Abstract:
BACKGROUND:Aberrant DNA methylation is a hallmark of many cancers. Classically there are two types of endometrial cancer, endometrioid adenocarcinoma (EAC), or Type I, and uterine papillary serous carcinoma (UPSC), or Type II. However, the whole genome DNA methylation changes in these two classical types of endometrial cancer is still unknown. RESULTS:Here we described complete genome-wide DNA methylome maps of EAC, UPSC, and normal endometrium by applying a combined strategy of methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylation-sensitive restriction enzyme digestion sequencing (MRE-seq). We discovered distinct genome-wide DNA methylation patterns in EAC and UPSC: 27,009 and 15,676 recurrent differentially methylated regions (DMRs) were identified respectively, compared with normal endometrium. Over 80% of DMRs were in intergenic and intronic regions. The majority of these DMRs were not interrogated on the commonly used Infinium 450K array platform. Large-scale demethylation of chromosome X was detected in UPSC, accompanied by decreased XIST expression. Importantly, we discovered that the majority of the DMRs harbored promoter or enhancer functions and are specifically associated with genes related to uterine development and disease. Among these, abnormal methylation of transposable elements (TEs) may provide a novel mechanism to deregulate normal endometrium-specific enhancers derived from specific TEs. CONCLUSIONS:DNA methylation changes are an important signature of endometrial cancer and regulate gene expression by affecting not only proximal promoters but also distal enhancers.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Zhang B,Xing X,Li J,Lowdon RF,Zhou Y,Lin N,Zhang B,Sundaram V,Chiappinelli KB,Hagemann IS,Mutch DG,Goodfellow PJ,Wang Tdoi
10.1186/1471-2164-15-868subject
Has Abstractpub_date
2014-10-06 00:00:00pages
868issn
1471-2164pii
1471-2164-15-868journal_volume
15pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:DNA methylation at promoters is largely correlated with inhibition of gene expression. However, the role of DNA methylation at enhancers is not fully understood, although a crosstalk with chromatin marks is expected. Actually, there exist contradictory reports about positive and negative correlations between...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4353-7
更新日期:2017-12-12 00:00:00
abstract:BACKGROUND:Poxviruses constitute one of the largest and most complex animal virus families known. The notorious smallpox disease has been eradicated and the virus contained, but its simian sister, monkeypox is an emerging, untreatable infectious disease, killing 1 to 10 % of its human victims. In the case of poxviruses...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2826-8
更新日期:2016-08-31 00:00:00
abstract:BACKGROUND:In a previous genome-wide analysis of FXR binding to hepatic chromatin, we noticed that an extra nuclear receptor (NR) half-site was co-enriched close to the FXR binding IR-1 elements and we provided limited support that the monomeric LRH-1 receptor that binds to NR half-sites might function together with FX...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-51
更新日期:2012-02-01 00:00:00
abstract:BACKGROUND:We present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the rhesus macaque. RESULTS:The assembly process consisted of multipl...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-180
更新日期:2009-04-24 00:00:00
abstract:BACKGROUND:The giant panda, one of the most primitive carnivores, is an endangered animal. Although it has been the subject of many interesting studies during recent years, little is known about its genome. In order to promote research on this genome, a bacterial artificial chromosome (BAC) library of the giant panda w...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-294
更新日期:2006-11-17 00:00:00
abstract:BACKGROUND:In contrast to wild species, which have typically evolved phenotypes over long periods of natural selection, domesticates rapidly gained human-preferred agronomic traits in a relatively short-time frame via artificial selection. Under domesticated conditions, many traits can be observed that cannot only be d...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-646
更新日期:2013-09-23 00:00:00
abstract:BACKGROUND:Understanding the genetic basis of adaptive evolution is one of the major goals in evolutionary biology. Recently, it has been revealed that gene copy number variations (GCNVs) constitute significant proportions of genomic diversities within natural populations. However, it has been unclear whether GCNVs are...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-735
更新日期:2014-08-29 00:00:00
abstract:BACKGROUND:The completed sequence of the Anopheles gambiae genome has enabled genome-wide analyses of gene expression and regulation in this principal vector of human malaria. These investigations have created a demand for efficient methods of cataloguing and analyzing the large quantities of data that have been produc...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-116
更新日期:2006-05-17 00:00:00
abstract:BACKGROUND:There are no commercially available vaccines against human protozoan parasitic diseases, despite the success of vaccination-induced long-term protection against infectious diseases. East Coast fever, caused by the protist Theileria parva, kills one million cattle each year in sub-Saharan Africa, and contribu...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1910-9
更新日期:2015-09-24 00:00:00
abstract:BACKGROUND:Coral reefs are hotspots of oceanic biodiversity, forming the foundation of ecosystems that are important both ecologically and for their direct practical impacts on humans. Corals are declining globally due to a number of stressors, including rising sea-surface temperatures and pollution; such stresses can ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-271
更新日期:2012-06-22 00:00:00
abstract:BACKGROUND:The Yesso scallop, Patinopecten (Mizuhopecten) yessoensis, is a commercially important bivalve in the coastal countries of Northeast Asia. It has complex modes of sex differentiation, but knowledge of the mechanisms underlying this sex determination and differentiation is limited. RESULTS:In this study, the...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6021-6
更新日期:2019-08-23 00:00:00
abstract:BACKGROUND:Aquaporins are a large family of transmembrane channel proteins that are present throughout all domains of life and are implicated in human disorders. These channels, allow the passive but selective movement of water and other small neutral solutes across cell membranes. Aquaporins have been classified into ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-S4-S8
更新日期:2011-12-22 00:00:00
abstract:BACKGROUND:Petal nectar spurs, which facilitate pollination through animal attraction and pollen placement, represent a key innovation promoting diversification in the genus Aquilegia (Ranunculaceae). Identifying the genetic components that contribute to the development of these three-dimensional structures will inform...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6002-9
更新日期:2019-08-22 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are a class of noncoding small RNAs (sRNAs) that are 20-24 nucleotides (nt) in length. Extensive studies have indicated that miRNAs play versatile roles in plants, functioning in processes such as growth, development and stress responses. Chilling is a common abiotic stress that seriously ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1130
更新日期:2014-12-17 00:00:00
abstract:BACKGROUND:Gaucher disease is caused by defective glucocerebrosidase activity and the consequent accumulation of glucosylceramide. The pathogenic pathways resulting from lipid laden macrophages (Gaucher cells) in visceral organs and their abnormal functions are obscure. RESULTS:To elucidate this pathogenic pathway, de...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-20
更新日期:2011-01-11 00:00:00
abstract:BACKGROUND:Computational methods that infer single nucleotide polymorphism (SNP) interactions from phenotype data may uncover new biological mechanisms in non-Mendelian diseases. However, practical aspects of such analysis face many problems. Present experimental studies typically use SNP arrays with hundreds of thousa...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-58
更新日期:2010-01-22 00:00:00
abstract:BACKGROUND:The environmental light-dark cycle is the dominant cue that maintains 24-h biological rhythms in multicellular organisms. In Drosophila, light entrainment is mediated by the photosensitive protein CRYPTOCHROME, but the role and extent of transcription regulation in light resetting of the dipteran clock is ye...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1787-7
更新日期:2015-08-01 00:00:00
abstract:BACKGROUND:Single cell transcriptome sequencing has become an increasingly valuable technology for dissecting complex biology at a resolution impossible with bulk sequencing. However, the gap between the technical expertise required to effectively work with the resultant high dimensional data and the biological experti...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6053-y
更新日期:2019-08-27 00:00:00
abstract:BACKGROUND:Gene expression variation is a key underlying factor influencing phenotypic variation, and can occur via cis- or trans-regulation. To understand the role of cis- and trans-regulatory variation on population divergence in chicken, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornis...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6342-5
更新日期:2019-12-05 00:00:00
abstract:BACKGROUND:Species of the crenarchaeon Sulfolobus harbour three replication origins in their single circular chromosome that are synchronously initiated during replication. RESULTS:We demonstrate that global gene expression in two Sulfolobus species is highly biased, such that early replicating genome regions are more...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-454
更新日期:2010-07-28 00:00:00
abstract:BACKGROUND:Little is known about the genome sequences of Euphausiacea (krill) although these crustaceans are abundant components of the pelagic ecosystems in all oceans and used for aquaculture and pharmaceutical industry. This study reports the results of an expressed sequence tag (EST) sequencing project from differe...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-45
更新日期:2008-01-28 00:00:00
abstract:BACKGROUND:RNA amplification is necessary for profiling gene expression from small tissue samples. Previous studies have shown that the T7 based amplification techniques are reproducible but may distort the true abundance of targets. However, the consequences of such distortions on the ability to detect biological vari...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-252
更新日期:2006-10-09 00:00:00
abstract:BACKGROUND:Panax notoginseng (Burk) F.H. Chen is important medicinal plant of the Araliacease family. Triterpene saponins are the bioactive constituents in P. notoginseng. However, available genomic information regarding this plant is limited. Moreover, details of triterpene saponin biosynthesis in the Panax species ar...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-S5-S5
更新日期:2011-12-23 00:00:00
abstract:BACKGROUND:Typhoid fever is an infectious disease of global importance that is caused by Salmonella enterica subsp. enterica serovar Typhi (S. Typhi). This disease causes an estimated 200,000 deaths per year and remains a serious global health threat. S. Typhi is strictly a human pathogen, and some recovered individual...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1007
更新日期:2014-11-20 00:00:00
abstract:BACKGROUND:The circadian rhythms regulate physiological functions and metabolism. Circadian Time (CT) is a unit to quantify the rhythm of endogenous circadian clock, independent of light influence. To understand the gene expression changes throughout CT, C57BL/6 J mice were maintained under constant darkness (DD) for 6...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6639-4
更新日期:2020-03-12 00:00:00
abstract:BACKGROUND:Two-component systems (TCS) play critical roles in sensing and responding to environmental cues. Azospirillum is a plant growth-promoting rhizobacterium living in the rhizosphere of many important crops. Despite numerous studies about its plant beneficial properties, little is known about how the bacterium s...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1962-x
更新日期:2015-10-22 00:00:00
abstract:BACKGROUND:The gilthead sea bream (Sparus aurata) is the main fish species cultured in the Mediterranean area and constitutes an interesting model of research. Nevertheless, transcriptomic and genomic data are still scarce for this highly valuable species. A transcriptome database was constructed by de novo assembly of...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-178
更新日期:2013-03-15 00:00:00
abstract:BACKGROUND:Post-translational glycosylation of the flagellin protein is relatively common among Gram-negative bacteria, and has been linked to several phenotypes, including flagellar biosynthesis and motility, biofilm formation, host immune evasion and manipulation and virulence. However to date, despite extensive phys...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2735-x
更新日期:2016-05-20 00:00:00
abstract:BACKGROUND:Interactions between fish and pathogens, that may be harmless under natural conditions, often result in serious diseases in aquaculture systems. This is especially important due to the fact that the strains used in aquaculture are derived from wild strains that may not have had enough time to adapt to new di...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-541
更新日期:2011-11-02 00:00:00
abstract:BACKGROUND:Cadmium (Cd) is a severe detrimental environmental pollutant. To adapt to Cd-induced deleterious effects, plants have evolved sophisticated defence mechanisms. In this study, a genome-wide transcriptome analysis was performed to identify the mechanisms of Cd tolerance using two barley genotypes with distinct...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-611
更新日期:2014-07-19 00:00:00