Abstract:
BACKGROUND:A-to-I RNA-editing mediated by ADAR (adenosine deaminase acting on RNA) enzymes that converts adenosine to inosine in RNA sequence can generate mutations and alter gene regulation in metazoans. Previous studies have shown that A-to-I RNA-editing plays vital roles in mouse embryogenesis. However, the RNA-editing activities in early human embryonic development have not been investigated. RESULTS:Here, we characterized genome-wide A-to-I RNA-editing activities during human early embryogenesis by profiling 68 single cells from 29 human embryos spanning from oocyte to morula stages. We demonstrate dynamic changes in genome-wide RNA-editing during early human embryogenesis in a stage-specific fashion. In parallel with ADAR expression level changes, the genome-wide A-to-I RNA-editing levels in cells remained relatively stable until 4-cell stage, but dramatically decreased at 8-cell stage, continually decreased at morula stage. We detected 37 non-synonymously RNA-edited genes, of which 5 were frequently found in cells of multiple embryonic stages. Moreover, we found that A-to-I editings in miRNA-targeted regions of a substantial number of genes preferably occurred in one or two sequential stages. CONCLUSIONS:Our single-cell analysis reveals dynamic changes in genome-wide RNA-editing during early human embryogenesis in a stage-specific fashion, and provides important insights into early human embryogenesis.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Qiu S,Li W,Xiong H,Liu D,Bai Y,Wu K,Zhang X,Yang H,Ma K,Hou Y,Li Bdoi
10.1186/s12864-016-3115-2subject
Has Abstractpub_date
2016-09-29 00:00:00pages
766issue
1issn
1471-2164pii
10.1186/s12864-016-3115-2journal_volume
17pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:The Iberian lynx (Lynx pardinus) has been acknowledged as the most endangered felid species in the world. An intense contraction and fragmentation during the twentieth century left less than 100 individuals split in two isolated and genetically eroded populations by 2002. Genetic monitoring and management so...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3946-5
更新日期:2017-07-21 00:00:00
abstract:BACKGROUND:The increased multi-omics information on carefully phenotyped patients in studies of complex diseases requires novel methods for data integration. Unlike continuous intensity measurements from most omics data sets, phenome data contain clinical variables that are binary, ordinal and categorical. RESULTS:In ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2170-4
更新日期:2015-11-11 00:00:00
abstract:BACKGROUND:Lipopolysaccharide (LPS) from Gram-negative bacteria cause innate immune responses in animals and plants. The molecules involved in LPS signaling in animals are well studied, whereas those in plants are not yet as well documented. Recently, we identified Arabidopsis AtLBR-2, which binds to LPS from Pseudomon...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4372-4
更新日期:2017-12-29 00:00:00
abstract:BACKGROUND:Periodic spacing of A-tracts (short runs of A or T) with the DNA helical period of ~10-11 bp is characteristic of intrinsically bent DNA. In eukaryotes, the DNA bending is related to chromatin structure and nucleosome positioning. However, the physiological role of strong sequence periodicity detected in man...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-188
更新日期:2012-05-15 00:00:00
abstract:BACKGROUND:Despite the importance of chromosomal translocations in the initiation and/or progression of cancer, a comprehensive catalog of translocation breakpoints in which these are precisely located on the reference sequence of the human genome is not available at present. DESCRIPTION:We have created a database tha...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-33
更新日期:2007-01-26 00:00:00
abstract:BACKGROUND:Although the needs for analyses of secondary structures of RNAs are increasing, prediction of the secondary structures of RNAs are not always reliable. Because an RNA may have a complicated energy landscape, comprehensive representations of the whole ensemble of the secondary structures, such as the probabil...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-S10-S6
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:The golden birdwing butterfly (Troides aeacus formosanus) is a rarely observed species in Taiwan. Recently, a typical symptom of nuclear polyhedrosis was found in reared T. aeacus larvae. From the previous Kimura-2 parameter (K-2-P) analysis based on the nucleotide sequence of three genes in this isolate, po...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5713-2
更新日期:2019-05-27 00:00:00
abstract:BACKGROUND:Precision medicine is a medical approach that takes into account individual genetic variability and often requires Next Generation Sequencing data in order to predict new treatments. Here we present GMIEC, Genomic Modules Identification et Characterization for genomics medicine, an application that is able t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06996-y
更新日期:2020-09-10 00:00:00
abstract:BACKGROUND:BCG is the most widely used vaccine of all time and remains the only licensed vaccine for use against tuberculosis in humans. BCG also protects other species such as cattle against tuberculosis, but due to its incompatibility with current tuberculin testing regimens remains unlicensed. BCG's efficacy relates...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5791-1
更新日期:2019-05-28 00:00:00
abstract:BACKGROUND:The freshwater snail Lymnaea stagnalis (L. stagnalis) has served as a successful model for studies in the field of Neuroscience. However, a serious drawback in the molecular analysis of the nervous system of L. stagnalis has been the lack of large-scale genomic or neuronal transcriptome information, thereby ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-451
更新日期:2009-09-23 00:00:00
abstract:BACKGROUND:HSP90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. HSP90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. In this study we investigate ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-156
更新日期:2006-06-17 00:00:00
abstract:BACKGROUND:Papain-like cysteine proteases (PLCPs), a large group of cysteine proteases structurally related to papain, play important roles in plant development, senescence, and defense responses. Papain, the first cysteine protease whose structure was determined by X-ray crystallography, plays a crucial role in protec...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4394-y
更新日期:2018-01-06 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:The use of RNAseq to resolve the transcriptional organization of an organism was established in recent years and also showed the complexity and dynamics of bacterial transcriptomes. The aim of this study was to comprehensively investigate the transcriptome of the industrially relevant amino acid producer and...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-888
更新日期:2013-12-17 00:00:00
abstract:BACKGROUND:Habitats colonized by acidophiles as an ideal physical barrier may induce genetic exchange of microbial members within the common communities, but little is known about how species in extremely acidic environments diverge and evolve. RESULTS:Using the acidophilic sulfur-oxidizer Acidithiobacillus as a case ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5827-6
更新日期:2019-05-30 00:00:00
abstract:BACKGROUND:In higher eukaryotes, small RNAs play a role in regulating gene expression. Overexpression (OE) lines of Arabidopsis thaliana purple acid phosphatase 2 (AtPAP2) were shown to grow faster and exhibit higher ATP and sugar contents. Leaf microarray studies showed that many genes involved in microRNAs (miRNAs) a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-116
更新日期:2014-02-10 00:00:00
abstract:BACKGROUND:JWB phytoplasma is a kind of insect-transmitted and uncultivable bacterial plant pathogen causeing a destructive Jujube disease. To date, no genome information about JWB phytoplasma has been published, which hindered its characterization at genomic level. To understand its pathogenicity and ecology, the geno...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5075-1
更新日期:2018-09-19 00:00:00
abstract:BACKGROUND:Next generation sequencing (NGS) has become a universal practice in modern molecular biology. As the throughput of sequencing experiments increases, the preparation of conventional multiplexed libraries becomes more labor intensive. Conventional library preparation typically requires quality control (QC) tes...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6481-8
更新日期:2020-01-28 00:00:00
abstract:BACKGROUND:With the advance of new massively parallel genotyping technologies, quantitative trait loci (QTL) fine mapping and map-based cloning become more achievable in identifying genes for important and complex traits. Development of high-density genetic markers in the QTL regions of specific mapping populations is ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-469
更新日期:2010-08-11 00:00:00
abstract:BACKGROUND:Cytoplasmic male sterility (CMS) is an inability to produce functional pollen that is caused by mutation of the mitochondrial genome. Comparative analyses of mitochondrial genomes of lines with and without CMS in several species have revealed structural differences between genomes, including extensive rearra...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-561
更新日期:2014-07-04 00:00:00
abstract:BACKGROUND:The human zinc finger protein 191 (ZNF191) is a member of the SCAN domain family of Krüppel-like zinc finger transcription factors. ZNF191 shows 94% identity to its mouse homologue zinc finger protein 191(Zfp191), which is the most highly conserved among the human-mouse SCAN family member orthologues pairs. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-241
更新日期:2009-05-22 00:00:00
abstract:BACKGROUND:Brown and white adipose tissues (BAT and WAT) play critical roles in controlling energy homeostasis and in the development of obesity and diabetes. The mouse Fat-Specific protein 27 (FSP27), a member of the cell death-inducing DFF45-like effector (CIDE) family, is expressed in both BAT and WAT and is associa...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-446
更新日期:2010-07-22 00:00:00
abstract:BACKGROUND:Transmembrane β-barrel proteins are a special class of transmembrane proteins which play several key roles in human body and diseases. Due to experimental difficulties, the number of transmembrane β-barrel proteins with known structures is very small. Over the years, a number of learning-based methods have b...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-S2-S5
更新日期:2012-04-12 00:00:00
abstract:BACKGROUND:Hard ticks (family Ixodidae) are obligatory hematophagous ectoparasites of worldwide medical and veterinary importance. The haploid genomes of multiple species of ixodid ticks exceed 1 Gbp, prompting questions regarding gene, segmental and whole genome duplication in this phyletic group. The availability of ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2350-2
更新日期:2016-03-16 00:00:00
abstract:BACKGROUND:The complex genome of rapeseed (Brassica napus) is not well understood despite the economic importance of the species. Good knowledge of sequence variation is needed for genetics approaches and breeding purposes. We used a diversity set of B. napus representing eight different germplasm types to sequence gen...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-281
更新日期:2012-06-24 00:00:00
abstract:BACKGROUND:Lower eggshell quality in the late laying period leads to economic loss. It is a major threat to the quality and safety of egg products. Age-related variations in ultrastructure were thought to induce this deterioration. Eggshell formation is a highly complex process under precise regulation of genes and bio...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07177-7
更新日期:2020-11-09 00:00:00
abstract:BACKGROUND:Evolution of novel protein-coding genes is the bedrock of adaptive evolution. Recently, we identified six protein-coding genes with similar signal sequence from Schistosoma japonicum egg stage mRNA using signal sequence trap (SST). To find the mechanism underlying the origination of these genes with similar ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-260
更新日期:2012-06-20 00:00:00
abstract:BACKGROUND:Major secondary metabolites, including flavonoids, caffeine, and theanine, are important components of tea products and are closely related to the taste, flavor, and health benefits of tea. Secondary metabolite biosynthesis in Camellia sinensis is differentially regulated in different tissues during growth a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1773-0
更新日期:2015-07-29 00:00:00
abstract:BACKGROUND:Streptococcus infantarius subsp. infantarius (Sii) belongs to the Streptococcus bovis/Streptococcus equinus complex associated with several human and animal infections. Sii is a predominant bacterium in spontaneously fermented milk products in Africa. The genome sequence of Sii strain CJ18 was compared with ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-200
更新日期:2013-03-22 00:00:00
abstract:BACKGROUND:Animals are thought to achieve lignocellulose digestion via symbiotic associations with gut microbes; this view leads to significant focus on bacteria and fungi for lignocellulolytic systems. The presence of biomass conversion systems hardwired into animal genomes has not yet been unequivocally demonstrated....
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4861-0
更新日期:2018-06-20 00:00:00