Abstract:
BACKGROUND:Diet is a major contributor to metabolic disease risk, but there is controversy as to whether increased incidences of diseases such as non-alcoholic fatty liver disease arise from consumption of saturated fats or free sugars. Here, we investigate whether a sub-set of triacylglycerols (TAGs) were associated with hepatic steatosis and whether they arise from de novo lipogenesis (DNL) from the consumption of carbohydrates. RESULTS:We conduct direct infusion mass spectrometry of lipids in plasma to study the association between specific TAGs and hepatic steatosis assessed by ultrasound and fatty liver index in volunteers from the UK-based Fenland Study and evaluate clustering of TAGs in the National Survey of Health and Development UK cohort. We find that TAGs containing saturated and monounsaturated fatty acids with 16-18 carbons are specifically associated with hepatic steatosis. These TAGs are additionally associated with higher consumption of carbohydrate and saturated fat, hepatic steatosis, and variations in the gene for protein phosphatase 1, regulatory subunit 3b (PPP1R3B), which in part regulates glycogen synthesis. DNL is measured in hyperphagic ob/ob mice, mice on a western diet (high in fat and free sugar) and in healthy humans using stable isotope techniques following high carbohydrate meals, demonstrating the rate of DNL correlates with increased synthesis of this cluster of TAGs. Furthermore, these TAGs are increased in plasma from patients with biopsy-confirmed steatosis. CONCLUSION:A subset of TAGs is associated with hepatic steatosis, even when correcting for common confounding factors. We suggest that hepatic steatosis risk in western populations is in part driven by increased DNL following carbohydrate rich meals in addition to the consumption of saturated fat.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Sanders FWB,Acharjee A,Walker C,Marney L,Roberts LD,Imamura F,Jenkins B,Case J,Ray S,Virtue S,Vidal-Puig A,Kuh D,Hardy R,Allison M,Forouhi N,Murray AJ,Wareham N,Vacca M,Koulman A,Griffin JLdoi
10.1186/s13059-018-1439-8subject
Has Abstractpub_date
2018-06-20 00:00:00pages
79issue
1eissn
1474-7596issn
1474-760Xpii
10.1186/s13059-018-1439-8journal_volume
19pub_type
杂志文章相关文献
GENOME BIOLOGY文献大全abstract:BACKGROUND:DNase-seq and ATAC-seq are broadly used methods to assay open chromatin regions genome-wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription factor binding sites (TFBSs) in regulatory regions through footprinting. Recent studies have demonstrated the sequence b...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1654-y
更新日期:2019-02-21 00:00:00
abstract:BACKGROUND:The function of the non-coding portion of the human genome remains one of the most important questions of our time. Its vast complexity is exemplified by the recent identification of an unusual and notable component of the transcriptome - very long intergenic non-coding RNAs, termed vlincRNAs. RESULTS:Here ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2013-14-7-r73
更新日期:2013-07-22 00:00:00
abstract:BACKGROUND:Massively parallel pyrosequencing systems have increased the efficiency of DNA sequencing, although the published per-base accuracy of a Roche GS20 is only 96%. In genome projects, highly redundant consensus assemblies can compensate for sequencing errors. In contrast, studies of microbial diversity that cat...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-7-r143
更新日期:2007-01-01 00:00:00
abstract::Absolute tumor DNA copy numbers can currently be achieved only on a single gene basis by using fluorescence in situ hybridization (FISH). We present GeneCount, a method for genome-wide calculation of absolute copy numbers from clinical array comparative genomic hybridization data. The tumor cell fraction is reliably e...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-5-r86
更新日期:2008-01-01 00:00:00
abstract:BACKGROUND:Methylation of nucleotides, notably in the forms of 5-methylcytosine (5mC) in DNA and N6-methyladenosine (m6A) in mRNA, carries important information for gene regulation. 5mC has been elucidated to participate in the regulation of fruit ripening, whereas the function of m6A in this process and the interplay ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1771-7
更新日期:2019-08-06 00:00:00
abstract:BACKGROUND:Chronic psychological stress is associated with accelerated aging and increased risk for aging-related diseases, but the underlying molecular mechanisms are unclear. RESULTS:We examined the effect of lifetime stressors on a DNA methylation-based age predictor, epigenetic clock. After controlling for blood c...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0828-5
更新日期:2015-12-17 00:00:00
abstract::A report of The Keystone Symposium on Plant Innate Immunity, Keystone, USA, 10-15 February 2008. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2008-9-4-304
更新日期:2008-01-01 00:00:00
abstract::The accurate placement of an ancient whole-genome duplication (WGD) in relation to the lineage divergence is important. Here, we re-investigated the Aquilegia coerulea WGD and found it is more likely lineage-specific rather than shared by all eudicots. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02212-y
更新日期:2020-12-08 00:00:00
abstract::A new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins is presented. The method is quantitative, reproducible, and computationally undemanding. It can be combined with genomic signature and/or phylogenetic tree-building procedures to improve accuracy and efficiency. T...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-2-r16
更新日期:2007-01-01 00:00:00
abstract::Cryptochromes are photoreceptors that regulate entrainment by light of the circadian clock in plants and animals. They also act as integral parts of the central circadian oscillator in animal brains and as receptors controlling photomorphogenesis in response to blue or ultraviolet (UV-A) light in plants. Cryptochromes...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2005-6-5-220
更新日期:2005-01-01 00:00:00
abstract:BACKGROUND:The relationships between proteins are often asymmetric: one protein (A) depends for its function on another protein (B), but the second protein does not depend on the first. In metabolic networks there are multiple pathways that converge into one central pathway. The enzymes in the converging pathways depen...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2009-10-2-r19
更新日期:2009-02-12 00:00:00
abstract::The ability to accurately quantify all the microRNAs (miRNAs) in a sample is important for understanding miRNA biology and for development of new biomarkers and therapeutic targets. We develop a new method for preparing miRNA sequencing libraries, RealSeq®-AC, that involves ligating the miRNAs with a single adapter an...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1488-z
更新日期:2018-09-03 00:00:00
abstract:BACKGROUND:In multicellular organisms, alternative splicing is central to tissue differentiation and identity. Unicellular protists lack multicellular tissue but differentiate into variable cell types during their life cycles. The role of alternative splicing in transitions between cell types and establishing cellular ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1756-6
更新日期:2019-08-01 00:00:00
abstract:BACKGROUND:Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is not known how common this mechanism is. We provide transcriptional evidence of widespread alternate splicing in the Toll-like rece...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-2-r10
更新日期:2006-01-01 00:00:00
abstract:BACKGROUND:Protein synthesis is tightly regulated and alterations to translation are characteristic of many cancers.Translation regulation is largely exerted at initiation through the eukaryotic translation initiation factor 4 F (eIF4F). eIF4F is pivotal for oncogenic signaling as it integrates mitogenic signals to amp...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-014-0476-1
更新日期:2014-01-01 00:00:00
abstract::Transcription factor binding sites compete for a limited pool of bioavailable transcription factor molecules to fine tune gene expression. ...
journal_title:Genome biology
pub_type: 评论,杂志文章
doi:10.1186/gb4174
更新日期:2014-04-28 00:00:00
abstract:BACKGROUND:Next-generation sequencing (NGS) is a powerful tool for understanding both patterns of descent over time and space (phylogeography) and the molecular processes underpinning genome divergence in pathogenic bacteria. Here, we describe a synthesis between these perspectives by employing a recently developed Bay...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-12-r126
更新日期:2012-12-27 00:00:00
abstract::The protein folding game Foldit shows that games are an effective way to recruit, engage and organize ordinary citizens to help solve difficult scientific problems. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2011-12-12-135
更新日期:2011-12-28 00:00:00
abstract:BACKGROUND:Concepts of orthology and paralogy are become increasingly important as whole-genome comparison allows their identification in complete genomes. Functional specificity of proteins is assumed to be conserved among orthologs and is different among paralogs. We used this assumption to identify residues which de...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2002-3-3-preprint0002
更新日期:2002-01-01 00:00:00
abstract::We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate variants for functional follow-up. We calibrate and test FineMAV using eight experimentally validated "gold...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1380-2
更新日期:2018-01-17 00:00:00
abstract::Your Gene structure Annotation Tool for Eukaryotes (yrGATE) provides an Annotation Tool and Community Utilities for worldwide web-based community genome and gene annotation. Annotators can evaluate gene structure evidence derived from multiple sources to create gene structure annotations. Administrators regulate the a...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-7-r58
更新日期:2006-01-01 00:00:00
abstract::DNA arrays are valuable tools in molecular biology laboratories. Their rapid acceptance was aided by the release of plans for a pin-spotting microarrayer by researchers at Stanford. Inkjet microarraying is a flexible, complementary technique that allows the synthesis of arrays of any oligonucleotide sequences de novo....
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2004-5-8-r58
更新日期:2004-01-01 00:00:00
abstract::Genetic mapping and determination of the organization of the wheat genome are changing the wheat-breeding process. New initiatives to analyze the expressed portion of the wheat genome and structural analysis of the genomes of Arabidopsis and rice are increasing our knowledge of the genes that are linked to key agronom...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2002-3-5-reviews1013
更新日期:2002-01-01 00:00:00
abstract:BACKGROUND:Parasitism is a highly successful mode of life and one that requires suites of gene adaptations to permit survival within a potentially hostile host. Among such adaptations is the secretion of proteins capable of modifying or manipulating the host environment. Nippostrongylus brasiliensis is a well-studied m...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2004-5-6-r39
更新日期:2004-01-01 00:00:00
abstract::The mouse is an important model of human genetic disease. Describing phenotypes of mutant mice in a standard, structured manner that will facilitate data mining is a major challenge for bioinformatics. Here we describe a novel, compositional approach to this problem which combines core ontologies from a variety of sou...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2004-6-1-r8
更新日期:2005-01-01 00:00:00
abstract::We used scaled factorial moments to search for intermittency in the log expression ratios (LERs) for thousands of genes spotted on cDNA microarrays (gene chips). Results indicate varying levels of intermittency in gene expression. The observation of intermittency in the data analyzed provides a complimentary handle on...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2002-3-7-preprint0005
更新日期:2002-05-29 00:00:00
abstract::Levels of transcripts sharing microRNA response elements are co-regulated. These RNA-RNA interactions imply that combinations of microRNAs modulate cell-specific transcript networks. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2011-12-11-132
更新日期:2011-11-21 00:00:00
abstract:BACKGROUND:Retrotransposons play a central role in plant evolution and could be a powerful endogenous source of genetic and epigenetic variability for crop breeding. To ensure genome integrity several silencing mechanisms have evolved to repress retrotransposon mobility. Even though retrotransposons fully depend on tra...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1265-4
更新日期:2017-07-07 00:00:00
abstract::Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA. ...
journal_title:Genome biology
pub_type: 历史文章,杂志文章,评审
doi:10.1186/s13059-015-0866-z
更新日期:2016-01-11 00:00:00
abstract::We present a graph-based method for the analysis of repeat families in a repeat library. We build a repeat domain graph that decomposes a repeat library into repeat domains, short subsequences shared by multiple repeat families, and reveals the mosaic structure of repeat families. Our method recovers documented mosaic...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-1-r7
更新日期:2006-01-01 00:00:00