Abstract:
:It appears that, for many genes, the two alleles possessed by an individual may produce different amounts of transcript. When such allelic differences in transcription are observed for some individuals but not others, a plausible explanation is genetic variation in the cis-acting elements that regulate the gene in question. Here we describe a novel analytical approach that uses such observations, combined with genotyping data from the HapMap project, to define the genomic location of cis-acting regulatory elements. When applied to the human 5q31 chromosomal region, where complex regulatory mechanisms are known to exist, we demonstrate the sensitivity of this approach by locating a highly significant cis-regulatory element operating on IL13 at long range from a position 250 kb upstream from the gene (P = 2 x 10(-6)). As this method is unaffected by other sources of variation, such as environmental and trans-acting genetic factors, it provides a tractable approach for dissecting the complexities of genetic variation in gene regulation.
journal_name
Genome Resjournal_title
Genome researchauthors
Forton JT,Udalova IA,Campino S,Rockett KA,Hull J,Kwiatkowski DPdoi
10.1101/gr.5663007subject
Has Abstractpub_date
2007-01-01 00:00:00pages
82-7issue
1eissn
1088-9051issn
1549-5469pii
gr.5663007journal_volume
17pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract::Primordial dwarfism (PD) is a disease in which severely impaired fetal growth persists throughout postnatal development and results in stunted adult size. The condition is highly heterogeneous clinically, but the use of certain phenotypic aspects such as head circumference and facial appearance has proven helpful in d...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.160572.113
更新日期:2014-02-01 00:00:00
abstract::The last 20 years have been a remarkable era for biology and medicine. One of the most significant achievements has been the sequencing of the first human genomes, which has laid the foundation for profound insights into human genetics, the intricacies of regulation and development, and the forces of evolution. Incred...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.191684.115
更新日期:2015-10-01 00:00:00
abstract::Transcription factors canonically bind nucleosome-free DNA, making the positioning of nucleosomes within regulatory regions crucial to the regulation of gene expression. Using the assay of transposase accessible chromatin (ATAC-seq), we observe a highly structured pattern of DNA fragment lengths and positions around n...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.192294.115
更新日期:2015-11-01 00:00:00
abstract::Single-cell sequencing (SCS) is a powerful new tool for investigating evolution and diversity in cancer and understanding the role of rare cells in tumor progression. These methods have begun to unravel key questions in cancer biology that have been difficult to address with bulk tumor measurements. Over the past five...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.191098.115
更新日期:2015-10-01 00:00:00
abstract::By applying graph representations to biochemical pathways, a new computational pipeline is proposed to find potential operons in microbial genomes. The algorithm relies on the fact that enzyme genes in operons tend to catalyze successive reactions in metabolic pathways. We applied this algorithm to 42 microbial genome...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.200602
更新日期:2002-08-01 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
pub_type: 杂志文章
doi:10.1101/gr.5016106
更新日期:2006-07-01 00:00:00
abstract::Using AP-PCR-based DNA profiling we examined some structural features of B chromosomes from yellow-necked mice Apodemus flavicollis. Mice harboring one, two, or three or lacking B chromosomes were examined. Chromosomal structure was scanned for variant bands by using a series of arbitrary primers and from these, infor...
journal_title:Genome research
pub_type: 杂志文章
doi:
更新日期:2000-01-01 00:00:00
abstract::Homeotic (Hox) genes are usually clustered and arranged in the same order as they are expressed along the anteroposterior body axis of metazoans. The mechanistic explanation for this colinearity has been elusive, and it may well be that a single and universal cause does not exist. The Hox-gene complex (HOM-C) has been...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.3468605
更新日期:2005-05-01 00:00:00
abstract::Although it is well understood that selection shapes the polymorphism pattern in Drosophila, signatures of classic selective sweeps are scarce. Here, we focus on Drosophila mauritiana, an island endemic, which is closely related to Drosophila melanogaster. Based on a new, annotated genome sequence, we characterized th...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.139873.112
更新日期:2013-01-01 00:00:00
abstract::Genomics data introduce a substantial computational burden as well as data privacy and ownership issues. Data sets generated by high-throughput sequencing platforms require immense amounts of computational resources to align to reference genomes and to call and annotate genomic variants. This problem is even more pron...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.207464.116
更新日期:2018-09-01 00:00:00
abstract::Knowledge of the genome-wide rate and spectrum of mutations is necessary to understand the origin of disease and the genetic variation driving all evolutionary processes. Here, we provide a genome-wide analysis of the rate and spectrum of mutations obtained in two Daphnia pulex genotypes via separate mutation-accumula...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.191338.115
更新日期:2016-01-01 00:00:00
abstract::The next-generation sequencing technology coupled with the growing number of genome sequences opens the opportunity to redesign genotyping strategies for more effective genetic mapping and genome analysis. We have developed a high-throughput method for genotyping recombinant populations utilizing whole-genome resequen...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.089516.108
更新日期:2009-06-01 00:00:00
abstract::The representation and discovery of transcription factor (TF) sequence binding specificities is critical for understanding gene regulatory networks and interpreting the impact of disease-associated noncoding genetic variants. We present a novel TF binding motif representation, the k-mer set memory (KSM), which consist...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.226852.117
更新日期:2018-06-01 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::Mutation rates of microsatellites vary greatly among loci. The causes of this heterogeneity remain largely enigmatic yet are crucial for understanding numerous human neurological diseases and genetic instability in cancer. In this first genome-wide study, the relative contributions of intrinsic features and regional g...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.7113408
更新日期:2008-01-01 00:00:00
abstract::The genome size of Pseudoalteromonas haloplanktis, a ubiquitous and easily cultured marine bacterium, was measured as a step toward estimating the genome complexity of marine bacterioplankton. To determine total genome size, we digested P. haloplanktis DNA with the restriction endonucleases Notl and Sfil, separated th...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6.12.1160
更新日期:1996-12-01 00:00:00
abstract::The human Y chromosome, because it is enriched in repetitive DNA, has been very intractable to genetic and molecular analyses. There is no previous evidence for developmental stage- and testis-specific transcription from the male-specific region of the Y (MSY). Here, we present evidence for the first time for a develo...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5155706
更新日期:2007-04-01 00:00:00
abstract::Regulatory sequences in higher genomes can map large distances from gene coding regions, and cannot yet be identified by simple inspection of primary DNA sequence information. Here we describe an efficient method of surveying large genomic regions for gene regulatory information, and subdividing complex sets of distan...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.1306003
更新日期:2003-09-01 00:00:00
abstract::Comparative genomics is a promising approach to the challenging problem of eukaryotic regulatory element identification, because functional noncoding sequences may be conserved across species from evolutionary constraints. We systematically analyzed known human and Saccharomyces cerevisiae regulatory elements and disc...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.1327604
更新日期:2004-03-01 00:00:00
abstract::Clusters of functionally related genes can be disrupted by a single copy number variant (CNV). We demonstrate that the simultaneous disruption of multiple functionally related genes is a frequent and significant characteristic of de novo CNVs in patients with developmental disorders (P = 1 × 10(-3)). Using three diffe...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.184325.114
更新日期:2015-06-01 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::Noncoding RNA (ncRNA) constitutes a significant portion of the mammalian transcriptome. Emerging evidence suggests that it regulates gene expression in cis or trans by modulating the chromatin structure. To uncover the functional role of ncRNA in chromatin organization, we deep sequenced chromatin-associated RNAs (CAR...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.103473.109
更新日期:2010-07-01 00:00:00
abstract::Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of post-transcriptional gene regulatory evolution are largely unknown. Here we used ri...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.164996.113
更新日期:2014-03-01 00:00:00
abstract::We have cloned the human gene encoding the transcription factor T. T protein is vital for the formation of posterior mesoderm and axial development in all vertebrates. Brachyury mutant mice, which lack T protein, die in utero with abnormal notochord, posterior somites, and allantois. We have identified human T genomic...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6.3.226
更新日期:1996-03-01 00:00:00
abstract::Few methods are available for mapping the local structure of DNA throughout a genome. The hydroxyl radical cleavage pattern is a measure of the local variation in solvent-accessible surface area of duplex DNA, and thus provides information on the local shape and structure of DNA. We report the construction of a relati...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6073107
更新日期:2007-06-01 00:00:00
abstract::One of the first useful products from the human genome will be a set of predicted genes. Besides its intrinsic scientific interest, the accuracy and completeness of this data set is of considerable importance for human health and medicine. Though progress has been made on computational gene identification in terms of ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.122800
更新日期:2000-10-01 00:00:00
abstract::Chronic neuropathic pain is affected by specifics of the precipitating neural pathology, psychosocial factors, and by genetic predisposition. Little is known about the identity of predisposing genes. Using an integrative approach, we discovered that CACNG2 significantly affects susceptibility to chronic pain following...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.104976.110
更新日期:2010-09-01 00:00:00
abstract::In addition to mediating sister chromatid cohesion during the cell cycle, the cohesin complex associates with CTCF and with active gene regulatory elements to form long-range interactions between its binding sites. Genome-wide chromosome conformation capture had shown that cohesin's main role in interphase genome orga...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.184986.114
更新日期:2015-04-01 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::The Collaborative Cross (CC) is a mouse recombinant inbred strain panel that is being developed as a resource for mammalian systems genetics. Here we describe an experiment that uses partially inbred CC lines to evaluate the genetic properties and utility of this emerging resource. Genome-wide analysis of the incipien...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.111310.110
更新日期:2011-08-01 00:00:00