메뉴 건너뛰기




Volumn 23, Issue 3, 2015, Pages 421-426

Completing the human genome: the progress and challenge of satellite DNA assembly

Author keywords

acrocentric repeats; assembly; centromere; pericentromeric heterochromatin; Satellite DNA

Indexed keywords

SATELLITE DNA; HETEROCHROMATIN;

EID: 84947492787     PISSN: 09673849     EISSN: 15736849     Source Type: Journal    
DOI: 10.1007/s10577-015-9488-2     Document Type: Article
Times cited : (65)

References (37)
  • 1
    • 34848890323 scopus 로고    scopus 로고
    • Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data
    • COI: 1:CAS:528:DC%2BD2sXhtFKmtrjO, PID: 17907796
    • Alkan C, Ventura M, Archidiacono N et al (2007) Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data. PLoS Comput Biol 3:1807–1818
    • (2007) PLoS Comput Biol , vol.3 , pp. 1807-1818
    • Alkan, C.1    Ventura, M.2    Archidiacono, N.3
  • 2
    • 84901684467 scopus 로고    scopus 로고
    • Genomic characterization of large heterochromatic gaps in the human genome assembly
    • PID: 24831296
    • Altemose N, Miga KH, Maggioni M et al (2014) Genomic characterization of large heterochromatic gaps in the human genome assembly. PLoS Comput Biol 10:e1003628
    • (2014) PLoS Comput Biol , vol.10 , pp. e1003628
    • Altemose, N.1    Miga, K.H.2    Maggioni, M.3
  • 3
    • 84922537404 scopus 로고    scopus 로고
    • Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing
    • COI: 1:CAS:528:DC%2BC2cXhslOisrnN, PID: 25326703
    • Amini S, Pushkarev D, Christiansen L et al (2014) Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nat Genet 46:1343–1349
    • (2014) Nat Genet , vol.46 , pp. 1343-1349
    • Amini, S.1    Pushkarev, D.2    Christiansen, L.3
  • 4
    • 55549089660 scopus 로고    scopus 로고
    • Accurate whole human genome sequencing using reversible terminator chemistry
    • COI: 1:CAS:528:DC%2BD1cXhtlCjtr3E, PID: 18987734
    • Bentley DR, Balasubramanian S, Swerdlow HP et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59
    • (2008) Nature , vol.456 , pp. 53-59
    • Bentley, D.R.1    Balasubramanian, S.2    Swerdlow, H.P.3
  • 6
    • 84890034912 scopus 로고    scopus 로고
    • Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
    • COI: 1:CAS:528:DC%2BC3sXhslWjtLvM, PID: 24185095
    • Burton JN, Adey A, Patwardhan RP et al (2013) Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat Biotechnol 31:1119–1125
    • (2013) Nat Biotechnol , vol.31 , pp. 1119-1125
    • Burton, J.N.1    Adey, A.2    Patwardhan, R.P.3
  • 7
    • 84925497196 scopus 로고    scopus 로고
    • Resolving the complexity of the human genome using single-molecule sequencing
    • COI: 1:CAS:528:DC%2BC2cXhvFGlt7bJ, PID: 25383537
    • Chaisson MJ, Huddleston J, Dennis MY et al (2015) Resolving the complexity of the human genome using single-molecule sequencing. Nature 517:608–611
    • (2015) Nature , vol.517 , pp. 608-611
    • Chaisson, M.J.1    Huddleston, J.2    Dennis, M.Y.3
  • 8
    • 1942499458 scopus 로고    scopus 로고
    • An assessment of the sequence gaps: unfinished business in a finished human genome
    • COI: 1:CAS:528:DC%2BD2cXjsl2iu7w%3D, PID: 15143317
    • Eichler EE, Clark RA, She X (2004) An assessment of the sequence gaps: unfinished business in a finished human genome. Nat Rev Genet 5:345–354
    • (2004) Nat Rev Genet , vol.5 , pp. 345-354
    • Eichler, E.E.1    Clark, R.A.2    She, X.3
  • 9
    • 84869814079 scopus 로고    scopus 로고
    • Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology
    • COI: 1:CAS:528:DC%2BC38XhvVagsr3E, PID: 23185243
    • English AC, Richards S, Han Y et al (2012) Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One 7:e47768
    • (2012) PLoS One , vol.7 , pp. e47768
    • English, A.C.1    Richards, S.2    Han, Y.3
  • 10
    • 84864874774 scopus 로고    scopus 로고
    • Human centromere genomics: now it’s personal
    • COI: 1:CAS:528:DC%2BC38XhtFWntr3O
    • Hayden KE (2012) Human centromere genomics: now it’s personal. Chromosom Res 20:621–633
    • (2012) Chromosom Res , vol.20 , pp. 621-633
    • Hayden, K.E.1
  • 11
    • 84873805996 scopus 로고    scopus 로고
    • Sequences associated with centromere competency in the human genome
    • COI: 1:CAS:528:DC%2BC3sXltVOiur4%3D, PID: 23230266
    • Hayden KE, Strome ED, Merrett SL et al (2013) Sequences associated with centromere competency in the human genome. Mol Cell Biol 33:763–772
    • (2013) Mol Cell Biol , vol.33 , pp. 763-772
    • Hayden, K.E.1    Strome, E.D.2    Merrett, S.L.3
  • 12
    • 84897965254 scopus 로고    scopus 로고
    • Reconstructing complex regions of genomes using long-read sequencing technology
    • COI: 1:CAS:528:DC%2BC2cXmt1CrsLo%3D, PID: 24418700
    • Huddleston J, Ranade S, Malig M et al (2014) Reconstructing complex regions of genomes using long-read sequencing technology. Genome Res 24:688–696
    • (2014) Genome Res , vol.24 , pp. 688-696
    • Huddleston, J.1    Ranade, S.2    Malig, M.3
  • 13
    • 84926472171 scopus 로고    scopus 로고
    • Improved data analysis for the MinION nanopore sequencer
    • COI: 1:CAS:528:DC%2BC2MXivVSitrY%3D, PID: 25686389
    • Jain M, Fiddes IT, Miga KH et al (2015) Improved data analysis for the MinION nanopore sequencer. Nat Methods 12:351–356
    • (2015) Nat Methods , vol.12 , pp. 351-356
    • Jain, M.1    Fiddes, I.T.2    Miga, K.H.3
  • 14
    • 84863651532 scopus 로고    scopus 로고
    • Hybrid error correction and de novo assembly of single-molecule sequencing reads
    • COI: 1:CAS:528:DC%2BC38XpsVWjsL4%3D, PID: 22750884
    • Koren S, Schatz MC, Walenz BP et al (2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol 30:693–700
    • (2012) Nat Biotechnol , vol.30 , pp. 693-700
    • Koren, S.1    Schatz, M.C.2    Walenz, B.P.3
  • 15
    • 0030884929 scopus 로고    scopus 로고
    • Human centromeric DNAs
    • COI: 1:CAS:528:DyaK2sXkvF2nu7o%3D, PID: 9272147
    • Lee C, Wevrick R, Fisher RB et al (1997) Human centromeric DNAs. Hum Genet 100:291–304
    • (1997) Hum Genet , vol.100 , pp. 291-304
    • Lee, C.1    Wevrick, R.2    Fisher, R.B.3
  • 16
    • 35648976118 scopus 로고    scopus 로고
    • The diploid genome sequence of an individual human
    • PID: 17803354
    • Levy S, Sutton G, Ng PC et al (2007) The diploid genome sequence of an individual human. PLoS Biol 5:e254
    • (2007) PLoS Biol , vol.5 , pp. e254
    • Levy, S.1    Sutton, G.2    Ng, P.C.3
  • 17
    • 33750452293 scopus 로고    scopus 로고
    • Precise centromere mapping using a combination of repeat junction markers and chromatin immunoprecipitation-polymerase chain reaction
    • COI: 1:CAS:528:DC%2BD28Xht12mur3N, PID: 16951073
    • Luce AC, Sharma A, Mollere OS et al (2006) Precise centromere mapping using a combination of repeat junction markers and chromatin immunoprecipitation-polymerase chain reaction. Genetics 174:1057–1061
    • (2006) Genetics , vol.174 , pp. 1057-1061
    • Luce, A.C.1    Sharma, A.2    Mollere, O.S.3
  • 18
    • 0018274661 scopus 로고
    • Chromosomal localization of complex and simple repeated human DNAs
    • COI: 1:CAS:528:DyaE1cXhvVKqtbY%3D, PID: 639625
    • Manuelidis L (1978) Chromosomal localization of complex and simple repeated human DNAs. Chromosoma 66:23–32
    • (1978) Chromosoma , vol.66 , pp. 23-32
    • Manuelidis, L.1
  • 19
    • 84898762051 scopus 로고    scopus 로고
    • Centromere reference models for human chromosomes X and Y satellite arrays
    • COI: 1:CAS:528:DC%2BC2cXmt1CrsLs%3D, PID: 24501022
    • Miga KH, Newton Y, Jain M et al (2014) Centromere reference models for human chromosomes X and Y satellite arrays. Genome Res 24:697–707
    • (2014) Genome Res , vol.24 , pp. 697-707
    • Miga, K.H.1    Newton, Y.2    Jain, M.3
  • 20
    • 84950124321 scopus 로고    scopus 로고
    • Miga KH, Eisenhart C, Kent WJ (2015) Utilizing mapping targets of sequences underrepresented in the reference assembly to reduce false positive alignments. Nucleic Acids Res in press
    • Miga KH, Eisenhart C, Kent WJ (2015) Utilizing mapping targets of sequences underrepresented in the reference assembly to reduce false positive alignments. Nucleic Acids Res in press
  • 21
    • 84926417573 scopus 로고    scopus 로고
    • Building a pan-genome reference for a population
    • COI: 1:CAS:528:DC%2BC2MXnsVantbk%3D, PID: 25565268
    • Nguyen N, Hickey G, Zerbino DR et al (2015) Building a pan-genome reference for a population. J Comput Biol 22:387–401
    • (2015) J Comput Biol , vol.22 , pp. 387-401
    • Nguyen, N.1    Hickey, G.2    Zerbino, D.R.3
  • 25
    • 33645802774 scopus 로고    scopus 로고
    • Human centromeric alphoid domains are periodically homogenized so that they vary substantially between homologues. Mechanism and implications for centromere functioning
    • COI: 1:CAS:528:DC%2BD28XjslOjs7s%3D, PID: 16598075
    • Roizes G (2006) Human centromeric alphoid domains are periodically homogenized so that they vary substantially between homologues. Mechanism and implications for centromere functioning. Nucleic Acids Res 34:1912–1924
    • (2006) Nucleic Acids Res , vol.34 , pp. 1912-1924
    • Roizes, G.1
  • 26
    • 4744339350 scopus 로고    scopus 로고
    • Analysis of the centromeric regions of the human genome assembly
    • COI: 1:CAS:528:DC%2BD2cXotlajs7k%3D, PID: 15475110
    • Rudd MK, Willard HF (2004) Analysis of the centromeric regions of the human genome assembly. Trends Genet 20:529–533
    • (2004) Trends Genet , vol.20 , pp. 529-533
    • Rudd, M.K.1    Willard, H.F.2
  • 27
    • 0035812788 scopus 로고    scopus 로고
    • Genomic and genetic definition of a functional human centromere
    • COI: 1:CAS:528:DC%2BD3MXnsFyitr4%3D, PID: 11588252
    • Schueler MG, Higgins AW, Rudd MK et al (2001) Genomic and genetic definition of a functional human centromere. Science 294:109–115
    • (2001) Science , vol.294 , pp. 109-115
    • Schueler, M.G.1    Higgins, A.W.2    Rudd, M.K.3
  • 28
    • 0026080822 scopus 로고
    • Four distinct alpha satellite subfamilies shared by human chromosomes 13, 14 and 21
    • COI: 1:CAS:528:DyaK3MXhsl2ntbo%3D, PID: 2014167
    • Vissel B, Choo KH (1991) Four distinct alpha satellite subfamilies shared by human chromosomes 13, 14 and 21. Nucleic Acids Res 19:271–277
    • (1991) Nucleic Acids Res , vol.19 , pp. 271-277
    • Vissel, B.1    Choo, K.H.2
  • 29
    • 84864258558 scopus 로고    scopus 로고
    • Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm
    • COI: 1:CAS:528:DC%2BC38XhtVymtr7P, PID: 22817899
    • Wang J, Fan HC, Behr B et al (2012) Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell 150:402–412
    • (2012) Cell , vol.150 , pp. 402-412
    • Wang, J.1    Fan, H.C.2    Behr, B.3
  • 30
    • 0025049328 scopus 로고
    • Genomic analysis of sequence variation in tandemly repeated DNA. Evidence for localized homogeneous sequence domains within arrays of alpha-satellite DNA
    • COI: 1:CAS:528:DyaK3MXhvVKksA%3D%3D, PID: 2122000
    • Warburton PE, Willard HF (1990) Genomic analysis of sequence variation in tandemly repeated DNA. Evidence for localized homogeneous sequence domains within arrays of alpha-satellite DNA. J Mol Biol 216:3–16
    • (1990) J Mol Biol , vol.216 , pp. 3-16
    • Warburton, P.E.1    Willard, H.F.2
  • 31
    • 0342390179 scopus 로고
    • Pulsed-field and two-dimensional gel electrophoresis of long arrays of tandemly repeated DNA: analysis of human centromeric alpha satellite
    • COI: 1:CAS:528:DyaK38Xmt1Ois7c%3D, PID: 21409641
    • Warburton PE, Wevrick R, Mahtani MM et al (1992) Pulsed-field and two-dimensional gel electrophoresis of long arrays of tandemly repeated DNA: analysis of human centromeric alpha satellite. Methods Mol Biol 12:299–317
    • (1992) Methods Mol Biol , vol.12 , pp. 299-317
    • Warburton, P.E.1    Wevrick, R.2    Mahtani, M.M.3
  • 32
    • 0022432047 scopus 로고
    • Chromosome-specific alpha satellite DNA: nucleotide sequence analysis of the 2.0 kilobasepair repeat from the human X chromosome
    • COI: 1:CAS:528:DyaL2MXktVWntbk%3D, PID: 2987865
    • Waye JS, Willard HF (1985) Chromosome-specific alpha satellite DNA: nucleotide sequence analysis of the 2.0 kilobasepair repeat from the human X chromosome. Nucleic Acids Res 13:2731–2743
    • (1985) Nucleic Acids Res , vol.13 , pp. 2731-2743
    • Waye, J.S.1    Willard, H.F.2
  • 33
    • 0024379003 scopus 로고
    • Long-range organization of tandem arrays of alpha satellite DNA at the centromeres of human chromosomes: High-frequency array-length polymorphism and meiotic stability
    • COI: 1:CAS:528:DyaK3cXkvFyisQ%3D%3D, PID: 2594775
    • Wevrick R, Willard HF (1989) Long-range organization of tandem arrays of alpha satellite DNA at the centromeres of human chromosomes: High-frequency array-length polymorphism and meiotic stability. Proc Natl Acad Sci U S A 86:9394–9398
    • (1989) Proc Natl Acad Sci U S A , vol.86 , pp. 9394-9398
    • Wevrick, R.1    Willard, H.F.2
  • 34
    • 0025806731 scopus 로고
    • Physical map of the centromeric region of human chromosome 7: relationship between two distinct alpha satellite arrays
    • COI: 1:CAS:528:DyaK3MXks1Grtbo%3D, PID: 2041770
    • Wevrick R, Willard HF (1991) Physical map of the centromeric region of human chromosome 7: relationship between two distinct alpha satellite arrays. Nucleic Acids Res 19:2295–2301
    • (1991) Nucleic Acids Res , vol.19 , pp. 2295-2301
    • Wevrick, R.1    Willard, H.F.2
  • 35
    • 0023066343 scopus 로고
    • Chromosome-specific subsets of human alpha satellite DNA: analysis of sequence divergence within and between chromosomal subsets and evidence for an ancestral pentameric repeat
    • COI: 1:CAS:528:DyaL2sXlsVygur4%3D, PID: 2822935
    • Willard HF, Waye JS (1987) Chromosome-specific subsets of human alpha satellite DNA: analysis of sequence divergence within and between chromosomal subsets and evidence for an ancestral pentameric repeat. J Mol Evol 25:207–214
    • (1987) J Mol Evol , vol.25 , pp. 207-214
    • Willard, H.F.1    Waye, J.S.2
  • 36
    • 0015230639 scopus 로고
    • Heterochromatin, satellite DNA, and cell function
    • COI: 1:CAS:528:DyaE38XpsFyisw%3D%3D, PID: 4943851
    • Yunis JJ, Yasmineh WG (1971) Heterochromatin, satellite DNA, and cell function. Science 174:1200–1209
    • (1971) Science , vol.174 , pp. 1200-1209
    • Yunis, J.J.1    Yasmineh, W.G.2
  • 37
    • 84861735098 scopus 로고    scopus 로고
    • Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research
    • COI: 1:CAS:528:DC%2BC38XivVChurk%3D, PID: 22343429
    • Zhang M, Zhang Y, Scheuring CF et al (2012) Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research. Nat Protoc 7:467–478
    • (2012) Nat Protoc , vol.7 , pp. 467-478
    • Zhang, M.1    Zhang, Y.2    Scheuring, C.F.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.