Abstract:
BACKGROUND:Long non-coding RNAs (lncRNAs) regulate adipose tissue metabolism, however, their function on testosterone deficiency related obesity in humans is less understood. For this research, intact and castrated male pigs are the best model animal because of their similar proportional organ sizes, cardiovascular systems and metabolic features. RESULTS:We identified lncRNAs in subcutaneous adipose tissue by deep RNA-sequencing using the intact and castrated Huainan male pigs. The results showed that castration reduced serum testosterone but increased body fatness-related traits (serum triglyceride levels, backfat thickness, intramuscular fat content, and adipocyte size). Meanwhile, 343 lncRNAs from subcutaneous adipose tissue were identified, including 223 intergenic lncRNAs (lincRNAs), 68 anti-sense lncRNAs, and 52 intronic lncRNAs. It was predicted that there were 416 recognition sites for C/EBPα in the 303 lncRNA promoter region, and 13 adipogenesis-promoting miRNAs and five adipogenesis-depressing miRNAs target these lncRNAs. Eighteen lncRNAs, including nine up- and nine down-regulated had more than 2-fold differential expression between the castrated and intact male pigs (q-value < 0.05). Functional analysis indicated that these 18 lncRNAs and their target genes were involved in fatty acid, insulin, and the adipocytokine signaling pathway. We further analyzed the features of a conserved mouse lncRNA gene ENSMUST00000189966 and found it mainly expressed in the cell nucleus and target the Nuclear Receptor Subfamily 2 Group F Member 2 (NR2F2) gene. In 3 T3-L1 cells, differentiation down-regulated their expression, but dihydrotestosterone (DHT) significantly up-regulated their expression in a concentration-dependent manner (P < 0.05). CONCLUSIONS:These results suggested that lncRNAs and their target genes might participated in the castration-induced fat deposition and provide a new therapeutic target for combatting testosterone deficiency-related obesity.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Wang J,Hua L,Chen J,Zhang J,Bai X,Gao B,Li C,Shi Z,Sheng W,Gao Y,Xing Bdoi
10.1186/s12864-017-3907-zsubject
Has Abstractpub_date
2017-07-19 00:00:00pages
542issue
1issn
1471-2164pii
10.1186/s12864-017-3907-zjournal_volume
18pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Understanding the genome sequence-specific positioning of nucleosomes is essential to understand various cellular processes, such as transcriptional regulation and replication. As a typical example, the 10-bp periodicity of AA/TT and GC dinucleotides has been reported in several species, but it is still uncl...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-309
更新日期:2010-05-17 00:00:00
abstract:BACKGROUND:Cancer is a complex disease driven by somatic genomic alterations (SGAs) that perturb signaling pathways and consequently cellular function. Identifying patterns of pathway perturbations would provide insights into common disease mechanisms shared among tumors, which is important for guiding treatment and pr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3494-z
更新日期:2017-03-14 00:00:00
abstract:BACKGROUND:Cucumber, Cucumis sativus L. (2n = 2 × = 14) and melon, C. melo L. (2n = 2 × = 24) are two important vegetable species in the genus Cucumis (family Cucurbitaceae). Both species have an Asian origin that diverged approximately nine million years ago. Cucumber is believed to have evolved from melon through chr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-396
更新日期:2011-08-05 00:00:00
abstract:BACKGROUND:Intensive selection has resulted in increased growth rates and muscularity in broiler chickens, in addition to adverse effects, including delayed organ development, sudden death syndrome, and altered metabolic rates. The biological mechanisms underlying selection responses remain largely unknown. Non-artific...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3845-9
更新日期:2017-06-20 00:00:00
abstract:BACKGROUND:Genomic inversion is one type of structural variations (SVs) and is known to play an important biological role. An established problem in sequence data analysis is calling inversions from high-throughput sequence data. It is more difficult to detect inversions because they are surrounded by duplication or ot...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6585-1
更新日期:2020-03-05 00:00:00
abstract:BACKGROUND:Protein phosphorylation by kinases plays crucial roles in various biological processes including signal transduction and tumorigenesis, thus a better understanding of protein phosphorylation events in cells is fundamental for studying protein functions and designing drugs to treat diseases caused by the malf...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06895-2
更新日期:2020-08-04 00:00:00
abstract:BACKGROUND:Dystonia1 (DYT1) dystonia is caused by a glutamic acid deletion (ΔE) mutation in the gene encoding Torsin A in humans (HTorA). To investigate the unknown molecular and cellular mechanisms underlying DYT1 dystonia, we performed an unbiased proteomic analysis. RESULTS:We found that the amount of proteins and ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1518-0
更新日期:2015-04-23 00:00:00
abstract:BACKGROUND:The development of second generation sequencing methods has enabled large scale DNA variation studies at moderate cost. For the high throughput discovery of single nucleotide polymorphisms (SNPs) in species lacking a sequenced reference genome, we set-up an analysis pipeline based on a short read de novo seq...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-479
更新日期:2009-10-16 00:00:00
abstract:BACKGROUND:Horizontal gene transfer has shaped the evolution of the ammonium transporter/ammonia permease gene family. Horizontal transfers of ammonium transporter/ammonia permease genes into the fungi include one transfer from archaea to the filamentous ascomycetes associated with the adaptive radiation of the leotiom...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-225
更新日期:2013-04-04 00:00:00
abstract:BACKGROUND:Sugarcane is an economically important crop contributing about 80% and 40% to the world sugar and ethanol production, respectively. The complicated genetics consequential to its complex polyploid genome, however, have impeded efforts to improve sugar yield and related important agronomic traits. Modern sugar...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-314
更新日期:2013-05-10 00:00:00
abstract:BACKGROUND:gammadelta T cells differ from alphabeta T cells with regard to the types of antigen with which their T cell receptors interact; gammadelta T cell antigens are not necessarily peptides nor are they presented on MHC. Cattle are considered a "gammadelta T cell high" species indicating they have an increased pr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-100
更新日期:2010-02-09 00:00:00
abstract:BACKGROUND:The Zap1 transcription factor is a central player in the response of yeast to changes in zinc status. We previously used transcriptome profiling with DNA microarrays to identify 46 potential Zap1 target genes in the yeast genome. In this new study, we used complementary methods to identify additional Zap1 ta...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-370
更新日期:2008-08-01 00:00:00
abstract:BACKGROUND:The approaches for shotgun-based sequencing of vertebrate genomes are now well-established, and have resulted in the generation of numerous draft whole-genome sequence assemblies. In contrast, the process of refining those assemblies to improve contiguity and increase accuracy (known as 'sequence finishing')...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-21
更新日期:2010-01-11 00:00:00
abstract:INTRODUCTION:In the classification of Mass Spectrometry (MS) proteomics data, peak detection, feature selection, and learning classifiers are critical to classification accuracy. To better understand which methods are more accurate when classifying data, some publicly available peak detection algorithms for Matrix assi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-S1-S3
更新日期:2009-07-07 00:00:00
abstract:MOTIVATION:With the rapid growth rate of newly sequenced genomes, species tree inference from multiple genes has become a basic bioinformatics task in comparative and evolutionary biology. However, accurate species tree estimation is difficult in the presence of gene tree discordance, which is often due to incomplete l...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-S6-S7
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Missing data is an inevitable phenomenon in gene expression microarray experiments due to instrument failure or human error. It has a negative impact on performance of downstream analysis. Technically, most existing approaches suffer from this prevalent problem. Imputation is one of the frequently used metho...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-16-S9-S1
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:As economically relevant traits, feeding behavior and food preference domestication determine production cost and profitability. Although there are intensive research efforts on feeding behavior and food intake, little is known about food preference. Mandarin fish accept only live prey fish and refuse dead p...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-601
更新日期:2013-09-05 00:00:00
abstract:BACKGROUND:Identification of genes with ascending or descending monotonic expression patterns over time or stages of stem cells is an important issue in time-series microarray data analysis. We propose a method named Monotonic Feature Selector (MFSelector) based on a concept of total discriminating error (DEtotal) to i...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-16-S2-S2
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Rapid acquisition of accurate genotyping information is essential for all genetic marker-based studies. For species with relatively small genomes, complete genome resequencing is a feasible approach for genotyping; however, for species with large and highly repetitive genomes, the acquisition of whole genome...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-448
更新日期:2013-07-05 00:00:00
abstract:BACKGROUND:Helicobacter pylori is presumed to be co-evolved with its human host and is a highly diverse gastric pathogen at genetic levels. Ancient origins of H. pylori in the New World are still debatable. It is not clear how different waves of human migrations in South America contributed to the evolution of strain d...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-191
更新日期:2006-07-27 00:00:00
abstract:BACKGROUND:Rainbow trout is a significant fish farming species under temperate climates. Female reproduction traits play an important role in the economy of breeding companies with the sale of fertilized eggs. The objectives of this study are threefold: to estimate the genetic parameters of female reproduction traits, ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06955-7
更新日期:2020-08-14 00:00:00
abstract:BACKGROUND:Ramie (Boehmeria nivea L.), popularly known as "China grass", is one of the oldest crops in China and the second most important fiber crop in terms of area sown. Ramie fiber, extracted from the plant bast, is important in the textile industry. However, the molecular mechanism of ramie fiber development remai...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-919
更新日期:2014-10-22 00:00:00
abstract:BACKGROUND:Leaf blight caused by Calonectria spp. is one of the most destructive diseases to affect Eucalyptus nurseries and plantations. These pathogens mainly attack Eucalyptus, a tree with a diversity of secondary metabolites employed as defense-related phytoalexins. To unravel the fungal adaptive mechanisms to vari...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4739-1
更新日期:2018-05-10 00:00:00
abstract:BACKGROUND:Magnaporthe oryzae (anamorph Pyricularia oryzae) is the causal agent of blast disease of Poaceae crops and their wild relatives. To understand the genetic mechanisms that drive host specialization of M. oryzae, we carried out whole genome resequencing of four M. oryzae isolates from rice (Oryza sativa), one ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2690-6
更新日期:2016-05-18 00:00:00
abstract:BACKGROUND:Numerous human genes encode potentially active DNA transposases or recombinases, but our understanding of their functions remains limited due to shortage of methods to profile their activities on endogenous genomic substrates. RESULTS:To enable functional analysis of human transposase-derived genes, we comb...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2877-x
更新日期:2016-08-04 00:00:00
abstract:BACKGROUND:Free asparagine is the precursor for acrylamide formation during cooking and processing of grains, tubers, beans and other crop products. In wheat grain, free asparagine, free glutamine and total free amino acids accumulate to high levels in response to sulphur deficiency. In this study, RNA-seq data were ac...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5991-8
更新日期:2019-08-01 00:00:00
abstract:BACKGROUND:Musa species (Zingiberaceae, Zingiberales) including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning Musa genome structure and the origin of distinct cultivars has greatly increased over the last few years. Until now, however, no large-scale...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-58
更新日期:2008-01-30 00:00:00
abstract:BACKGROUND:The monophyly of flatfishes has not been supported in many molecular phylogenetic studies. The monophyly of Pleuronectoidei, which comprises all but one family of flatfishes, is broadly supported. However, the Psettodoidei, comprising the single family Psettodidae, is often found to be most closely related t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4788-5
更新日期:2018-05-25 00:00:00
abstract:BACKGROUND:Gene duplication underlies a significant proportion of gene functional diversity and genome complexity in both eukaryotes and prokaryotes. Although several reports in the literature described the duplication of specific genes in E. coli, a detailed analysis of the extent of gene duplications in this microorg...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5683-4
更新日期:2019-04-24 00:00:00
abstract:BACKGROUND:Thousands of intragenic long interspersed element 1 sequences (LINE-1 elements or L1s) reside within genes. These intragenic L1 sequences are conserved and regulate the expression of their host genes. When L1 methylation is decreased, either through chemical induction or in cancer, the intragenic L1 transcri...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-205
更新日期:2013-03-27 00:00:00