple collections of biological scores and/or one or more interaction networks. We present an overview of the state of the art of bioinformatics pipelines that use network diffusion processes for the integrative analysis of omics data. We discuss the fundamental ways in which network diffusion is exploited, open issues and potential developments in the field. Current trends suggest that network diffusion is a tool of broad utility in omics data analysis. It is reasonable to think that it will continue to be used and further refined as new data types arise (e.g. single cell datasets) and the identification of system-level patterns will be considered more and more important in omics data analysis. Copyright © 2020 Di Nanni, Bersanelli, Milanesi and Mosca.The regulation of mitochondrial proteome is unique in that its components have origins in both mitochondria and nucleus. With the development of OMICS technologies, emerging evidence indicates an interaction between mitochondria and nucleus based not only on the proteins but also on the non-coding RNAs (ncRNAs). It is now accepted that large parts of the non-coding genome are transcribed into various ncRNA species. Although their characterization has been a hot topic in recent years, the function of the majority remains unknown. Recently, ncRNA species microRNA (miRNA) and long-non coding RNAs (lncRNA) have been gaining attention as direct or indirect modulators of the mitochondrial proteome homeostasis. These ncRNA can impact mitochondria indirectly by affecting transcripts encoding for mitochondrial proteins in the cytoplasm. Furthermore, reports of mitochondria-localized miRNAs, termed mitomiRs, and lncRNAs directly regulating mitochondrial gene expression suggest the import of RNA to mitochondria, but also transcription from the mitochondrial genome. Interestingly, ncRNAs have been also shown to hide small open reading frames (sORFs) encoding for small functional peptides termed micropeptides, with several examples reported with a role in mitochondria. In this review, we provide a literature overview on ncRNAs and micropeptides found to be associated with mitochondrial biology in the context of both health and disease. Although reported, small study overlap and rare replications by other groups make the presence, transport, and role of ncRNA in mitochondria an attractive, but still challenging subject. Finally, we touch the topic of their potential as prognosis markers and therapeutic targets. Copyright © 2020 Gusic and Prokisch.Yanbian cattle is inhabitant of North of China, exhibiting many phenotypic features, such as long, dense body hair, and abundant intramuscular fat, designed to combat the extreme cold climate adaption. In the current study, we studied the cold tolerance of nine Yanbian cattle by whole genome resequencing and compared with African tropical cattle, N'Dama, as a control group. Yanbian cattle was aligned to the Bos taurus reference genome (ARS-UCD1.2) yielding an average of 10.8 fold coverage. The positive selective sweep analysis for the cold adaption in Yanbian cattle were analyzed using composite likelihood ratio (CLR) and nucleotide diversity (θπ), resulting in 292 overlapped genes. The strongest selective signal was found on BTA16 with potential mutation in CORT gene, a regulatory gene of primary hormone in the hypothalamic-pituitary-adrenal (HPA) axis, is reported to be associated with the cold stress, representedfour missense mutations (c.269C > T, p.Lys90Ile; c.251A > G, p.Glu84Gly; c.112C > T, p.Pro38Serrstanding of the cold climate adaptation of Yanbian cattle. Copyright © 2020 Shen, Hanif, Cao, Yu, Lei, Zhang and Zhao.Noncoding RNA (ncRNA) is a kind of RNA that plays an important role in many biological processes, diseases, and cancers, while cannot translate into proteins. With the development of next-generation sequence technology, thousands of novel RNAs with long open reading frames (ORFs, longest ORF length > 303 nt) and short ORFs (longest ORF length ≤ 303 nt) have been discovered in a short time. How to identify ncRNAs more precisely from novel unannotated RNAs is an important step for RNA functional analysis, RNA regulation, etc. However, most previous methods only utilize the information of sequence features. Meanwhile, most of them have focused on long-ORF RNA sequences, but not adapted to short-ORF RNA sequences. In this paper, we propose a new reliable method called NCResNet. NCResNet employs 57 hybrid features of four categories as inputs, including sequence, protein, RNA structure, and RNA physicochemical properties, and introduces feature enhancement and deep feature learning policies in a neural net model to adapt to this problem. The experiments on benchmark datasets of 8 species shows NCResNet has higher accuracy and higher Matthews correlation coefficient (MCC) compared with other state-of-the-art methods. Particularly, on four short-ORF RNA sequence datasets, specifically mouse, Saccharomyces cerevisiae, zebrafish, and cow, NCResNet achieves greater than 10 and 15% improvements over other state-of-the-art methods in terms of accuracy and MCC. Meanwhile, for long-ORF RNA sequence datasets, NCResNet also has better accuracy and MCC than other state-of-the-art methods on most test datasets. Codes and data are available at https//github.com/abcair/NCResNet. Copyright © 2020 Yang, Wang, Zhang, Hu, Ma and Tian.Osteoporosis is mainly characterized by low bone mineral density (BMD) and is an increasingly serious public health concern. DNA methylation is a major epigenetic mechanism that may contribute to the variation in BMD and may mediate the effects of genetic and environmental factors of osteoporosis. In this study, we performed an epigenome-wide DNA methylation analysis in peripheral blood monocytes of 118 Caucasian women with extreme BMD values. Further, we developed and implemented a novel analytical framework that integrates Mendelian randomization with genetic fine mapping and colocalization to evaluate the causal relationships between DNA methylation and BMD phenotype. Danicopan We identified 2,188 differentially methylated CpGs (DMCs) between the low and high BMD groups and distinguished 30 DMCs that may mediate the genetic effects on BMD. The causal relationship was further confirmed by eliminating the possibility of horizontal pleiotropy, linkage effect and reverse causality. The fine-mapping analysis determined 25 causal variants that are most likely to affect the methylation levels at these mediator DMCs.