Abstract:
:Long and short interspersed elements (LINEs and SINEs) are retroelements that make up almost half of the human genome. L1 and Alu represent the most prolific human LINE and SINE families, respectively. Only a few Alu elements are able to retropose, and the factors determining their retroposition capacity are poorly understood. The data presented in this paper indicate that the length of Alu "A-tails" is one of the principal factors in determining the retropositional capability of an Alu element. The A stretches of the Alu subfamilies analyzed, both old (Alu S and J) and young (Ya5), had a Poisson distribution of A-tail lengths with a mean size of 21 and 26, respectively. In contrast, the A-tails of very recent Alu insertions (disease causing) were all between 40 and 97 bp in length. The L1 elements analyzed displayed a similar tendency, in which the "disease"-associated elements have much longer A-tails (mean of 77) than do the elements even from the young Ta subfamily (mean of 41). Analysis of the draft sequence of the human genome showed that only about 1000 of the over one million Alu elements have tails of 40 or more adenosine residues in length. The presence of these long A stretches shows a strong bias toward the actively amplifying subfamilies, consistent with their playing a major role in the amplification process. Evaluation of the 19 Alu elements retrieved from the draft sequence of the human genome that are identical to the Alu Ya5a2 insert in the NF1 gene showed that only five have tails with 40 or more adenosine residues. Sequence analysis of the loci with the Alu elements containing the longest A-tails (7 of the 19) from the genomes of the NF1 patient and the father revealed that there are at least two loci with A-tails long enough to serve as source elements within our model. Analysis of the A-tail lengths of 12 Ya5a2 elements in diverse human population groups showed substantial variability in both the Alu A-tail length and sequence homogeneity. On the basis of these observations, a model is presented for the role of A-tail length in determining which Alu elements are active.
journal_name
Genome Resjournal_title
Genome researchauthors
Roy-Engel AM,Salem AH,Oyeniran OO,Deininger L,Hedges DJ,Kilroy GE,Batzer MA,Deininger PLdoi
10.1101/gr.384802subject
Has Abstractpub_date
2002-09-01 00:00:00pages
1333-44issue
9eissn
1088-9051issn
1549-5469journal_volume
12pub_type
杂志文章相关文献
GENOME RESEARCH文献大全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
pub_type: 杂志文章
doi:10.1101/gr.128652.111
更新日期:2012-03-01 00:00:00
abstract::It is widely accepted that newly arisen duplicate gene pairs experience an altered selective regime that is often manifested as an increase in the rate of protein sequence evolution. Many details about the nature of the rate acceleration remain unknown, however, including its typical magnitude and duration, and whethe...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6341207
更新日期:2008-01-01 00:00:00
abstract::Double minutes (dmin) and homogeneously staining regions (hsr) are the cytogenetic hallmarks of genomic amplification in cancer. Different mechanisms have been proposed to explain their genesis. Recently, our group showed that the MYC-containing dmin in leukemia cases arise by excision and amplification (episome model...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.106252.110
更新日期:2010-09-01 00:00:00
abstract::Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward thi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.212696.116
更新日期:2017-06-01 00:00:00
abstract::We present a database of copy number variations (CNVs) detected in 2026 disease-free individuals, using high-density, SNP-based oligonucleotide microarrays. This large cohort, comprised mainly of Caucasians (65.2%) and African-Americans (34.2%), was analyzed for CNVs in a single study using a uniform array platform an...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.083501.108
更新日期:2009-09-01 00:00:00
abstract::Comparative gene mapping in mammals typically involves identification of segments of conserved synteny in diverse genomes. The development of maps that permit comparison of gene order within conserved synteny has not advanced beyond the mouse map that takes advantage of linkage analysis in interspecific backcrosses. R...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.8.7.731
更新日期:1998-07-01 00:00:00
abstract::Mycoplasma mycoides subsp. mycoidesSC (MmymySC)is the etiological agent of contagious bovine pleuropneumonia (CBPP), a highly contagious respiratory disease in cattle. The genome of Mmymy SC type strain PG1(T) has been sequenced to map all the genes and to facilitate further studies regarding the cell function of the ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.1673304
更新日期:2004-02-01 00:00:00
abstract::Large numbers of expressed sequence tags (ESTs) continue to fill public and private databases with partial cDNA sequences. However, using this huge amount of ESTs to facilitate gene finding in genomic sequence imposes a challenge, especially to wet-lab scientists who often have limited computing resources. In an effor...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.8.3.268
更新日期:1998-03-01 00:00:00
abstract::Bidirectional promoters have received considerable attention because of their ability to regulate two downstream genes (divergent genes). They are also highly abundant, directing the transcription of approximately 11% of genes in the human genome. We categorized the presence of DNA sequence motifs, binding of transcri...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5623407
更新日期:2007-06-01 00:00:00
abstract::The need to translate genes to function has positioned the rat as an invaluable animal model for genomic research. The significant increase in genomic resources in recent years has had an immediate functional application in the rat. Many of the resources for translational research are already in place and are ready to...
journal_title:Genome research
pub_type: 杂志文章,评审
doi:10.1101/gr.3744005
更新日期:2005-12-01 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
pub_type: 杂志文章
doi:10.1101/gr.106732.110
更新日期:2010-10-01 00:00:00
abstract::High-throughput sequencing is a revolutionary technology for the analysis of metagenomic samples. However, querying large volumes of reads against comprehensive DNA/RNA databases in a sensitive manner can be compute-intensive. Here, we present taxMaps, a highly efficient, sensitive, and fully scalable taxonomic classi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.225276.117
更新日期:2018-05-01 00:00:00
abstract::To promote the clinical and epidemiological studies that improve our understanding of human genetic susceptibility to environmental exposure, the Environmental Genome Project (EGP) has scanned 213 environmental response genes involved in DNA repair, cell cycle regulation, apoptosis, and metabolism for single nucleotid...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.2730004
更新日期:2004-10-01 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::The remarkable olfactory power of insect species is thought to be generated by a combinatorial action of two large protein families, G protein-coupled olfactory receptors (ORs) and odorant binding proteins (OBPs). In olfactory sensilla, OBPs deliver hydrophobic airborne molecules to ORs, but their expression in nonolf...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5075706
更新日期:2006-11-01 00:00:00
abstract::Previous approaches to mutation detection in mRNA from the neurofibromatosis 1 (NF1) locus have required the PCR amplification of five or more overlapping cDNA segments to screen the entire 8.5-kb open reading frame (ORF). Systematically, these assays do not detect deletions that span the region of overlap (usually 1-...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6.1.58
更新日期:1996-01-01 00:00:00
abstract::Genomic imprinting is a developmentally important mechanism that involves both differential DNA methylation and allelic histone modifications. Through detailed comparative characterization, a large imprinted domain mapping to chromosome 7q21 in humans and proximal chromosome 6 in mice was redefined. This domain is org...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.077115.108
更新日期:2008-08-01 00:00:00
abstract::Integrating the genotype with epigenetic marks holds the promise of better understanding the biology that underlies the complex interactions of inherited and environmental components that define the developmental origins of a range of disorders. The quality of the in utero environment significantly influences health o...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.171439.113
更新日期:2014-07-01 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::Pre-mRNA processing often occurs in coordination with transcription thereby coupling these two key regulatory events. As such, many proteins involved in mRNA processing associate with the transcriptional machinery and are in proximity to DNA. This proximity allows for the mapping of the genomic associations of RNA bin...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5211806
更新日期:2006-07-01 00:00:00
abstract::Intra-tumor heterogeneity poses substantial challenges for cancer treatment. A tumor's composition can be deduced by reconstructing its mutational history. Central to current approaches is the infinite sites assumption that every genomic position can only mutate once over the lifetime of a tumor. The validity of this ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.220707.117
更新日期:2017-11-01 00:00:00
abstract::Integration of DNA viruses into the human genome plays an important role in various types of tumors, including hepatitis B virus (HBV)-related hepatocellular carcinoma. However, the molecular details and clinical impact of HBV integration on either human or HBV epigenomes are unknown. Here, we show that methylation of...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.175240.114
更新日期:2015-03-01 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::Identifying transcriptional regulatory elements represents a significant challenge in annotating the genomes of higher vertebrates. We have developed a computational tool, rVista, for high-throughput discovery of cis-regulatory elements that combines clustering of predicted transcription factor binding sites (TFBSs) a...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.225502
更新日期:2002-05-01 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
pub_type: 杂志文章
doi:10.1101/gr.130682.111
更新日期:2012-04-01 00:00:00
abstract::Identity-by-descent (IBD) inference is the problem of establishing a genetic connection between two individuals through a genomic segment that is inherited by both individuals from a recent common ancestor. IBD inference is an important preceding step in a variety of population genomic studies, ranging from demographi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.173641.114
更新日期:2015-02-01 00:00:00
abstract::Alternative splicing is a major mechanism for gene product regulation in many multicellular organisms. By using different exon combinations, some coding regions can encode amino acids in multiple reading frames in different transcripts. Here we performed a systematic search through a set of high-quality human transcri...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.4246506
更新日期:2006-02-01 00:00:00
abstract::The human pseudoautosomal region 1 (PAR1) is essential for meiotic pairing and recombination, and its deletion causes male sterility. Comparative studies of human and mouse pseudoautosomal genes are valuable in charting the evolution of this interesting region, but have been limited by the paucity of genes conserved b...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.197001
更新日期:2001-12-01 00:00:00
abstract::Long noncoding RNAs (lncRNAs) play a conserved role in regulating gene expression, chromatin dynamics, and cell differentiation. They serve as a platform for RNA interference (RNAi)-mediated heterochromatin formation or DNA methylation in many eukaryotic organisms. We found in Schizosaccharomyces pombe that heterochro...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.216986.116
更新日期:2017-07-01 00:00:00
abstract::Initially thought to play a restricted role in calcium homeostasis, the pleiotropic actions of vitamin D in biology and their clinical significance are only now becoming apparent. However, the mode of action of vitamin D, through its cognate nuclear vitamin D receptor (VDR), and its contribution to diverse disorders, ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.107920.110
更新日期:2010-10-01 00:00:00