Abstract：
:The alignment of full-length human cDNA sequences to the finished sequence of the human genome provides a unique opportunity to study the distribution of genes throughout the genome. By analyzing the distances between 23,752 genes, we identified a class of divergently transcribed gene pairs, representing more than 10% of the genes in the genome, whose transcription start sites are separated by less than 1000 base pairs. Although this bidirectional arrangement has been previously described in humans and other species, the prevalence of bidirectional gene pairs in the human genome is striking, and the mechanisms of regulation of all but a few bidirectional genes are unknown. Our work shows that the transcripts of many bidirectional pairs are coexpressed, but some are antiregulated. Further, we show that many of the promoter segments between two bidirectional genes initiate transcription in both directions and contain shared elements that regulate both genes. We also show that the bidirectional arrangement is often conserved among mouse orthologs. These findings demonstrate that a bidirectional arrangement provides a unique mechanism of regulation for a significant number of mammalian genes.
journal_name
Genome Resjournal_title
Genome researchauthors
Trinklein ND,Aldred SF,Hartman SJ,Schroeder DI,Otillar RP,Myers RMdoi
10.1101/gr.1982804subject
Has Abstractpub_date
2004-01-01 00:00:00pages
62-6issue
1eissn
1088-9051issn
1549-5469pii
14/1/62journal_volume
14pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract：:The determination of the phylogenetic relationships among microorganisms has long relied primarily on gene sequence information. Given that prokaryotic organisms often lack morphological characteristics amenable to phylogenetic analysis, prokaryotic phylogenies, in particular, are often based on sequence data. In this...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.3033805
更新日期：2005-03-01 00:00:00
abstract：:The genetic positions of the five Arabidopsis thaliana centromere regions have been identified by mapping size polymorphisms in the centromeric 180-bp repeat arrays. Structural and genetic analysis indicates that 180-bp repeat arrays of up to 1000 kb are found in the centromere region of each chromosome. The genetic b...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.7.11.1045
更新日期：1997-11-01 00:00:00
abstract：:In vivo analyses of the occurrence, subcellular localization, and dynamics of protein-protein interactions (PPIs) are important issues in functional proteomic studies. The bimolecular fluorescence complementation (BiFC) assay has many advantages in that it provides a reliable way to detect PPIs in living cells with mi...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.231860.117
更新日期：2019-01-01 00:00:00
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
pub_type： 杂志文章
doi：10.1101/gr.123745.111
更新日期：2011-09-01 00:00:00
abstract：:We have constructed a detailed map of the genomic region containing the ETS-variant gene 6 (ETV6), involved in translocations and deletions associated with hematologic malignancies. Thirty-eight cosmids were characterized belonging to two contigs spanning 340 kb, and an EcoRl restriction map was developed. The gap bet...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.6.5.404
更新日期：1996-05-01 00:00:00
abstract：:Although often considered "minimal" organisms, mycoplasmas show a wide range of diversity with respect to host environment, phenotypic traits, and pathogenicity. Here we report the complete genomic sequence and proteogenomic map for the piscine mycoplasma Mycoplasma mobile, noted for its robust gliding motility. For t...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.2674004
更新日期：2004-08-01 00:00:00
abstract：:Metabolic homeostasis is sustained by complex biological networks that respond to nutrient availability. Genetic and environmental factors may disrupt this equilibrium, leading to metabolic disorders, including obesity and type 2 diabetes. To identify the genetic factors controlling metabolism, we performed quantitati...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.232322.117
更新日期：2018-09-01 00:00:00
abstract：:Giardia duodenalis is the best-characterized example of the most ancient eukaryotes, which are primitively amitochondrial and anaerobic. The surface of Giardia is coated with cysteine-rich proteins. One family of these proteins, CRP136, varies among isolates and upon environmental stress. A repeat region within the CR...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.7.1.37
更新日期：1997-01-01 00:00:00
abstract：:Human chromosomal regions enriched in segmental duplications are subject to extensive genomic reorganization. Such regions are particularly informative for illuminating the evolutionary history of a given chromosome. We have analyzed 866 kb of Y-chromosomal non-palindromic segmental duplications delineating four euchr...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.076711.108
更新日期：2008-07-01 00:00:00
abstract：:A-to-I RNA editing is a conserved widespread phenomenon in which adenosine (A) is converted to inosine (I) by adenosine deaminases (ADARs) in double-stranded RNA regions, mainly noncoding. Mutations in ADAR enzymes in Caenorhabditis elegans cause defects in normal development but are not lethal as in human and mouse. ...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.211169.116
更新日期：2017-03-01 00:00:00
abstract：:Evolutionary constraints on gene regulatory elements are poorly understood: Little is known about how the strength of transcription factor binding correlates with DNA sequence conservation, and whether transcription factor binding sites can evolve rapidly while retaining their function. Here we use the model of the NF...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.6490707
更新日期：2007-09-01 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
pub_type： 杂志文章
doi：10.1101/gr.1549503
更新日期：2003-12-01 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
pub_type： 杂志文章
doi：10.1101/gr.5.5.488
更新日期：1995-12-01 00:00:00
abstract：:The draft genome ( approximately 160 Mb) of the urochordate ascidian Ciona intestinalis has been sequenced by the whole-genome shotgun method and should provide important insights into the origin and evolution of chordates as well as vertebrates. However, because this genomic data has not yet been mapped onto chromoso...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.4156606
更新日期：2006-02-01 00:00:00
abstract：:Biophysical, chemical, and nanoscience approaches to the study of nuclear structure and activity have been developing recently and hold considerable promise. A selection of fundamental problems in genome organization and function are reviewed and discussed in the context of these new perspectives and approaches. Advan...
journal_title：Genome research
pub_type： 杂志文章,评审
doi：10.1101/gr.946403
更新日期：2003-06-01 00:00:00
abstract：:Variation in the composition of the human oral microbiome in health and disease has been observed. We have characterized inter- and intra-individual variation of microbial communities of 107 individuals in one of the largest cohorts to date (264 saliva samples), using culture-independent 16S rRNA pyrosequencing. We ex...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.140608.112
更新日期：2012-11-01 00:00:00
abstract：:A genome-wide search for multiple loci influencing salt-loaded systolic blood pressure (NaSBP) variation among 188 F2 progeny from a cross between the Brown-Norway and spontaneously hypertensive rat strains was pursued in an effort to gain insight into the polygenic basis of blood pressure regulation. The results sugg...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.5.2.164
更新日期：1995-09-01 00:00:00
abstract：:Paternal X chromosome inactivation occurs in rodent extraembryonic membranes and in all tissues of marsupials. Methylation of CpG islands occurs on the inactive X in eutherians and is considered to be a stabilizing mechanism. The only previous study of a marsupial X-linked CpG island was of the G6PD gene of the Virgin...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.6.2.114
更新日期：1996-02-01 00:00:00
abstract：:We describe a new method, Tag-seq, which employs ultra high-throughput sequencing of 21 base pair cDNA tags for sensitive and cost-effective gene expression profiling. We compared Tag-seq data to LongSAGE data and observed improved representation of several classes of rare transcripts, including transcription factors,...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.094482.109
更新日期：2009-10-01 00:00:00
abstract：:The tumor microenvironment of colorectal carcinoma is a complex community of genomically altered cancer cells, nonneoplastic cells, and a diverse collection of microorganisms. Each of these components may contribute to carcinogenesis; however, the role of the microbiota is the least well understood. We have characteri...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.126573.111
更新日期：2012-02-01 00:00:00
abstract：:Cellular senescence is a mechanism that virtually irreversibly suppresses the proliferative capacity of cells in response to various stress signals. This includes the expression of activated oncogenes, which causes Oncogene-Induced Senescence (OIS). A body of evidence points to the involvement in OIS of chromatin reor...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.225763.117
更新日期：2017-10-01 00:00:00
abstract：:To elucidate the role of exon shuffling in shaping the complexity of the human genome/proteome, we have systematically analyzed intron phase distributions in the coding sequence of human protein domains. We found that introns at the boundaries of domains show high excess of symmetrical phase combinations (i.e., 0-0, 1...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.520702
更新日期：2002-11-01 00:00:00
abstract：:The densities of transposable elements (TEs) in the human genome display substantial variation both within individual chromosomes and among chromosome types (autosomes and the two sex chromosomes). Finding an explanation for this variability has been challenging, especially in light of genome landscapes unique to the ...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.099044.109
更新日期：2010-05-01 00:00:00
abstract：:In mammals, genetic recombination during meiosis is limited to a set of 1- to 2-kb regions termed hotspots. Their locations are predominantly determined by the zinc finger protein PRDM9, which binds to DNA in hotspots and subsequently uses its SET domain to locally trimethylate histone H3 at lysine 4 (H3K4me3). This s...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.170167.113
更新日期：2014-05-01 00:00:00
abstract：:Cys2-His2 zinc finger proteins (ZFPs) are the largest group of transcription factors in higher metazoans. A complete characterization of these ZFPs and their associated target sequences is pivotal to fully annotate transcriptional regulatory networks in metazoan genomes. As a first step in this process, we have charac...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.151472.112
更新日期：2013-06-01 00:00:00
abstract：:Many thousands of proteins encoded by the genome of Plasmodium falciparum, the causal organism of the deadliest form of human malaria, are of unknown function. It is of utmost importance that these proteins be characterized if we are to develop combative strategies against malaria based on the biology of the parasite....
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.4573206
更新日期：2006-04-01 00:00:00
abstract：:Organisms with large genomes contain vast amounts of repetitive DNA sequences, much of which is composed of retrotransposons. Amplification of retrotransposons has been postulated to be a major mechanism increasing genome size and leading to "genomic obesity." To gain insights into the relation between retrotransposon...
journal_title：Genome research
pub_type： 评论,杂志文章
doi：10.1101/gr.10.7.908
更新日期：2000-07-01 00:00:00
abstract：:The identification and interpretation of the regulatory signals within the human genome remain among the greatest goals and most difficult challenges in genome analysis. The ability to predict the temporal and spatial control of transcription is likely to require a combination of methods to address the contribution of...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.180601
更新日期：2001-09-01 00:00:00
abstract：:Genes with sex-biased expression in Drosophila are thought to underlie sexually dimorphic phenotypes and have been shown to possess unique evolutionary properties. However, the forces and constraints governing the evolution of sex-biased genes in the somatic tissues of Drosophila are largely unknown. By using populati...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.259069.119
更新日期：2020-06-01 00:00:00
abstract：:The Y centromere sequence of house mouse, Mus musculus, remains unknown despite our otherwise significant knowledge of the genome sequence of this important mammalian model organism. Here, we report the complete molecular characterization of the C57BL/6J chromosome Y centromere, which comprises a highly diverged minor...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.092080.109
更新日期：2009-12-01 00:00:00
