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Identification of a unique library of complex, but ordered, arrays of repetitive elements in the human genome and implication of their potential involvement in pathobiology.

Abstract Approximately 2% of the human genome is reported to be occupied by genes. Various forms of repetitive elements (REs), both characterized and uncharacterized, are presumed to make up the vast majority of the rest of the genomes of human and other species. In conjunction with a comprehensive annotation of genes, information regarding components of genome biology, such as gene polymorphisms, non-coding RNAs, and certain REs, is found in human genome databases. However, the genome-wide profile of unique RE arrangements formed by different groups of REs has not been fully characterized yet. In this study, the entire human genome was subjected to an unbiased RE survey to establish a whole-genome profile of REs and their arrangements. Due to the limitation in query size within the bl2seq alignment program (National Center for Biotechnology Information [NCBI]) utilized for the RE survey, the entire NCBI reference human genome was fragmented into 6206 units of 0.5M nucleotides. A number of RE arrangements with varying complexities and patterns were identified throughout the genome. Each chromosome had unique profiles of RE arrangements and density, and high levels of RE density were measured near the centromere regions. Subsequently, 175 complex RE arrangements, which were selected throughout the genome, were subjected to a comparison analysis using five different human genome sequences. Interestingly, three of the five human genome databases shared the exactly same arrangement patterns and sequences for all 175 RE arrangement regions (a total of 12,765,625 nucleotides). The findings from this study demonstrate that a substantial fraction of REs in the human genome are clustered into various forms of ordered structures. Further investigations are needed to examine whether some of these ordered RE arrangements contribute to the human pathobiology as a functional genome unit.
PMID
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Authors

Mayor MeshTerms

Gene Library

Genetic Predisposition to Disease

Genome, Human

Keywords
Journal Title experimental and molecular pathology
Publication Year Start
%A Lee, Kang-Hoon; Lee, Young-Kwan; Kwon, Deug-Nam; Chiu, Sophia; Chew, Victoria; Rah, Hyungchul; Kujawski, Gregory; Melhem, Ramzi; Hsu, Karen; Chung, Cecilia; Greenhalgh, David G.; Cho, Kiho
%T Identification of a unique library of complex, but ordered, arrays of repetitive elements in the human genome and implication of their potential involvement in pathobiology.
%J Experimental and molecular pathology, vol. 90, no. 3, pp. 300-311
%D 06/2011
%V 90
%N 3
%M eng
%B Approximately 2% of the human genome is reported to be occupied by genes. Various forms of repetitive elements (REs), both characterized and uncharacterized, are presumed to make up the vast majority of the rest of the genomes of human and other species. In conjunction with a comprehensive annotation of genes, information regarding components of genome biology, such as gene polymorphisms, non-coding RNAs, and certain REs, is found in human genome databases. However, the genome-wide profile of unique RE arrangements formed by different groups of REs has not been fully characterized yet. In this study, the entire human genome was subjected to an unbiased RE survey to establish a whole-genome profile of REs and their arrangements. Due to the limitation in query size within the bl2seq alignment program (National Center for Biotechnology Information [NCBI]) utilized for the RE survey, the entire NCBI reference human genome was fragmented into 6206 units of 0.5M nucleotides. A number of RE arrangements with varying complexities and patterns were identified throughout the genome. Each chromosome had unique profiles of RE arrangements and density, and high levels of RE density were measured near the centromere regions. Subsequently, 175 complex RE arrangements, which were selected throughout the genome, were subjected to a comparison analysis using five different human genome sequences. Interestingly, three of the five human genome databases shared the exactly same arrangement patterns and sequences for all 175 RE arrangement regions (a total of 12,765,625 nucleotides). The findings from this study demonstrate that a substantial fraction of REs in the human genome are clustered into various forms of ordered structures. Further investigations are needed to examine whether some of these ordered RE arrangements contribute to the human pathobiology as a functional genome unit.
%K Chromosome Mapping, Gene Library, Genetic Predisposition to Disease, Genome, Human, Humans, Repetitive Sequences, Nucleic Acid
%P 300
%L 311
%Y 10.1016/j.yexmp.2011.02.007
%W PHY
%G AUTHOR
%R 2011.......90..300L

@Article{Lee2011,
author="Lee, Kang-Hoon
and Lee, Young-Kwan
and Kwon, Deug-Nam
and Chiu, Sophia
and Chew, Victoria
and Rah, Hyungchul
and Kujawski, Gregory
and Melhem, Ramzi
and Hsu, Karen
and Chung, Cecilia
and Greenhalgh, David G.
and Cho, Kiho",
title="Identification of a unique library of complex, but ordered, arrays of repetitive elements in the human genome and implication of their potential involvement in pathobiology.",
journal="Experimental and molecular pathology",
year="2011",
month="Jun",
day="01",
volume="90",
number="3",
pages="300--311",
keywords="Chromosome Mapping",
keywords="Gene Library",
keywords="Genetic Predisposition to Disease",
keywords="Genome, Human",
keywords="Humans",
keywords="Repetitive Sequences, Nucleic Acid",
abstract="Approximately 2\% of the human genome is reported to be occupied by genes. Various forms of repetitive elements (REs), both characterized and uncharacterized, are presumed to make up the vast majority of the rest of the genomes of human and other species. In conjunction with a comprehensive annotation of genes, information regarding components of genome biology, such as gene polymorphisms, non-coding RNAs, and certain REs, is found in human genome databases. However, the genome-wide profile of unique RE arrangements formed by different groups of REs has not been fully characterized yet. In this study, the entire human genome was subjected to an unbiased RE survey to establish a whole-genome profile of REs and their arrangements. Due to the limitation in query size within the bl2seq alignment program (National Center for Biotechnology Information [NCBI]) utilized for the RE survey, the entire NCBI reference human genome was fragmented into 6206 units of 0.5M nucleotides. A number of RE arrangements with varying complexities and patterns were identified throughout the genome. Each chromosome had unique profiles of RE arrangements and density, and high levels of RE density were measured near the centromere regions. Subsequently, 175 complex RE arrangements, which were selected throughout the genome, were subjected to a comparison analysis using five different human genome sequences. Interestingly, three of the five human genome databases shared the exactly same arrangement patterns and sequences for all 175 RE arrangement regions (a total of 12,765,625 nucleotides). The findings from this study demonstrate that a substantial fraction of REs in the human genome are clustered into various forms of ordered structures. Further investigations are needed to examine whether some of these ordered RE arrangements contribute to the human pathobiology as a functional genome unit.",
issn="1096-0945",
doi="10.1016/j.yexmp.2011.02.007",
url="http://www.ncbi.nlm.nih.gov/pubmed/21376035",
language="eng"
}

%0 Journal Article
%T Identification of a unique library of complex, but ordered, arrays of repetitive elements in the human genome and implication of their potential involvement in pathobiology.
%A Lee, Kang-Hoon
%A Lee, Young-Kwan
%A Kwon, Deug-Nam
%A Chiu, Sophia
%A Chew, Victoria
%A Rah, Hyungchul
%A Kujawski, Gregory
%A Melhem, Ramzi
%A Hsu, Karen
%A Chung, Cecilia
%A Greenhalgh, David G.
%A Cho, Kiho
%J Experimental and molecular pathology
%D 2011
%8 Jun 01
%V 90
%N 3
%@ 1096-0945
%G eng
%F Lee2011
%X Approximately 2% of the human genome is reported to be occupied by genes. Various forms of repetitive elements (REs), both characterized and uncharacterized, are presumed to make up the vast majority of the rest of the genomes of human and other species. In conjunction with a comprehensive annotation of genes, information regarding components of genome biology, such as gene polymorphisms, non-coding RNAs, and certain REs, is found in human genome databases. However, the genome-wide profile of unique RE arrangements formed by different groups of REs has not been fully characterized yet. In this study, the entire human genome was subjected to an unbiased RE survey to establish a whole-genome profile of REs and their arrangements. Due to the limitation in query size within the bl2seq alignment program (National Center for Biotechnology Information [NCBI]) utilized for the RE survey, the entire NCBI reference human genome was fragmented into 6206 units of 0.5M nucleotides. A number of RE arrangements with varying complexities and patterns were identified throughout the genome. Each chromosome had unique profiles of RE arrangements and density, and high levels of RE density were measured near the centromere regions. Subsequently, 175 complex RE arrangements, which were selected throughout the genome, were subjected to a comparison analysis using five different human genome sequences. Interestingly, three of the five human genome databases shared the exactly same arrangement patterns and sequences for all 175 RE arrangement regions (a total of 12,765,625 nucleotides). The findings from this study demonstrate that a substantial fraction of REs in the human genome are clustered into various forms of ordered structures. Further investigations are needed to examine whether some of these ordered RE arrangements contribute to the human pathobiology as a functional genome unit.
%K Chromosome Mapping
%K Gene Library
%K Genetic Predisposition to Disease
%K Genome, Human
%K Humans
%K Repetitive Sequences, Nucleic Acid
%U http://dx.doi.org/10.1016/j.yexmp.2011.02.007
%U http://www.ncbi.nlm.nih.gov/pubmed/21376035
%P 300-311

PT Journal
AU Lee, K
   Lee, Y
   Kwon, D
   Chiu, S
   Chew, V
   Rah, H
   Kujawski, G
   Melhem, R
   Hsu, K
   Chung, C
   Greenhalgh, DG
   Cho, K
TI Identification of a unique library of complex, but ordered, arrays of repetitive elements in the human genome and implication of their potential involvement in pathobiology.
SO Experimental and molecular pathology
JI Exp. Mol. Pathol.
PD Jun
PY 2011
BP 300
EP 311
VL 90
IS 3
DI 10.1016/j.yexmp.2011.02.007
LA eng
DE Chromosome Mapping; Gene Library; Genetic Predisposition to Disease; Genome, Human; Humans; Repetitive Sequences, Nucleic Acid
AB Approximately 2% of the human genome is reported to be occupied by genes. Various forms of repetitive elements (REs), both characterized and uncharacterized, are presumed to make up the vast majority of the rest of the genomes of human and other species. In conjunction with a comprehensive annotation of genes, information regarding components of genome biology, such as gene polymorphisms, non-coding RNAs, and certain REs, is found in human genome databases. However, the genome-wide profile of unique RE arrangements formed by different groups of REs has not been fully characterized yet. In this study, the entire human genome was subjected to an unbiased RE survey to establish a whole-genome profile of REs and their arrangements. Due to the limitation in query size within the bl2seq alignment program (National Center for Biotechnology Information [NCBI]) utilized for the RE survey, the entire NCBI reference human genome was fragmented into 6206 units of 0.5M nucleotides. A number of RE arrangements with varying complexities and patterns were identified throughout the genome. Each chromosome had unique profiles of RE arrangements and density, and high levels of RE density were measured near the centromere regions. Subsequently, 175 complex RE arrangements, which were selected throughout the genome, were subjected to a comparison analysis using five different human genome sequences. Interestingly, three of the five human genome databases shared the exactly same arrangement patterns and sequences for all 175 RE arrangement regions (a total of 12,765,625 nucleotides). The findings from this study demonstrate that a substantial fraction of REs in the human genome are clustered into various forms of ordered structures. Further investigations are needed to examine whether some of these ordered RE arrangements contribute to the human pathobiology as a functional genome unit.
ER

PMID- 21376035
OWN - NLM
STAT- MEDLINE
DA  - 20110510
DCOM- 20110719
LR  - 20150317
IS  - 1096-0945 (Electronic)
IS  - 0014-4800 (Linking)
VI  - 90
IP  - 3
DP  - 2011 Jun
TI  - Identification of a unique library of complex, but ordered, arrays of repetitive 
      elements in the human genome and implication of their potential involvement in
      pathobiology.
PG  - 300-11
LID - 10.1016/j.yexmp.2011.02.007 [doi]
AB  - Approximately 2% of the human genome is reported to be occupied by genes. Various
      forms of repetitive elements (REs), both characterized and uncharacterized, are
      presumed to make up the vast majority of the rest of the genomes of human and
      other species. In conjunction with a comprehensive annotation of genes,
      information regarding components of genome biology, such as gene polymorphisms,
      non-coding RNAs, and certain REs, is found in human genome databases. However,
      the genome-wide profile of unique RE arrangements formed by different groups of
      REs has not been fully characterized yet. In this study, the entire human genome 
      was subjected to an unbiased RE survey to establish a whole-genome profile of REs
      and their arrangements. Due to the limitation in query size within the bl2seq
      alignment program (National Center for Biotechnology Information [NCBI]) utilized
      for the RE survey, the entire NCBI reference human genome was fragmented into
      6206 units of 0.5M nucleotides. A number of RE arrangements with varying
      complexities and patterns were identified throughout the genome. Each chromosome 
      had unique profiles of RE arrangements and density, and high levels of RE density
      were measured near the centromere regions. Subsequently, 175 complex RE
      arrangements, which were selected throughout the genome, were subjected to a
      comparison analysis using five different human genome sequences. Interestingly,
      three of the five human genome databases shared the exactly same arrangement
      patterns and sequences for all 175 RE arrangement regions (a total of 12,765,625 
      nucleotides). The findings from this study demonstrate that a substantial
      fraction of REs in the human genome are clustered into various forms of ordered
      structures. Further investigations are needed to examine whether some of these
      ordered RE arrangements contribute to the human pathobiology as a functional
      genome unit.
CI  - Copyright (c) 2011 Elsevier Inc. All rights reserved.
FAU - Lee, Kang-Hoon
AU  - Lee KH
AD  - Burn Research, Shriners Hospitals for Children Northern California and Department
      of Surgery, University of California-Davis, 2425 Stockton Blvd., Sacramento, CA
      95817, USA.
FAU - Lee, Young-Kwan
AU  - Lee YK
FAU - Kwon, Deug-Nam
AU  - Kwon DN
FAU - Chiu, Sophia
AU  - Chiu S
FAU - Chew, Victoria
AU  - Chew V
FAU - Rah, Hyungchul
AU  - Rah H
FAU - Kujawski, Gregory
AU  - Kujawski G
FAU - Melhem, Ramzi
AU  - Melhem R
FAU - Hsu, Karen
AU  - Hsu K
FAU - Chung, Cecilia
AU  - Chung C
FAU - Greenhalgh, David G
AU  - Greenhalgh DG
FAU - Cho, Kiho
AU  - Cho K
LA  - eng
GR  - R01 GM071360/GM/NIGMS NIH HHS/United States
GR  - R01 GM071360/GM/NIGMS NIH HHS/United States
GR  - R01 GM071360-05/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20110301
PL  - United States
TA  - Exp Mol Pathol
JT  - Experimental and molecular pathology
JID - 0370711
SB  - IM
MH  - Chromosome Mapping
MH  - *Gene Library
MH  - *Genetic Predisposition to Disease
MH  - *Genome, Human
MH  - Humans
MH  - Repetitive Sequences, Nucleic Acid/*genetics
PMC - PMC3092023
MID - NIHMS278679
OID - NLM: NIHMS278679
OID - NLM: PMC3092023
EDAT- 2011/03/08 06:00
MHDA- 2011/07/20 06:00
CRDT- 2011/03/08 06:00
PHST- 2011/02/03 [received]
PHST- 2011/02/18 [accepted]
PHST- 2011/03/01 [aheadofprint]
AID - S0014-4800(11)00023-2 [pii]
AID - 10.1016/j.yexmp.2011.02.007 [doi]
PST - ppublish
SO  - Exp Mol Pathol. 2011 Jun;90(3):300-11. doi: 10.1016/j.yexmp.2011.02.007. Epub
      2011 Mar 1.
TY  - JOUR
AU  - Lee, Kang-Hoon
AU  - Lee, Young-Kwan
AU  - Kwon, Deug-Nam
AU  - Chiu, Sophia
AU  - Chew, Victoria
AU  - Rah, Hyungchul
AU  - Kujawski, Gregory
AU  - Melhem, Ramzi
AU  - Hsu, Karen
AU  - Chung, Cecilia
AU  - Greenhalgh, David G.
AU  - Cho, Kiho
PY  - 2011/Jun/01
TI  - Identification of a unique library of complex, but ordered, arrays of repetitive elements in the human genome and implication of their potential involvement in pathobiology.
T2  - Exp. Mol. Pathol.
JO  - Experimental and molecular pathology
SP  - 300
EP  - 311
VL  - 90
IS  - 3
KW  - Chromosome Mapping
KW  - Gene Library
KW  - Genetic Predisposition to Disease
KW  - Genome, Human
KW  - Humans
KW  - Repetitive Sequences, Nucleic Acid
N2  - Approximately 2% of the human genome is reported to be occupied by genes. Various forms of repetitive elements (REs), both characterized and uncharacterized, are presumed to make up the vast majority of the rest of the genomes of human and other species. In conjunction with a comprehensive annotation of genes, information regarding components of genome biology, such as gene polymorphisms, non-coding RNAs, and certain REs, is found in human genome databases. However, the genome-wide profile of unique RE arrangements formed by different groups of REs has not been fully characterized yet. In this study, the entire human genome was subjected to an unbiased RE survey to establish a whole-genome profile of REs and their arrangements. Due to the limitation in query size within the bl2seq alignment program (National Center for Biotechnology Information [NCBI]) utilized for the RE survey, the entire NCBI reference human genome was fragmented into 6206 units of 0.5M nucleotides. A number of RE arrangements with varying complexities and patterns were identified throughout the genome. Each chromosome had unique profiles of RE arrangements and density, and high levels of RE density were measured near the centromere regions. Subsequently, 175 complex RE arrangements, which were selected throughout the genome, were subjected to a comparison analysis using five different human genome sequences. Interestingly, three of the five human genome databases shared the exactly same arrangement patterns and sequences for all 175 RE arrangement regions (a total of 12,765,625 nucleotides). The findings from this study demonstrate that a substantial fraction of REs in the human genome are clustered into various forms of ordered structures. Further investigations are needed to examine whether some of these ordered RE arrangements contribute to the human pathobiology as a functional genome unit.
SN  - 1096-0945
UR  - http://dx.doi.org/10.1016/j.yexmp.2011.02.007
UR  - http://www.ncbi.nlm.nih.gov/pubmed/21376035
ID  - Lee2011
ER  - 
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