Abstract：
:Contamination by present-day human and microbial DNA is one of the major hindrances for large-scale genomic studies using ancient biological material. We describe a new molecular method, U selection, which exploits one of the most distinctive features of ancient DNA--the presence of deoxyuracils--for selective enrichment of endogenous DNA against a complex background of contamination during DNA library preparation. By applying the method to Neanderthal DNA extracts that are heavily contaminated with present-day human DNA, we show that the fraction of useful sequence information increases ∼ 10-fold and that the resulting sequences are more efficiently depleted of human contamination than when using purely computational approaches. Furthermore, we show that U selection can lead to a four- to fivefold increase in the proportion of endogenous DNA sequences relative to those of microbial contaminants in some samples. U selection may thus help to lower the costs for ancient genome sequencing of nonhuman samples also.
journal_name
Genome Resjournal_title
Genome researchauthors
Gansauge MT,Meyer Mdoi
10.1101/gr.174201.114subject
Has Abstractpub_date
2014-09-01 00:00:00pages
1543-9issue
9eissn
1088-9051issn
1549-5469pii
gr.174201.114journal_volume
24pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract：:To gauge the complexity of gene regulation in yeast, it is essential to know how much promoter sequence is functional. Conservation across species can be a sensitive means of detecting functional sequences, provided that the significance of conservation can be accurately calibrated with the local neutral mutation rate...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.3243305
更新日期：2005-02-01 00:00:00
abstract：:During meiosis, chromatin undergoes extensive changes to facilitate recombination, homolog pairing, and chromosome segregation. To investigate the relationship between chromatin organization and meiotic processes, we used formaldehyde-assisted isolation of regulatory elements (FAIRE) to map open chromatin during the t...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.096297.109
更新日期：2009-12-01 00:00:00
abstract：:The primate-specific multisequence family chAB4 is represented with approximately 40 copies within the haploid human genome. Former analyis revealed that unusually long repetition units ( > 35 kb) are distributed to at least eight different chromosomal loci. Remarkably varying copy-numbers within the genomes of closel...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.6.4.267
更新日期：1996-04-01 00:00:00
abstract：:Single-nucleotide polymorphisms (SNPs) are the most frequently found DNA sequence variations in the human genome. It has been argued that a dense set of SNP markers can be used to identify genetic factors associated with complex disease traits. Because all high-throughput genotyping methods require precise sequence kn...
journal_title：Genome research
pub_type： 杂志文章
doi：
更新日期：1999-05-01 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：:C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2-ZF arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. In addition, little is known about whether ...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.209643.116
更新日期：2016-12-01 00:00:00
abstract：:Many CpG islands have tissue-dependent and differentially methylated regions (T-DMRs) in normal cells and tissues. To elucidate how DNA methyltransferases (Dnmts) participate in methylation of the genomic components, we investigated the genome-wide DNA methylation pattern of the T-DMRs with Dnmt1-, Dnmt3a-, and/or Dnm...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.2431504
更新日期：2004-09-01 00:00:00
abstract：:Notwithstanding their biological importance, Y chromosomes remain poorly known in most species. A major obstacle to their study is the identification of Y chromosome sequences; due to its high content of repetitive DNA, in most genome projects, the Y chromosome sequence is fragmented into a large number of small, unma...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.156034.113
更新日期：2013-11-01 00:00:00
abstract：:Translocations are known to affect the expression of genes at the breakpoints and, in the case of unbalanced translocations, alter the gene copy number. However, a comprehensive understanding of the functional impact of this class of variation is lacking. Here, we have studied the effect of balanced chromosomal rearra...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.103622.109
更新日期：2010-05-01 00:00:00
abstract：:A rigorous analysis of the Merck-sponsored EST data with respect to known gene sequences increases the utility of the data set and helps refine methods for building a gene index. A highly curated human transcript data base was used as a reference data set of known genes. A detailed analysis of EST sequences derived fr...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.6.9.829
更新日期：1996-09-01 00:00:00
abstract：:The regulation of gene expression is mediated at the transcriptional level by enhancer regions that are bound by sequence-specific transcription factors (TFs). Recent studies have shown that the in vivo binding sites of single TFs differ between developmental or cellular contexts. How this context-specific binding is ...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.132811.111
更新日期：2012-10-01 00:00:00
abstract：:Elucidating the pathophysiology and molecular attributes of common disorders as well as developing targeted and effective treatments hinges on the study of the relevant cell type and tissues. Pancreatic beta cells within the islets of Langerhans are centrally involved in the pathogenesis of both type 1 and type 2 diab...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.150706.112
更新日期：2013-09-01 00:00:00
abstract：:A detailed comparative map of Brassica oleracea and Arabidopsis thaliana has been established based largely on mapping of Arabidopsis ESTs in two Arabidopsis and four Brassica populations. Based on conservative criteria for inferring synteny, "one to one correspondence" between Brassica and Arabidopsis chromosomes acc...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.10.6.776
更新日期：2000-06-01 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：:Recent advances toward the characterization of Alzheimer's disease (AD) have permitted the identification of a dozen of genetic risk factors, although many more remain undiscovered. In parallel, works in the field of network biology have shown a strong link between protein connectivity and disease. In this manuscript,...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.114280.110
更新日期：2011-03-01 00:00:00
abstract：:Transcription factors (TFs) are key mediators that propagate extracellular and intracellular signals through to changes in gene expression profiles. However, the rules by which promoters decode the amount of active TF into target gene expression are not well understood. To determine the mapping between promoter DNA se...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.212316.116
更新日期：2017-01-01 00:00:00
abstract：:The rate of transcription elongation plays an important role in the timing of expression of full-length transcripts as well as in the regulation of alternative splicing. In this study, we coupled Bru-seq technology with 5,6-dichlorobenzimidazole 1-β-D-ribofuranoside (DRB) to estimate the elongation rates of over 2000 ...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.171405.113
更新日期：2014-06-01 00:00:00
abstract：:Maize (Zea mays L. ssp. mays), one of the most important agricultural crops in the world, originated by hybridization of two closely related progenitors. To investigate the fate of its genes after tetraploidization, we analyzed the sequence of five duplicated regions from different chromosomal locations. We also compa...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.2701104
更新日期：2004-10-01 00:00:00
abstract：:We have identified three new families of insulin homologs in Caenorhabditis elegans. In two of these families, concerted mutations suggest that an additional disulfide bond links B and A domains, and that the A-domain internal disulfide bond is substituted by a hydrophobic interaction. Homology modeling remarkably con...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.8.4.348
更新日期：1998-04-01 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：:Aberrant DNA methylation (DNAm) was first linked to cancer over 25 yr ago. Since then, many studies have associated hypermethylation of tumor suppressor genes and hypomethylation of oncogenes to the tumorigenic process. However, most of these studies have been limited to the analysis of promoters and CpG islands (CGIs...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.109678.110
更新日期：2011-04-01 00:00:00
abstract：:We assessed the content, structure, and distribution of segmental duplications (> or =90% sequence identity, > or =5 kb length) within the published version of the Rattus norvegicus genome assembly (v.3.1). The overall fraction of duplicated sequence within the rat assembly (2.92%) is greater than that of the mouse (1...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.1907504
更新日期：2004-04-01 00:00:00
abstract：:Molecular evolution studies are usually based on the analysis of individual genes and thus reflect only small-range variations in genomic sequences. A complementary approach is to study the evolutionary history of rearrangements in entire genomes based on the analysis of gene orders. The progress in whole genome seque...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.3002305
更新日期：2005-01-01 00:00:00
abstract：:Repetitive DNA is a significant component of eukaryotic genomes. We have developed a strategy to efficiently and accurately sequence repetitive DNA in the nematode Caenorhabditis elegans using integrated artificial transposons and automated fluorescent sequencing. Mapping and assembly tools represent important compone...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.7.5.551
更新日期：1997-05-01 00:00:00
abstract：:We have developed a computer program that aligns spliced sequences to genomic sequences, using local alignment algorithms and heuristics to put together a global spliced alignment. Spidey can produce reliable alignments quickly, even when confronted with noise from alternative splicing, polymorphisms, sequencing error...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.195301
更新日期：2001-11-01 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：:LSH, a member of the SNF2 family of chromatin remodeling ATPases encoded by the Hells gene, is essential for normal levels of DNA methylation in the mammalian genome. While the role of LSH in the methylation of repetitive DNA sequences is well characterized, its contribution to the regulation of DNA methylation and th...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.108498.110
更新日期：2011-01-01 00:00:00
abstract：:Interindividual variability in response to chemicals and drugs is a common regulatory concern. It is assumed that xenobiotic-induced adverse reactions have a strong genetic basis, but many mechanism-based investigations have not been successful in identifying susceptible individuals. While recent advances in pharmacog...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.090241.108
更新日期：2009-09-01 00:00:00
abstract：:An open question in bacterial genomics is the role that adaptive evolution of the core genome plays in diversification and adaptation of bacterial species, and how this might differ between groups of bacteria occupying different environmental circumstances. The genus Campylobacter encompasses several important human a...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.089250.108
更新日期：2009-07-01 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
