Common gene expression strategies revealed by genome-wide analysis in yeast.

abstract：BACKGROUND:MicroRNAs (miRNAs) are a class of small, non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition. So far, identification of miRNAs has been limited to a few model plant species, such as Arabidopsis, rice and Populus, whose genomes have been sequenc...

journal_title：Genome biology

authors： Yao Y,Guo G,Ni Z,Sunkar R,Du J,Zhu JK,Sun Q

更新日期：2007-01-01 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

authors： Mirny LA,Gelfand MS

更新日期：2002-01-01 00:00:00

abstract：BACKGROUND:Plant-microbe interactions feature complex signal interplay between pathogens and their hosts. Phytophthora species comprise a destructive group of fungus-like plant pathogens, collectively affecting a wide range of plants important to agriculture and natural ecosystems. Despite the availability of genome se...

journal_title：Genome biology

authors： Jupe J,Stam R,Howden AJ,Morris JA,Zhang R,Hedley PE,Huitema E

更新日期：2013-06-25 00:00:00

abstract：BACKGROUND:Growth rate is central to the development of cells in all organisms. However, little is known about the impact of changing growth rates. We used continuous cultures to control growth rate and studied the transcriptional program of the model eukaryote Saccharomyces cerevisiae, with generation times varying be...

journal_title：Genome biology

authors： Regenberg B,Grotkjaer T,Winther O,Fausbøll A,Akesson M,Bro C,Hansen LK,Brunak S,Nielsen J

更新日期：2006-01-01 00:00:00

abstract：:The explosive growth in taxonomic metagenome profiling methods over the past years has created a need for systematic comparisons using relevant performance criteria. The Open-community Profiling Assessment tooL (OPAL) implements commonly used performance metrics, including those of the first challenge of the initiativ...

journal_title：Genome biology

authors： Meyer F,Bremges A,Belmann P,Janssen S,McHardy AC,Koslicki D

更新日期：2019-03-04 00:00:00

abstract：BACKGROUND:Immunolabeling of metaphase chromosome spreads can map components of the human epigenome at the single cell level. Previously, there has been no systematic attempt to explore the potential of this approach for epigenomic mapping and thereby to complement approaches based on chromatin immunoprecipitation (ChI...

journal_title：Genome biology

authors： Terrenoire E,McRonald F,Halsall JA,Page P,Illingworth RS,Taylor AM,Davison V,O'Neill LP,Turner BM

更新日期：2010-01-01 00:00:00

abstract：:Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction associations for entire metabolic genes in an organism, and can be simulated to predict metabolic fluxes for various systems-level metabolic studies. Since the first GEM for Haemophilus influenzae was reported in 1999, advances have be...

journal_title：Genome biology

authors： Gu C,Kim GB,Kim WJ,Kim HU,Lee SY

更新日期：2019-06-13 00:00:00

abstract：BACKGROUND:DNA methylation and the Polycomb repression system are epigenetic mechanisms that play important roles in maintaining transcriptional repression. Recent evidence suggests that DNA methylation can attenuate the binding of Polycomb protein components to chromatin and thus plays a role in determining their geno...

journal_title：Genome biology

authors： Reddington JP,Perricone SM,Nestor CE,Reichmann J,Youngson NA,Suzuki M,Reinhardt D,Dunican DS,Prendergast JG,Mjoseng H,Ramsahoye BH,Whitelaw E,Greally JM,Adams IR,Bickmore WA,Meehan RR

更新日期：2013-03-25 00:00:00

abstract：:We describe here our experience in annotating the Drosophila melanogaster genome sequence, in the course of which we developed several new open-source software tools and a database schema to support large-scale genome annotation. We have developed these into an integrated and reusable software system for whole-genome ...

journal_title：Genome biology

authors： Mungall CJ,Misra S,Berman BP,Carlson J,Frise E,Harris N,Marshall B,Shu S,Kaminker JS,Prochnik SE,Smith CD,Smith E,Tupy JL,Wiel C,Rubin GM,Lewis SE

更新日期：2002-01-01 00:00:00

abstract：:Gene-expression profiling has yielded important information about simple systems, but complex tissues have not yet been widely profiled. Four recent studies of mammalian skeletal muscles have added to the catalogs of their gene expression differences, but have yet to lead to better understanding of the molecular proce...

journal_title：Genome biology

authors： Hampson R,Hughes SM

更新日期：2001-01-01 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:The genetic provenance of domesticated plants and the routes along which they were disseminated in prehistory have been a long-standing source of debate. Much of this debate has focused on identifying centers of origins for individual crops. However, many important crops show clear genetic signatures of mult...

journal_title：Genome biology

authors： Poets AM,Fang Z,Clegg MT,Morrell PL

更新日期：2015-08-21 00:00:00

abstract：:Piwi-interacting RNAs (piRNAs) originate from genomic regions dubbed piRNA clusters. How cluster transcripts are selected for processing into piRNAs is not understood. We discuss evidence for the involvement of chromatin structure and maternally inherited piRNAs in determining their fate. ...

journal_title：Genome biology

authors： Le Thomas A,Tóth KF,Aravin AA

更新日期：2014-01-27 00:00:00

abstract：BACKGROUND:Protein domains are commonly used to assess the functional roles and evolutionary relationships of proteins and protein families. Here, we use the Pfam protein family database to examine a set of candidate partial domains. Pfam protein domains are often thought of as evolutionarily indivisible, structurally ...

journal_title：Genome biology

authors： Triant DA,Pearson WR

更新日期：2015-05-15 00:00:00

abstract：:The key molecules involved in regulating the assembly and function of the mitotic spindle are shared by evolutionarily divergent species. Studies in different model systems are leading to convergent conclusions about the central role of microtubule nucleation and dynamics and of kinesin-related motor proteins in spind...

journal_title：Genome biology

authors： Walczak CE

更新日期：2000-01-01 00:00:00

abstract：BACKGROUND:The development of complex organisms is believed to involve progressive restrictions in cellular fate. Understanding the scope and features of chromatin dynamics during embryogenesis, and identifying regulatory elements important for directing developmental processes remain key goals of developmental biology...

journal_title：Genome biology

authors： Thomas S,Li XY,Sabo PJ,Sandstrom R,Thurman RE,Canfield TK,Giste E,Fisher W,Hammonds A,Celniker SE,Biggin MD,Stamatoyannopoulos JA

更新日期：2011-01-01 00:00:00

abstract：:An exciting recent study examining the methylation profile of human brain tissue implicates early-life epigenetic disruption in the neurodevelopmental origin of schizophrenia. ...

journal_title：Genome biology

authors： Ryan J,Saffery R

更新日期：2014-10-29 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：:From worms to humans, recognizing and modifying a specific chromosome is essential for dosage compensation, the mechanism by which equal X-linked gene expression in males and females is achieved. Recent molecular genetic and biochemical studies have provided new insights into how regulatory factors in Drosophila are r...

journal_title：Genome biology

authors： Amrein H

更新日期：2000-01-01 00:00:00

abstract：:A new generation of DNA-sequencing platforms will become commercially available over the next few years. These instruments will enable re-sequencing of human genomes at a previously unimagined throughput and low cost. Here, I examine why the 1,000 dollar human genome is an important goal for research and clinical diag...

journal_title：Genome biology

authors： Mardis ER

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Transcription factors (TFs) play a central role in regulating gene expression by interacting with cis-regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding specificities of most Saccharomyces cerevisiae TFs, but a comprehensive evaluation of their data has b...

journal_title：Genome biology

authors： Gordân R,Murphy KF,McCord RP,Zhu C,Vedenko A,Bulyk ML

更新日期：2011-12-21 00:00:00

abstract：BACKGROUND:Mutation rates vary across the genome. Many trans factors that influence mutation rates have been identified, as have specific sequence motifs at the 1-7-bp scale, but cis elements remain poorly characterized. The lack of understanding regarding why different sequences have different mutation rates hampers o...

journal_title：Genome biology

authors： Duan C,Huan Q,Chen X,Wu S,Carey LB,He X,Qian W

更新日期：2018-09-14 00:00:00

abstract：:Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here we present superTranscripts, a substitute for a reference genome, where each gene with multiple transcripts is represented by a si...

journal_title：Genome biology

authors： Davidson NM,Hawkins ADK,Oshlack A

更新日期：2017-08-04 00:00:00

abstract：BACKGROUND:Despite decades of research, the agent responsible for transmitting spongiform encephalopathies (TSEs) has not been identified. The Prion hypothesis, which dominates the field, supposes that modified host PrP protein, termed PrPSc, acts as the transmissible agent. This model fits the observation that TSE dis...

journal_title：Genome biology

authors： Gibson TJ

更新日期：2001-01-01 00:00:00

abstract：BACKGROUND:Nucleosome deposition downstream of transcription initiation and DNA methylation in the gene body suggest that control of transcription elongation is a key aspect of epigenetic regulation. RESULTS:Here we report a genome-wide observation of distinct peaks of nucleosomes and methylation at both ends of a pro...

journal_title：Genome biology

authors： Choi JK,Bae JB,Lyu J,Kim TY,Kim YJ

更新日期：2009-01-01 00:00:00

abstract：:Fine-tuning quantitative traits for continuous subtle phenotypes is highly advantageous. We engineer the highly conserved upstream open reading frame (uORF) of FvebZIPs1.1 in strawberry (Fragaria vesca), using base editor A3A-PBE. Seven novel alleles are generated. Sugar content of the homozygous T1 mutant lines is 33...

journal_title：Genome biology

authors： Xing S,Chen K,Zhu H,Zhang R,Zhang H,Li B,Gao C

更新日期：2020-09-03 00:00:00

abstract：BACKGROUND:Targeted deep sequencing is increasingly used to detect low-allelic fraction variants; it is therefore essential that errors that constitute baseline noise and impose a practical limit on detection are characterized. In the present study, we systematically evaluate the extent to which errors are incurred dur...

journal_title：Genome biology

authors： Park G,Park JK,Shin SH,Jeon HJ,Kim NKD,Kim YJ,Shin HT,Lee E,Lee KH,Son DS,Park WY,Park D

更新日期：2017-07-21 00:00:00

abstract：:Genomic regions with altered gene expression are a characteristic feature of cancer cells. We present a novel method for identifying such regions in gene expression maps. This method is based on total variation minimization, a classical signal restoration technique. In systematic evaluations, we show that our method c...

journal_title：Genome biology

authors： Nilsson B,Johansson M,Heyden A,Nelander S,Fioretos T

更新日期：2008-01-21 00:00:00

abstract：BACKGROUND:DNA damage leads to cellular responses that include the increased expression of DNA repair genes, repression of DNA replication and alterations in cellular metabolism. Archaeal information processing pathways resemble those in eukaryotes, but archaeal damage response pathways remain poorly understood. RESUL...

journal_title：Genome biology

authors： Götz D,Paytubi S,Munro S,Lundgren M,Bernander R,White MF

更新日期：2007-01-01 00:00:00

abstract：:A report of the Wellcome Trust Functional Genomics and Systems Biology Conference, Hinxton, UK, 29 November to 1 December 2011. ...

journal_title：Genome biology

authors： Bakal C

更新日期：2012-01-30 00:00:00