Bacillus subtilis during feast and famine: visualization of the overall regulation of protein synthesis during glucose starvation by proteome analysis.

abstract：:Genome-wide association studies (GWAS) have consistently implicated noncoding variation within the TCF7L2 locus with type 2 diabetes (T2D) risk. While this locus represents the strongest genetic determinant for T2D risk in humans, it remains unclear how these noncoding variants affect disease etiology. To test the hyp...

journal_title：Genome research

authors： Savic D,Ye H,Aneas I,Park SY,Bell GI,Nobrega MA

更新日期：2011-09-01 00:00:00

abstract：:MicroRNAs (miRNAs) are known to post-transcriptionally regulate target mRNAs through the 3'-UTR, which interacts mainly with the 5'-end of miRNA in animals. Here we identify many endogenous motifs within human 5'-UTRs specific to the 3'-ends of miRNAs. The 3'-end of conserved miRNAs in particular has significant inter...

journal_title：Genome research

authors： Lee I,Ajay SS,Yook JI,Kim HS,Hong SH,Kim NH,Dhanasekaran SM,Chinnaiyan AM,Athey BD

更新日期：2009-07-01 00:00:00

abstract：:We herein study genetic recombination in three cattle populations from France, New Zealand, and the Netherlands. We identify 2,395,177 crossover (CO) events in 94,516 male gametes, and 579,996 CO events in 25,332 female gametes. The average number of COs was found to be larger in males (23.3) than in females (21.4). T...

journal_title：Genome research

authors： Kadri NK,Harland C,Faux P,Cambisano N,Karim L,Coppieters W,Fritz S,Mullaart E,Baurain D,Boichard D,Spelman R,Charlier C,Georges M,Druet T

更新日期：2016-10-01 00:00:00

abstract：:Low-copy repeats, or segmental duplications, are highly dynamic regions in the genome. The low-copy repeats on chromosome 22q11.2 (LCR22) are a complex mosaic of genes and pseudogenes formed by duplication processes; they mediate chromosome rearrangements associated with velo-cardio-facial syndrome/DiGeorge syndrome, ...

journal_title：Genome research

authors： Babcock M,Pavlicek A,Spiteri E,Kashork CD,Ioshikhes I,Shaffer LG,Jurka J,Morrow BE

更新日期：2003-12-01 00:00:00

abstract：:Caenorhabditis elegans was the first multicellular eukaryotic genome sequenced to apparent completion. Although this assembly employed a standard C. elegans strain (N2), it used sequence data from several laboratories, with DNA propagated in bacteria and yeast. Thus, the N2 assembly has many differences from any C. el...

journal_title：Genome research

authors： Yoshimura J,Ichikawa K,Shoura MJ,Artiles KL,Gabdank I,Wahba L,Smith CL,Edgley ML,Rougvie AE,Fire AZ,Morishita S,Schwarz EM

更新日期：2019-06-01 00:00:00

abstract：:While copy number variation (CNV) is an active area of research, de novo mutation rates within human populations are not well characterized. By focusing on large (>100 kbp) events, we estimate the rate of de novo CNV formation in humans by analyzing 4394 transmissions from human pedigrees with and without neurocogniti...

journal_title：Genome research

authors： Itsara A,Wu H,Smith JD,Nickerson DA,Romieu I,London SJ,Eichler EE

更新日期：2010-11-01 00:00:00

abstract：:Comparative genomics provides a general methodology for discovering functional DNA elements and understanding their evolution. The availability of many related genomes enables more powerful analyses, but requires rigorous phylogenetic methods to resolve orthologous genes and regions. Here, we use 12 recently sequenced...

journal_title：Genome research

authors： Rasmussen MD,Kellis M

更新日期：2007-12-01 00:00:00

abstract：:Animal microRNA sequences are subject to 3' nucleotide addition. Through detailed analysis of deep-sequenced short RNA data sets, we show adenylation and uridylation of miRNA is globally present and conserved across Drosophila and vertebrates. To better understand 3' adenylation function, we deep-sequenced RNA after k...

journal_title：Genome research

authors： Burroughs AM,Ando Y,de Hoon MJ,Tomaru Y,Nishibu T,Ukekawa R,Funakoshi T,Kurokawa T,Suzuki H,Hayashizaki Y,Daub CO

更新日期：2010-10-01 00:00:00

abstract：:Microsatellites--tandem repeats of short DNA motifs--are abundant in the human genome and have high mutation rates. While microsatellite instability is implicated in numerous genetic diseases, the molecular processes involved in their emergence and disappearance are still not well understood. Microsatellites are hypot...

journal_title：Genome research

authors： Kelkar YD,Eckert KA,Chiaromonte F,Makova KD

更新日期：2011-12-01 00:00:00

abstract：:Gene expression can be regulated at multiple levels, but it is not known if and how there is broad coordination between regulation at the transcriptional and post-transcriptional levels. Transcription factors and chromatin regulate gene expression transcriptionally, whereas microRNAs (miRNAs) are small regulatory RNAs...

journal_title：Genome research

authors： Shivram H,Le SV,Iyer VR

更新日期：2019-02-01 00:00:00

abstract：:By analyzing 1,780,295 5'-end sequences of human full-length cDNAs derived from 164 kinds of oligo-cap cDNA libraries, we identified 269,774 independent positions of transcriptional start sites (TSSs) for 14,628 human RefSeq genes. These TSSs were clustered into 30,964 clusters that were separated from each other by m...

journal_title：Genome research

authors： Kimura K,Wakamatsu A,Suzuki Y,Ota T,Nishikawa T,Yamashita R,Yamamoto J,Sekine M,Tsuritani K,Wakaguri H,Ishii S,Sugiyama T,Saito K,Isono Y,Irie R,Kushida N,Yoneyama T,Otsuka R,Kanda K,Yokoi T,Kondo H,Wagatsuma M

更新日期：2006-01-01 00:00:00

abstract：:Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencin...

journal_title：Genome research

authors： Heidari N,Phanstiel DH,He C,Grubert F,Jahanbani F,Kasowski M,Zhang MQ,Snyder MP

更新日期：2014-12-01 00:00:00

abstract：:Essential genes refer to those whose null mutation leads to lethality or sterility. Theoretical reasoning and empirical data both suggest that the fatal effect of inactivating an essential gene can be attributed to either the loss of indispensable core cellular function (Type I), or the gain of fatal side effects afte...

journal_title：Genome research

authors： Chen P,Wang D,Chen H,Zhou Z,He X

更新日期：2016-10-01 00:00:00

abstract：:Highly overlapping patterns of genome-wide binding of many distinct transcription factors have been observed in worms, insects, and mammals, but the origins and consequences of this overlapping binding remain unclear. While analyzing chromatin immunoprecipitation data sets from 21 sequence-specific transcription facto...

journal_title：Genome research

authors： Satija R,Bradley RK

更新日期：2012-04-01 00:00:00

abstract：:Somatic transposon expression in neural tissue is commonly considered as a measure of mobilization and has therefore been linked to neuropathology and organismal individuality. We combined genome sequencing data with single-cell mRNA sequencing of the same inbred fly strain to map transposon expression in the Drosophi...

journal_title：Genome research

authors： Treiber CD,Waddell S

更新日期：2020-11-01 00:00:00

abstract：:Pigmentation of skin, eye, and hair reflects some of the most evident common phenotypes in humans. Several candidate genes for human pigmentation are identified. The SNP rs12913832 has strong statistical association with human pigmentation. It is located within an intron of the nonpigment gene HERC2, 21 kb upstream of...

journal_title：Genome research

authors： Visser M,Kayser M,Palstra RJ

更新日期：2012-03-01 00:00:00

abstract：:The higher-order structural organization and dynamics of the chromosomes play a central role in gene regulation. To explore this structure-function relationship, it is necessary to directly visualize genomic elements in living cells. Genome imaging based on the CRISPR system is a powerful approach but has limited appl...

journal_title：Genome research

authors： Chaudhary N,Nho SH,Cho H,Gantumur N,Ra JS,Myung K,Kim H

更新日期：2020-09-01 00:00:00

abstract：:We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94 had been sequenced already in the course of studying the biology of their gene products, and examples of 12 different tran...

journal_title：Genome research

authors： Benos PV,Gatt MK,Murphy L,Harris D,Barrell B,Ferraz C,Vidal S,Brun C,Demaille J,Cadieu E,Dreano S,Gloux S,Lelaure V,Mottier S,Galibert F,Borkova D,Miñana B,Kafatos FC,Bolshakov S,Sidén-Kiamos I,Papagiannakis G,S

更新日期：2001-05-01 00:00:00

abstract：:We have developed a simplified method for multiplex PCR based on the use of chimeric primers. Each primer contains a 3' region complementary to sequence-specific recognition sites and a 5' region made up of an unrelated 20-nucleotide sequence. Identical reaction conditions, cycling times, and annealing temperatures ha...

journal_title：Genome research

authors： Shuber AP,Grondin VJ,Klinger KW

更新日期：1995-12-01 00:00:00

abstract：:Mouse chromosome 7F4/F5, where the imprinting domain is located, is syntenic to human 11p15.5, the locus for Beckwith-Wiedemann syndrome. The domain is thought to consist of the two subdomains Kip2 (p57(kip2))/Lit1 and Igf2/H19. Because DNA methylation is believed to be a key factor in genomic imprinting, we performed...

journal_title：Genome research

authors： Yatsuki H,Joh K,Higashimoto K,Soejima H,Arai Y,Wang Y,Hatada I,Obata Y,Morisaki H,Zhang Z,Nakagawachi T,Satoh Y,Mukai T

更新日期：2002-12-01 00:00:00

abstract：:Disturbance of DNA methylation leading to aberrant gene expression has been implicated in the etiology of many diseases. Whereas variation at the genetic level has been studied extensively, less is known about the extent and function of epigenetic variation. To explore variation and heritability of DNA methylation, we...

journal_title：Genome research

authors： Gervin K,Hammerø M,Akselsen HE,Moe R,Nygård H,Brandt I,Gjessing HK,Harris JR,Undlien DE,Lyle R

更新日期：2011-11-01 00:00:00

abstract：:DNA transposons, or class 2 transposable elements, have successfully propagated in a wide variety of genomes. However, it is widely believed that DNA transposon activity has ceased in mammalian genomes for at least the last 40 million years. We recently reported evidence for the relatively recent activity of hAT and H...

journal_title：Genome research

authors： Ray DA,Feschotte C,Pagan HJ,Smith JD,Pritham EJ,Arensburger P,Atkinson PW,Craig NL

更新日期：2008-05-01 00:00:00

abstract：:Coevolution maintains interactions between phenotypic traits through the process of reciprocal natural selection. Detecting molecular coevolution can expose functional interactions between molecules in the cell, generating insights into biological processes, pathways, and the networks of interactions important for cel...

journal_title：Genome research

authors： Tillier ER,Charlebois RL

更新日期：2009-10-01 00:00:00

abstract：:Sequencing of the human Y chromosome has uncovered the peculiarities of the genomic organization of a heterogametic sex chromosome of old evolutionary age, and has led to many insights into the evolutionary changes that occurred during its long history. We have studied the genomic organization of the medaka fish Y chr...

journal_title：Genome research

authors： Kondo M,Hornung U,Nanda I,Imai S,Sasaki T,Shimizu A,Asakawa S,Hori H,Schmid M,Shimizu N,Schartl M

更新日期：2006-07-01 00:00:00

abstract：:The expression of most genes is regulated by multiple transcription factors. The interactions between transcription factors produce complex patterns of gene expression that are not always obvious from the arrangement of cis-regulatory elements in a promoter. One critical element of promoters is the TATA box, the docki...

journal_title：Genome research

authors： Mogno I,Vallania F,Mitra RD,Cohen BA

更新日期：2010-10-01 00:00:00

abstract：:Hearing impairment is clinically and genetically heterogeneous. There are >400 disorders in which hearing impairment is a characteristic of the syndrome, and family studies demonstrate that there are at least 30 autosomal loci for nonsyndromic hearing impairment. The genes that have been identified encode diaphanous (...

journal_title：Genome research

authors： Keats BJ,Berlin CI

更新日期：1999-01-01 00:00:00

abstract：:Yeasts and filamentous fungi do not have adenosine deaminase acting on RNA (ADAR) orthologs and are believed to lack A-to-I RNA editing, which is the most prevalent editing of mRNA in animals. However, during this study with the PUK1(FGRRES_01058) pseudokinase gene important for sexual reproduction in Fusarium gramine...

journal_title：Genome research

authors： Liu H,Wang Q,He Y,Chen L,Hao C,Jiang C,Li Y,Dai Y,Kang Z,Xu JR

更新日期：2016-04-01 00:00:00

abstract：:Natural selection that affected modern humans early in their evolution has likely shaped some of the traits that set present-day humans apart from their closest extinct and living relatives. The ability to detect ancient natural selection in the human genome could provide insights into the molecular basis for these hu...

journal_title：Genome research

authors： Peyrégne S,Boyle MJ,Dannemann M,Prüfer K

更新日期：2017-09-01 00:00:00

abstract：:We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes. Three principal change...

journal_title：Genome research

authors： Jaffe DB,Butler J,Gnerre S,Mauceli E,Lindblad-Toh K,Mesirov JP,Zody MC,Lander ES

更新日期：2003-01-01 00:00:00

abstract：:Meiotic DNA double-stranded breaks (DSBs) initiate genetic recombination in discrete areas of the genome called recombination hotspots. DSBs can be directly mapped using chromatin immunoprecipitation followed by sequencing (ChIP-seq). Nevertheless, the genome-wide mapping of recombination hotspots in mammals is still ...

journal_title：Genome research

authors： Khil PP,Smagulova F,Brick KM,Camerini-Otero RD,Petukhova GV

更新日期：2012-05-01 00:00:00