Abstract：
:The nature and pace of genome mutation is largely unknown. Because standard methods sequence DNA from populations of cells, the genetic composition of individual cells is lost, de novo mutations in cells are concealed within the bulk signal and per cell cycle mutation rates and mechanisms remain elusive. Although single-cell genome analyses could resolve these problems, such analyses are error-prone because of whole-genome amplification (WGA) artefacts and are limited in the types of DNA mutation that can be discerned. We developed methods for paired-end sequence analysis of single-cell WGA products that enable (i) detecting multiple classes of DNA mutation, (ii) distinguishing DNA copy number changes from allelic WGA-amplification artefacts by the discovery of matching aberrantly mapping read pairs among the surfeit of paired-end WGA and mapping artefacts and (iii) delineating the break points and architecture of structural variants. By applying the methods, we capture DNA copy number changes acquired over one cell cycle in breast cancer cells and in blastomeres derived from a human zygote after in vitro fertilization. Furthermore, we were able to discover and fine-map a heritable inter-chromosomal rearrangement t(1;16)(p36;p12) by sequencing a single blastomere. The methods will expedite applications in basic genome research and provide a stepping stone to novel approaches for clinical genetic diagnosis.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Voet T,Kumar P,Van Loo P,Cooke SL,Marshall J,Lin ML,Zamani Esteki M,Van der Aa N,Mateiu L,McBride DJ,Bignell GR,McLaren S,Teague J,Butler A,Raine K,Stebbings LA,Quail MA,D'Hooghe T,Moreau Y,Futreal PA,Stratton MRdoi
10.1093/nar/gkt345subject
Has Abstractpub_date
2013-07-01 00:00:00pages
6119-38issue
12eissn
0305-1048issn
1362-4962pii
gkt345journal_volume
41pub_type
杂志文章abstract：:The human transcription factor EF-1A binds to the purine-rich E1A core enhancer sequence in the adenovirus E1A and E4 and polyomavirus enhancer regions. The consensus binding site for EF-1A resembles that of members of the ets domain protein family. EF-1A activation of transcription requires a dimeric binding site. An...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.24.6555
更新日期：1992-12-25 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.17.6205
更新日期：1985-09-11 00:00:00
abstract：:Mitochondrial DNA (mtDNA) is entirely dependent on nuclear genes for its transcription and replication. One of these genes is TOP1MT, which encodes the mitochondrial DNA topoisomerase IB, involved in mtDNA relaxation. To elucidate TOP1MT regulation, we performed genome-wide profiling across the 60-cell line panel (the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr208
更新日期：2011-08-01 00:00:00
abstract：:Phylogenetic analysis of Y-family DNA polymerases suggests that it can be subdivided into several discrete branches consisting of UmuC/DinB/Rev1/Rad30/Rad30A and Rad30B. The most diverse is the DinB family that is found in all three kingdoms of life. Searches of the complete genome of the crenarchaeon Sulfolobus solfa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.22.4607
更新日期：2001-11-15 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.1.102
更新日期：1998-01-01 00:00:00
abstract：:Recent advances in DNA-sequencing technology have made it possible to obtain large datasets of small RNA sequences. Here we demonstrate that not all non-perfectly matched small RNA sequences are simple technological sequencing errors, but many hold valuable biological information. Analysis of three small RNA datasets ...
journal_title：Nucleic acids research
pub_type： 杂志文章,meta分析
doi：10.1093/nar/gkp093
更新日期：2009-05-01 00:00:00
abstract：:1731, a Drosophila retrotransposon was first described as having a transcription activity which was negatively regulated by 20-hydroxyecdysone (20-OH), the steroid molting hormone of insects. Using constructions expressing the bacterial chloramphenicol-acetyltransferase (CAT) gene under the control of the entire or de...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.20.5689
更新日期：1991-10-25 00:00:00
abstract：:A simple and efficient gene replacement method, based on the recombination and repair activities of the cell, was developed. The method permits the targeted construction of markerless deletions, insertions and point mutations in the Escherichia coli chromosome. A suicide plasmid, carrying the mutant allele and the rec...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.22.4409
更新日期：1999-11-15 00:00:00
abstract：:Ovarian poly (A) + RNA from Xenopus laevis and Xenopus borealis was used to construct two cDNA libraries which were screened for histone sequences. cDNA clones to H4 mRNA were obtained from both species and an H3 cDNA clone from Xenopus laevis. The complete DNA sequences of these clones have been determined and are pr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.12.3769
更新日期：1982-06-25 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.21.4395
更新日期：1994-10-25 00:00:00
abstract：:The RNA sequences boxA, boxB and boxC constitute the nut regions of phage lambda. They nucleate the formation of a termination-resistant RNA polymerase complex on the lambda chromosome. The complex includes E. coli proteins NusA, NusB, NusG and NusE, and the lambda N protein. A complex that includes the Nus proteins a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp452
更新日期：2009-08-01 00:00:00
abstract：:Eukaryotic topoisomerase II (topo II) is the essential decatenase of newly replicated chromosomes and the main relaxase of nucleosomal DNA. Apart from these general tasks, topo II participates in more specialized functions. In mammals, topo IIα interacts with specific RNA polymerases and chromatin-remodeling complexes...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt707
更新日期：2013-11-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.4.1835
更新日期：1987-02-25 00:00:00
abstract：:The thermal stabilities of the duplexes formed between 4'-thio-modified oligodeoxynucleotides and their DNA and RNA complementary strands were determined and compared with those of the corresponding unmodified oligodeoxynucleotides. A 16mer oligodeoxynucleotide containing 10 contiguous 4'-thiothymidylate modifications...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.21.4117
更新日期：1996-11-01 00:00:00
abstract：:Early in its differentiative pathway, a given B lymphocyte expresses immunoglobulin of the mu heavy chain class (IgM). Subsequent differentiative processes may involve rearrangement within the immunoglobulin heavy chain chromosomal locus to enable cells of the same lineage to synthesize immunoglobulins of other heavy ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.1.225
更新日期：1985-01-11 00:00:00
abstract：:DNA mismatches that occur between vector homology arms and chromosomal target sequences reduce gene targeting frequencies in several species; however, this has not been reported in human cells. Here we demonstrate that even a single mismatched base pair can significantly decrease human gene targeting frequencies. In a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1303
更新日期：2014-03-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.16.3821
更新日期：1993-08-11 00:00:00
abstract：:A sensitive gel retention assay has been utilized to detect proteins from uninfected Hela nuclei which interact with the adenovirus type 2 enhancer. This assay has been employed to monitor fractionation of nuclear extracts. Three enhancer binding factors were resolved by chromatography on DEAE-Sepharose and one of the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.6.2719
更新日期：1987-03-25 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.17.4239
更新日期：1981-09-11 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1234
更新日期：2021-01-25 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnh068
更新日期：2004-05-20 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.17.3603
更新日期：2001-09-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2000-11-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz1203
更新日期：2020-03-18 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.22.6313
更新日期：1991-11-25 00:00:00
abstract：:Small nucleolar RNAs (snoRNAs) are among the first discovered and most extensively studied group of small non-coding RNA. However, most studies focused on a small subset of snoRNAs that guide the modification of ribosomal RNA. In this study, we annotated the expression pattern of all box C/D snoRNAs in normal and canc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku664
更新日期：2014-09-01 00:00:00
abstract：:Human adenovirus mutants that carry a large deletion in early region 4 (E4) are severely defective in the synthesis of viral late proteins. Plasmids that carry intact E4 sequences can complement the late protein synthetic defect of such mutants when introduced into infected cells by transfection, presumably due to the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.8.3037
更新日期：1989-04-25 00:00:00
abstract：:Homologous recombination provides a means for the in vivo construction of recombinant DNA molecules that may be problematic to assemble in vitro. We have investigated the efficiency of recombination within the Caenorhabditis elegans germ line as a function of the length of homology between recombining molecules. Our f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm857
更新日期：2007-01-01 00:00:00
abstract：:A fraction of the ribosomal 28S genes in some insects are interrupted at specific sites by insertion elements R1 and R2 (also called Type I and II). These elements contain long open-reading frames with homology to reverse transcriptase. We have identified in the silkmoth, Bombyx mori, copies of these elements which ha...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.22.10561
更新日期：1988-11-25 00:00:00
abstract：:Smarcal1 is a SWI/SNF-family protein with an ATPase domain involved in DNA-annealing activities and a binding site for the RPA single-strand-DNA-binding protein. Although the role played by Smarcal1 in the maintenance of replication forks has been established, it remains unknown whether Smarcal1 contributes to genomic...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv621
更新日期：2015-07-27 00:00:00
