Nucleosome deposition and DNA methylation at coding region boundaries.

abstract：BACKGROUND:Bread wheat is an allohexaploid species with a 16-Gb genome that has large intergenic regions, which presents a big challenge for pinpointing regulatory elements and further revealing the transcriptional regulatory mechanisms. Chromatin profiling to characterize the combinatorial patterns of chromatin signat...

journal_title：Genome biology

authors： Li Z,Wang M,Lin K,Xie Y,Guo J,Ye L,Zhuang Y,Teng W,Ran X,Tong Y,Xue Y,Zhang W,Zhang Y

更新日期：2019-07-15 00:00:00

abstract：BACKGROUND:RNA sequencing has opened new avenues for the study of transcriptome composition. Significant evidence has accumulated showing that the human transcriptome contains in excess of a hundred thousand different transcripts. However, it is still not clear to what extent this diversity prevails when considering th...

journal_title：Genome biology

authors： Gonzàlez-Porta M,Frankish A,Rung J,Harrow J,Brazma A

更新日期：2013-07-01 00:00:00

abstract：:A report on the 18th Congress of the European Society for Evolutionary Biology (ESEB), Aarhus, Denmark, 20-25 August, 2001. ...

journal_title：Genome biology

authors： Liberles DA

更新日期：2001-01-01 00:00:00

abstract：BACKGROUND:The discovery of cytosine hydroxymethylation (5hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behaviour in colon cancer. 5hmC is globally reduced in proliferating cells such as colon tumours and the gut crypt progenitors, from which t...

journal_title：Genome biology

authors： Uribe-Lewis S,Stark R,Carroll T,Dunning MJ,Bachman M,Ito Y,Stojic L,Halim S,Vowler SL,Lynch AG,Delatte B,de Bony EJ,Colin L,Defrance M,Krueger F,Silva AL,Ten Hoopen R,Ibrahim AE,Fuks F,Murrell A

更新日期：2015-04-01 00:00:00

abstract：:Single-cell RNA-seq in samples from the human neocortex demonstrate that long noncoding RNAs (lncRNAs) are abundantly expressed in specific individual brain cells, despite being hard to detect in bulk samples. This result suggests that the lncRNAs might have important functions in specific cell types in the brain. ...

journal_title：Genome biology

authors： Ma Q,Chang HY

更新日期：2016-04-14 00:00:00

abstract：BACKGROUND:Mutations in genes encoding ribosomal proteins (RPs) have been shown to cause an array of cellular and developmental defects in a variety of organisms. In Drosophila melanogaster, disruption of RP genes can result in the 'Minute' syndrome of dominant, haploinsufficient phenotypes, which include prolonged dev...

journal_title：Genome biology

authors： Marygold SJ,Roote J,Reuter G,Lambertsson A,Ashburner M,Millburn GH,Harrison PM,Yu Z,Kenmochi N,Kaufman TC,Leevers SJ,Cook KR

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:While the song of all songbirds is controlled by the same neural circuit, the hormone dependence of singing behavior varies greatly between species. For this reason, songbirds are ideal organisms to study ultimate and proximate mechanisms of hormone-dependent behavior and neuronal plasticity. RESULTS:We pre...

journal_title：Genome biology

authors： Frankl-Vilches C,Kuhl H,Werber M,Klages S,Kerick M,Bakker A,de Oliveira EH,Reusch C,Capuano F,Vowinckel J,Leitner S,Ralser M,Timmermann B,Gahr M

更新日期：2015-01-29 00:00:00

abstract：:The subcellular localization of the entire proteome of an organism, the yeast Saccharomyces cerevisiae, has been revealed for the first time. Comparison with less comprehensive studies of mammalian cells provides insights into the localization of the mammalian proteome. ...

journal_title：Genome biology

authors： Simpson JC,Pepperkok R

更新日期：2003-01-01 00:00:00

abstract：BACKGROUND:Over the past years a variety of host restriction genes have been identified in human and mammals that modulate retrovirus infectivity, replication, assembly, and/or cross-species transmission. Among these host-encoded restriction factors, the APOBEC3 (A3; apolipoprotein B mRNA-editing catalytic polypeptide ...

journal_title：Genome biology

authors： Münk C,Beck T,Zielonka J,Hotz-Wagenblatt A,Chareza S,Battenberg M,Thielebein J,Cichutek K,Bravo IG,O'Brien SJ,Löchelt M,Yuhki N

更新日期：2008-01-01 00:00:00

abstract：:MAP1-family proteins are classical microtubule-associated proteins (MAPs) that bind along the microtubule lattice. The founding members, MAP1A and MAP1B, are predominantly expressed in neurons, where they are thought to be important in the formation and development of axons and dendrites. Mammalian genomes usually con...

journal_title：Genome biology

authors： Halpain S,Dehmelt L

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Many different methods exist to adjust for variability in cell-type mixture proportions when analyzing DNA methylation studies. Here we present the result of an extensive simulation study, built on cell-separated DNA methylation profiles from Illumina Infinium 450K methylation data, to compare the performanc...

journal_title：Genome biology

authors： McGregor K,Bernatsky S,Colmegna I,Hudson M,Pastinen T,Labbe A,Greenwood CM

更新日期：2016-05-03 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：:Gene regulatory networks (GRNs) are rapidly being delineated, but their quality and biological meaning are often questioned. Here, I argue that biological meaning is challenging to define and discuss reasons why GRN validation should be interpreted cautiously. ...

journal_title：Genome biology

authors： Walhout AJ

更新日期：2011-01-01 00:00:00

abstract：:The eXtensible Genome Data Broker (xGDB) provides a software infrastructure consisting of integrated tools for the storage, display, and analysis of genome features in their genomic context. Common features include gene structure annotations, spliced alignments, mapping of repetitive sequence, and microarray probes, b...

journal_title：Genome biology

authors： Schlueter SD,Wilkerson MD,Dong Q,Brendel V

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Light and carbon are two essential signals influencing plant growth and development. Little is known about how carbon and light signaling pathways intersect or influence one another to affect gene expression. RESULTS:Microarrays are used to investigate carbon and light signaling interactions at a genome-wid...

journal_title：Genome biology

authors： Thum KE,Shin MJ,Palenchar PM,Kouranov A,Coruzzi GM

更新日期：2004-01-01 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:The lifelong accumulation of somatic mutations underlies age-related phenotypes and cancer. Mutagenic forces are thought to shape the genome of aging cells in a tissue-specific way. Whole genome analyses of somatic mutation patterns, based on both types and genomic distribution of variants, can shed light on...

journal_title：Genome biology

authors： Franco I,Helgadottir HT,Moggio A,Larsson M,Vrtačnik P,Johansson A,Norgren N,Lundin P,Mas-Ponte D,Nordström J,Lundgren T,Stenvinkel P,Wennberg L,Supek F,Eriksson M

更新日期：2019-12-18 00:00:00

abstract：:We describe a method for extracting Boolean implications (if-then relationships) in very large amounts of gene expression microarray data. A meta-analysis of data from thousands of microarrays for humans, mice, and fruit flies finds millions of implication relationships between genes that would be missed by other meth...

journal_title：Genome biology

authors： Sahoo D,Dill DL,Gentles AJ,Tibshirani R,Plevritis SK

更新日期：2008-10-30 00:00:00

abstract：:We introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel simulation-based composite likelihood method that uses the blockwise site frequency spectrum to jointly infer past demography and recombination. ABLE is explicitly designed for a wide variety of data from unphased diploid genomes to genome-wide m...

journal_title：Genome biology

authors： Beeravolu CR,Hickerson MJ,Frantz LAF,Lohse K

更新日期：2018-09-25 00:00:00

abstract：:Open chromatin profiling integrates information across diverse regulatory elements to reveal the transcriptionally active genome. Tn5 transposase and DNase I sequencing-based methods prefer native or high cell numbers. Here, we describe NicE-seq (nicking enzyme assisted sequencing) for high-resolution open chromatin p...

journal_title：Genome biology

authors： Ponnaluri VKC,Zhang G,Estève PO,Spracklin G,Sian S,Xu SY,Benoukraf T,Pradhan S

更新日期：2017-06-28 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

authors： Rubio CA,Weisburd B,Holderfield M,Arias C,Fang E,DeRisi JL,Fanidi A

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Hypoxia-inducible factor 1 (HIF-1) plays a key role in cellular adaptation to hypoxia. To better understand the determinants of HIF-1 binding and transactivation, we used ChIP-chip and gene expression profiling to define the relationship between the epigenetic landscape, sites of HIF-1 binding, and genes tra...

journal_title：Genome biology

authors： Xia X,Kung AL

更新日期：2009-01-01 00:00:00

abstract：:A report on the 11th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, Cold Spring Harbor Laboratories, New York, USA, November 2-5, 2011. ...

journal_title：Genome biology

authors： Chambers EV,Kindt AS,Semple CA

更新日期：2011-12-28 00:00:00

abstract：BACKGROUND:The control of energy metabolism is fundamental for cell growth and function and anomalies in it are implicated in complex diseases and ageing. Metabolism in yeast cells can be manipulated by supplying different carbon sources: yeast grown on glucose rapidly proliferates by fermentation, analogous to tumour ...

journal_title：Genome biology

authors： Malecki M,Bitton DA,Rodríguez-López M,Rallis C,Calavia NG,Smith GC,Bähler J

更新日期：2016-11-25 00:00:00

abstract：:The nuclear genome sequence of Amborella trichopoda, the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics. ...

journal_title：Genome biology

authors： Soltis DE,Albert VA,Leebens-Mack J,Palmer JD,Wing RA,dePamphilis CW,Ma H,Carlson JE,Altman N,Kim S,Wall PK,Zuccolo A,Soltis PS

更新日期：2008-01-01 00:00:00

abstract：:Protein kinases are critical to cellular signalling and post-translational gene regulation, but their biological substrates are difficult to identify. We show that cyclin-dependent kinase (CDK) consensus motifs are frequently clustered in CDK substrate proteins. Based on this, we introduce a new computational strategy...

journal_title：Genome biology

authors： Moses AM,Hériché JK,Durbin R

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:Pluripotency of embryonic stem (ES) cells is controlled in part by chromatin-modifying factors that regulate histone H3 lysine 4 (H3K4) methylation. However, it remains unclear how H3K4 demethylation contributes to ES cell function. RESULTS:Here, we show that KDM5B, which demethylates lysine 4 of histone H3...

journal_title：Genome biology

authors： Kidder BL,Hu G,Zhao K

更新日期：2014-02-04 00:00:00

abstract：:Exome sequencing is poised to yield substantial insights into human genetic variation and evolutionary history, but there are significant challenges to overcome before this becomes a reality. ...

journal_title：Genome biology

authors： Tennessen JA,O'Connor TD,Bamshad MJ,Akey JM

更新日期：2011-09-14 00:00:00

abstract：BACKGROUND:Aberrant activation of the Hedgehog pathway drives tumorigenesis of many cancers, including glioblastoma. However, the sensitization mechanism of the G protein-coupled-like receptor smoothened (SMO), a key component of Hedgehog signaling, remains largely unknown. RESULTS:In this study, we describe a novel p...

journal_title：Genome biology

authors： Wu X,Xiao S,Zhang M,Yang L,Zhong J,Li B,Li F,Xia X,Li X,Zhou H,Liu D,Huang N,Yang X,Xiao F,Zhang N

更新日期：2021-01-14 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