Impact of transposable elements on genome structure and evolution in bread wheat.

abstract：BACKGROUND:While CRISPR-Cas systems hold tremendous potential for engineering the human genome, it is unclear how well each system performs against one another in both non-homologous end joining (NHEJ)-mediated and homology-directed repair (HDR)-mediated genome editing. RESULTS:We systematically compare five different...

journal_title：Genome biology

authors： Wang Y,Liu KI,Sutrisnoh NB,Srinivasan H,Zhang J,Li J,Zhang F,Lalith CRJ,Xing H,Shanmugam R,Foo JN,Yeo HT,Ooi KH,Bleckwehl T,Par YYR,Lee SM,Ismail NNB,Sanwari NAB,Lee STV,Lew J,Tan MH

更新日期：2018-05-29 00:00:00

abstract：BACKGROUND:The C2H2 zinc finger (C2H2-ZF) is the most numerous protein domain in many metazoans, but is not as frequent or diverse in other eukaryotes. The biochemical and evolutionary mechanisms that underlie the diversity of this DNA-binding domain exclusively in metazoans are, however, mostly unknown. RESULTS:Here,...

journal_title：Genome biology

authors： Najafabadi HS,Garton M,Weirauch MT,Mnaimneh S,Yang A,Kim PM,Hughes TR

更新日期：2017-09-06 00:00:00

abstract：BACKGROUND:Differences in 5-hydroxymethylcytosine, 5hmC, distributions may complicate previous observations of abnormal cytosine methylation statuses that are used for the identification of new tumor suppressor gene candidates that are relevant to human hepatocarcinogenesis. The simultaneous detection of 5-methylcytosi...

journal_title：Genome biology

authors： Gao F,Xia Y,Wang J,Lin Z,Ou Y,Liu X,Liu W,Zhou B,Luo H,Zhou B,Wen B,Zhang X,Huang J

更新日期：2014-12-03 00:00:00

abstract：BACKGROUND:The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence showed that ankylosing spondylitis may be a microbiome-driven disease. RESULTS:To investigate the relat...

journal_title：Genome biology

authors： Wen C,Zheng Z,Shao T,Liu L,Xie Z,Le Chatelier E,He Z,Zhong W,Fan Y,Zhang L,Li H,Wu C,Hu C,Xu Q,Zhou J,Cai S,Wang D,Huang Y,Breban M,Qin N,Ehrlich SD

更新日期：2017-07-27 00:00:00

abstract：:The iCLIP and eCLIP techniques facilitate the detection of protein-RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the specifics of iCLIP and eCLIP truncation patterns and possible biases. We developed PureCLIP ( https://github....

journal_title：Genome biology

authors： Krakau S,Richard H,Marsico A

更新日期：2017-12-28 00:00:00

abstract：:Key components of the programmed cell death pathway are conserved between Caenorhabditis elegans, Drosophila melanogaster and humans. The search for additional homologs has been facilitated by the availability of the entire genomic sequence for each of these organisms. ...

journal_title：Genome biology

authors： Tittel JN,Steller H

更新日期：2000-01-01 00:00:00

abstract：:DNA transposons are efficient tools in transgenesis and have therefore become popular in the analysis of the regulatory genome in vertebrates via enhancer trap screens. Here, I discuss recent progress in this field of research, with a focus on the application of one of these transposons, namely the medaka fish derived...

journal_title：Genome biology

authors： Korzh V

更新日期：2007-01-01 00:00:00

abstract：:Recent experiments show that properly controlled recombination between homologous DNA molecules is essential for the maintenance of genome stability and for the prevention of tumorigenesis. ...

journal_title：Genome biology

authors： Modesti M,Kanaar R

更新日期：2001-01-01 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

authors： Thieme M,Lanciano S,Balzergue S,Daccord N,Mirouze M,Bucher E

更新日期：2017-07-07 00:00:00

abstract：:CRISPR-Cas9 gene editing has transformed our ability to rapidly interrogate the functional impact of somatic mutations in human cancers. Droplet-based technology enables the analysis of Cas9-introduced gene edits in thousands of single cells. Using this technology, we analyze Ba/F3 cells engineered to express single o...

journal_title：Genome biology

authors： Ten Hacken E,Clement K,Li S,Hernández-Sánchez M,Redd R,Wang S,Ruff D,Gruber M,Baranowski K,Jacob J,Flynn J,Jones KW,Neuberg D,Livak KJ,Pinello L,Wu CJ

更新日期：2020-10-20 00:00:00

abstract：:Gene expression analysis of microRNA molecules is becoming increasingly important. In this study we assess the use of the mean expression value of all expressed microRNAs in a given sample as a normalization factor for microRNA real-time quantitative PCR data and compare its performance to the currently adopted approa...

journal_title：Genome biology

authors： Mestdagh P,Van Vlierberghe P,De Weer A,Muth D,Westermann F,Speleman F,Vandesompele J

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:Simple sequence repeats (SSRs) in DNA have been traditionally thought of as functionally unimportant and have been studied mainly as genetic markers. A recent handful of studies have shown, however, that SSRs in different positions of a gene can play important roles in determining protein function, genetic d...

journal_title：Genome biology

authors： Lawson MJ,Zhang L

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Pseudomonas aeruginosa is a ubiquitous environmental bacterium and an important opportunistic human pathogen. Generally, the acquisition of genes in the form of pathogenicity islands distinguishes pathogenic isolates from nonpathogens. We therefore sequenced a highly virulent strain of P. aeruginosa, PA14, a...

journal_title：Genome biology

authors： Lee DG,Urbach JM,Wu G,Liberati NT,Feinbaum RL,Miyata S,Diggins LT,He J,Saucier M,Déziel E,Friedman L,Li L,Grills G,Montgomery K,Kucherlapati R,Rahme LG,Ausubel FM

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are oligoribonucleotides with an important role in regulation of gene expression at the level of translation. Despite imperfect target complementarity, they can also significantly reduce mRNA levels. The validity of miRNA target gene predictions is difficult to assess at the protein level....

journal_title：Genome biology

authors： Arora A,Simpson DA

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Although 2,061 proteins of Pyrococcus horikoshii OT3, a hyperthermophilic archaeon, have been predicted from the recently completed genome sequence, the majority of proteins show no similarity to those from other organisms and are thus hypothetical proteins of unknown function. Because most proteins operate ...

journal_title：Genome biology

authors： Usui K,Katayama S,Kanamori-Katayama M,Ogawa C,Kai C,Okada M,Kawai J,Arakawa T,Carninci P,Itoh M,Takio K,Miyano M,Kidoaki S,Matsuda T,Hayashizaki Y,Suzuki H

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:Whole genome sequencing of marine cyanobacteria has revealed an unprecedented degree of genomic variation and streamlining. With a size of 1.66 megabase-pairs, Prochlorococcus sp. MED4 has the most compact of these genomes and it is enigmatic how the few identified regulatory proteins efficiently sustain the...

journal_title：Genome biology

authors： Axmann IM,Kensche P,Vogel J,Kohl S,Herzel H,Hess WR

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:Although aberrant DNA methylation has been observed previously in acute lymphoblastic leukemia (ALL), the patterns of differential methylation have not been comprehensively determined in all subtypes of ALL on a genome-wide scale. The relationship between DNA methylation, cytogenetic background, drug resista...

journal_title：Genome biology

authors： Nordlund J,Bäcklin CL,Wahlberg P,Busche S,Berglund EC,Eloranta ML,Flaegstad T,Forestier E,Frost BM,Harila-Saari A,Heyman M,Jónsson OG,Larsson R,Palle J,Rönnblom L,Schmiegelow K,Sinnett D,Söderhäll S,Pastinen T,Gusta

更新日期：2013-09-24 00:00:00

abstract：BACKGROUND:The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and regulate the expression of developmentally important genes. Here, we describe an unexpected role in...

journal_title：Genome biology

authors： Yang R,Zheng Z,Chen Q,Yang L,Huang H,Miki D,Wu W,Zeng L,Liu J,Zhou JX,Ogas J,Zhu JK,He XJ,Zhang H

更新日期：2017-05-31 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

authors： Haber M,Mezzavilla M,Xue Y,Tyler-Smith C

更新日期：2016-01-11 00:00:00

abstract：:The majority of disease resistance genes in plants encode nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins. This large family is encoded by hundreds of diverse genes per genome and can be subdivided into the functionally distinct TIR-domain-containing (TNL) and CC-domain-containing (CNL) subfamilies. The...

journal_title：Genome biology

authors： McHale L,Tan X,Koehl P,Michelmore RW

更新日期：2006-01-01 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

authors： Notebaart RA,Kensche PR,Huynen MA,Dutilh BE

更新日期：2009-02-12 00:00:00

abstract：BACKGROUND:CTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). However, despite the importance and conservation of TADs, the role of CTCF binding in their evolution and stability remains elusive. RESULTS...

journal_title：Genome biology

authors： Kentepozidou E,Aitken SJ,Feig C,Stefflova K,Ibarra-Soria X,Odom DT,Roller M,Flicek P

更新日期：2020-01-07 00:00:00

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

authors： Karabacak Calviello A,Hirsekorn A,Wurmus R,Yusuf D,Ohler U

更新日期：2019-02-21 00:00:00

abstract：BACKGROUND:Short-term laboratory evolution of bacteria followed by genomic sequencing provides insight into the mechanism of adaptive evolution, such as the number of mutations needed for adaptation, genotype-phenotype relationships, and the reproducibility of adaptive outcomes. RESULTS:In the present study, we descri...

journal_title：Genome biology

authors： Conrad TM,Joyce AR,Applebee MK,Barrett CL,Xie B,Gao Y,Palsson BØ

更新日期：2009-01-01 00:00:00

abstract：:Purification of proteins cross-linked to mRNAs has identified 800 mRNA-binding proteins and their characteristics. ...

journal_title：Genome biology

authors： Sibley CR,Attig J,Ule J

更新日期：2012-07-17 00:00:00

abstract：BACKGROUND:Circular RNAs are a class of endogenous RNAs with various functions in eukaryotic cells. Worthy of note, circular RNAs play a critical role in cancer. Currently, nothing is known about their role in head and neck squamous cell carcinoma (HNSCC). The identification of circular RNAs in HNSCC might become usefu...

journal_title：Genome biology

authors： Verduci L,Ferraiuolo M,Sacconi A,Ganci F,Vitale J,Colombo T,Paci P,Strano S,Macino G,Rajewsky N,Blandino G

更新日期：2017-12-20 00:00:00

abstract：BACKGROUND:The recent availability of genome sequences has provided unparalleled insights into the broad-scale patterns of transposable element (TE) sequences in eukaryotic genomes. Nevertheless, the difficulties that TEs pose for genome assembly and annotation have prevented detailed, quantitative inferences about the...

journal_title：Genome biology

authors： Bergman CM,Quesneville H,Anxolabéhère D,Ashburner M

更新日期：2006-01-01 00:00:00

abstract：:Early gene expression studies classified breast tumors into at least three clinically relevant subtypes. Although most current gene signatures are prognostic for estrogen receptor (ER) positive/human epidermal growth factor receptor 2 (HER2) negative breast cancers, few are informative for ER negative/HER2 negative an...

journal_title：Genome biology

authors： Haibe-Kains B,Desmedt C,Rothé F,Piccart M,Sotiriou C,Bontempi G

更新日期：2010-01-01 00:00:00

abstract：:We describe here a CRISPR simultaneous and wide-editing induced by a single system (SWISS), in which RNA aptamers engineered in crRNA scaffold recruit their cognate binding proteins fused with cytidine deaminase and adenosine deaminase to Cas9 nickase target sites to generate multiplexed base editing. By using paired ...

journal_title：Genome biology

authors： Li C,Zong Y,Jin S,Zhu H,Lin D,Li S,Qiu JL,Wang Y,Gao C

更新日期：2020-06-16 00:00:00

abstract：:How do naturally occurring polymorphisms in DNA sequence relate to variation in gene expression? Recent work to map genetic sources of expression variation has shown a surprising balance between cis and trans effects. Other work suggests some chromosomal clustering of genes by expression pattern. A synthesis of approa...

journal_title：Genome biology

authors： Hamilton BA

更新日期：2002-09-19 00:00:00