메뉴 건너뛰기




Volumn 34, Issue 20, 2006, Pages 5752-5763

Identification of insertion hot spots for non-LTR retrotransposons: Computational and biochemical application to Entamoeba histolytica

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; DNA; ENDONUCLEASE; GUANINE; THYMINE;

EID: 33845656427     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl710     Document Type: Article
Times cited : (8)

References (41)
  • 1
    • 0141950446 scopus 로고    scopus 로고
    • DNA: An Introduction
    • Mobile In Craig,N.L., Craigie,R., Gellert,M. and Lambowitz,A.M. (eds), American Society for Microbiology, Washington, D.C
    • Craig,N.L. (2002) Mobile DNA: An Introduction. In Craig,N.L., Craigie,R., Gellert,M. and Lambowitz,A.M. (eds), Mobile DNA II. American Society for Microbiology, Washington, D.C., pp. 3-11.
    • (2002) Mobile DNA II , pp. 3-11
    • Craig, N.L.1
  • 2
    • 0035674903 scopus 로고    scopus 로고
    • Biology of mammalian retrotransposons
    • Ostertag,E.M. and Kazazian,H.H. (2001) Biology of mammalian retrotransposons. Ann. Rev. Gen., 35, 501-538.
    • (2001) Ann. Rev. Gen. , vol.35 , pp. 501-538
    • Ostertag, E.M.1    Kazazian, H.H.2
  • 3
    • 0000602914 scopus 로고    scopus 로고
    • Report of a consultation of experts on Amoebiasis
    • WHO/PAHO/UNESCO
    • WHO/PAHO/UNESCO (1997) Report of a consultation of experts on Amoebiasis. Weekly Epidemiological Report of the World Health Organization, 72, 97-99.
    • (1997) Weekly Epidemiological Report of the World Health Organization , vol.72 , pp. 97-99
  • 4
    • 20444431839 scopus 로고    scopus 로고
    • The LINES and SINEs of Entamoeba histolytica: Comparative analysis and genomic distribution
    • Bakre,A.A., Rawal,K., Ramaswamy,R., Bhattacharya,A. and Bhattacharya,S. (2005) The LINES and SINEs of Entamoeba histolytica: Comparative analysis and genomic distribution. Exp. Parasitol., 110, 207-213.
    • (2005) Exp. Parasitol. , vol.110 , pp. 207-213
    • Bakre, A.A.1    Rawal, K.2    Ramaswamy, R.3    Bhattacharya, A.4    Bhattacharya, S.5
  • 5
    • 27744501724 scopus 로고    scopus 로고
    • Involvement of a short interspersed element in epigenetic transcriptional silencing of the amoebapore gene in Entamoeba histolytica
    • Anbar,M., Bracha,R., Nuchamowitz,Y., Li,Y., Florentin,A. and Mirelman,D. (2005) Involvement of a short interspersed element in epigenetic transcriptional silencing of the amoebapore gene in Entamoeba histolytica. Eukaryot. Cell, 4, 1775-1184.
    • (2005) Eukaryot. Cell , vol.4 , pp. 1184-1775
    • Anbar, M.1    Bracha, R.2    Nuchamowitz, Y.3    Li, Y.4    Florentin, A.5    Mirelman, D.6
  • 6
    • 0027450385 scopus 로고
    • Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: A mechanism for non-LTR retrotransposition
    • Luan,D.D., Korman,M.H., Jakubczak,J.L. and Eickbush,T.H. (1993) Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: A mechanism for non-LTR retrotransposition. Cell, 72, 595-605.
    • (1993) Cell , vol.72 , pp. 595-605
    • Luan, D.D.1    Korman, M.H.2    Jakubczak, J.L.3    Eickbush, T.H.4
  • 7
    • 85158069207 scopus 로고    scopus 로고
    • Origin and evolution of retrotransposons
    • In Craig,N.L., Craigie,R., Gellert,M. and Lambowitz,A.M. (eds), American Society for Microbiology, Washington, D.C.
    • Eickbush,T.H. and Malik,H.S. (2002) Origin and evolution of retrotransposons. In Craig,N.L., Craigie,R., Gellert,M. and Lambowitz,A.M. (eds), Mobile DNA II. American Society for Microbiology, Washington, D.C., pp. 1111-1144.
    • (2002) Mobile DNA II , pp. 1111-1144
    • Eickbush, T.H.1    Malik, H.S.2
  • 8
    • 0032478313 scopus 로고    scopus 로고
    • Retrotransposon R1Bm endonuclease cleaves the target sequence
    • Feng,Q., Schumann,G. and Boeke,J.D. (1998) Retrotransposon R1Bm endonuclease cleaves the target sequence, Proc. Natl Acad. Sci. USA, 95, 2083-2088.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 2083-2088
    • Feng, Q.1    Schumann, G.2    Boeke, J.D.3
  • 9
    • 0033959850 scopus 로고    scopus 로고
    • Target specificity of the endonuclease from the Xenopus laevis non-long terminal repeat retrotransposon, Tx1L
    • Christensen,S., Pont-Kingdon,G. and Carroll,D. (2000) Target specificity of the endonuclease from the Xenopus laevis non-long terminal repeat retrotransposon, Tx1L. Mol. Cell. Biol., 20, 1219-1226.
    • (2000) Mol. Cell. Biol. , vol.20 , pp. 1219-1226
    • Christensen, S.1    Pont-Kingdon, G.2    Carroll, D.3
  • 10
    • 85158011569 scopus 로고    scopus 로고
    • R2 and related site-specific non-long terminal repeat retrotransposons
    • In Craig,N.L., Craigie,R., Gellert,M. and Lambowitz,A.M. (eds), American Society for Microbiology, Washington, D.C
    • Eickbush,T.H. (2002) R2 and related site-specific non-long terminal repeat retrotransposons. In Craig,N.L., Craigie,R., Gellert,M. and Lambowitz,A.M. (eds), Mobile DNA II. American Society for Microbiology, Washington, D.C., pp. 813-835.
    • (2002) Mobile DNA II , pp. 813-835
    • Eickbush, T.H.1
  • 11
    • 0035052604 scopus 로고    scopus 로고
    • Non-LTR retrotransposons encoding a restriction enzyme-like endonuclease in vertebrates
    • Volff,J.N., Korting,C., Froschauer,A., Sweeney,K. and Schartl,M. (2001) Non-LTR retrotransposons encoding a restriction enzyme-like endonuclease in vertebrates. J. Mol. Evol., 52, 351-360.
    • (2001) J. Mol. Evol. , vol.52 , pp. 351-360
    • Volff, J.N.1    Korting, C.2    Froschauer, A.3    Sweeney, K.4    Schartl, M.5
  • 12
    • 0029039118 scopus 로고
    • Sequence-dependent bending propensity of DNA as revealed by DNase I: Parameters for trinucleotides
    • Brukner,I., Sanchez,R., Suck,D. and Pongor,S. (1995) Sequence-dependent bending propensity of DNA as revealed by DNase I: Parameters for trinucleotides. EMBO J., 18, 1812-1818.
    • (1995) EMBO J. , vol.18 , pp. 1812-1818
    • Brukner, I.1    Sanchez, R.2    Suck, D.3    Pongor, S.4
  • 13
    • 2542609960 scopus 로고    scopus 로고
    • Helix bending as a factor in protein/DNA recognition
    • Dickerson,R.E. and Chiu,T.K. (1997) Helix bending as a factor in protein/ DNA recognition. Biopolymers, 44, 361-403.
    • (1997) Biopolymers , vol.44 , pp. 361-403
    • Dickerson, R.E.1    Chiu, T.K.2
  • 14
    • 0030003963 scopus 로고    scopus 로고
    • Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA
    • Hassan,M.A.E. and Calladine,C.R. (1996) Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA. J. Mol. Biol., 259, 95-103.
    • (1996) J. Mol. Biol. , vol.259 , pp. 95-103
    • Hassan, M.A.E.1    Calladine, C.R.2
  • 15
    • 0018143102 scopus 로고
    • Optimized potential function for calculation of nucleic-acid interaction energies I. Base stacking
    • Ornstein,R.L., Rein,R., Breen,D.L. and MacElroy,R. (1978) Optimized potential function for calculation of nucleic-acid interaction energies I. Base stacking. Biopolymers, 17, 2341-2360.
    • (1978) Biopolymers , vol.17 , pp. 2341-2360
    • Ornstein, R.L.1    Rein, R.2    Breen, D.L.3    MacElroy, R.4
  • 16
    • 0029859713 scopus 로고    scopus 로고
    • Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes
    • Sugimoto,N., Nakano,S., Yoneyama,M, and Honda,K. (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res., 24, 4501-4505.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 4501-4505
    • Sugimoto, N.1    Nakano, S.2    Yoneyama, M.3    Honda, K.4
  • 19
    • 0032530555 scopus 로고    scopus 로고
    • DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
    • Olson,W.K., Gorin,A., Lu,X.J., Hock,L.M. and Zhurkin,V.B. (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl Acad. Sci. USA, 95, 11163-11168.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 11163-11168
    • Olson, W.K.1    Gorin, A.2    Lu, X.J.3    Hock, L.M.4    Zhurkin, V.B.5
  • 21
    • 0028624664 scopus 로고
    • Bending and curvature calculations in B-DNA
    • Goodsell,D.S. and Dickerson,R.E. (1994) Bending and curvature calculations in B-DNA. Nucleic Acids Res., 22, 5497-5503.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 5497-5503
    • Goodsell, D.S.1    Dickerson, R.E.2
  • 22
    • 1242277777 scopus 로고    scopus 로고
    • An Entamoeba histolytica LINE/SINE pair inserts at common target sites cleaved by the restriction enzyme-like LINE-encoded endonuclease
    • Mandal,P.K., Bagchi,A., Bhattacharya,A. and Bhattacharya,S. (2004) An Entamoeba histolytica LINE/SINE pair inserts at common target sites cleaved by the restriction enzyme-like LINE-encoded endonuclease. Eukaryot. Cell., 3, 170-179.
    • (2004) Eukaryot. Cell. , vol.3 , pp. 170-179
    • Mandal, P.K.1    Bagchi, A.2    Bhattacharya, A.3    Bhattacharya, S.4
  • 25
    • 0034724393 scopus 로고    scopus 로고
    • Insertion site preferences of the P transposable element in Drosophila melanogaster
    • Liao,G.C., Rehm,E.J. and Rubin,G.M. (2000) Insertion site preferences of the P transposable element in Drosophila melanogaster. Proc. Natl Acad. Sci. USA, 97, 3347-3351.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 3347-3351
    • Liao, G.C.1    Rehm, E.J.2    Rubin, G.M.3
  • 26
    • 0015104902 scopus 로고
    • A comparison of genome sizes and thermal denaturation-derived base composition of DNAs from several members of Entamoeba (histolytica group)
    • Gelderman,A.H., Bartgis,I.L., Keister,D.B. and Diamond,L.S. (1971) A comparison of genome sizes and thermal denaturation-derived base composition of DNAs from several members of Entamoeba (histolytica group). J. Parasitol., 57, 912-916.
    • (1971) J. Parasitol. , vol.57 , pp. 912-916
    • Gelderman, A.H.1    Bartgis, I.L.2    Keister, D.B.3    Diamond, L.S.4
  • 27
    • 0023905188 scopus 로고
    • Comparison of repeated DNA from strains of Entamoeba histolytica and other Entamoeba
    • Bhattacharya,S., Bhattacharya,A. and Diamond,L.S. (1988) Comparison of repeated DNA from strains of Entamoeba histolytica and other Entamoeba. Mol. Biochem. Parasitol., 27, 257-262.
    • (1988) Mol. Biochem. Parasitol. , vol.27 , pp. 257-262
    • Bhattacharya, S.1    Bhattacharya, A.2    Diamond, L.S.3
  • 28
    • 0004012196 scopus 로고
    • Fundamentals of Bayesian
    • Inference In Gelman,A. and Stern,H.S. (eds), Chapman & Hall, NY
    • Gelman,A., Carlin,J.B., Stern,H.S. and Rubin,D.B. (1995) Fundamentals of Bayesian Inference. In Gelman,A. and Stern,H.S. (eds), Bayesian Data Analysis. Chapman & Hall, NY, pp. 1-27.
    • (1995) Bayesian Data Analysis , pp. 1-27
    • Gelman, A.1    Carlin, J.B.2    Stern, H.S.3    Rubin, D.B.4
  • 30
    • 0028936684 scopus 로고
    • Translational positioning of nucleosomes on DNA: The role of sequence-dependent isotropic DNA bending stiffness
    • Sivolob,A.V. and Kharpunov,S.N. (1995) Translational positioning of nucleosomes on DNA: The role of sequence-dependent isotropic DNA bending stiffness. J. Mol. Biol., 247, 918-931.
    • (1995) J. Mol. Biol. , vol.247 , pp. 918-931
    • Sivolob, A.V.1    Kharpunov, S.N.2
  • 31
    • 0023001414 scopus 로고
    • Sequence periodicities in chicken nucleosome core DNA
    • Satchwell,S.C., Drew,H.R. and Traves,A.A. (1986) Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol., 191, 659-675.
    • (1986) J. Mol. Biol. , vol.191 , pp. 659-675
    • Satchwell, S.C.1    Drew, H.R.2    Traves, A.A.3
  • 32
    • 0035863793 scopus 로고    scopus 로고
    • Target DNA chromatinization modulates nicking by L1 endonuclease
    • Cost,G.J., Golding,A., Schlissel,M.S. and Boeke,J.D. (2001) Target DNA chromatinization modulates nicking by L1 endonuclease. Nucleic Acids Res., 29, 573-577.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 573-577
    • Cost, G.J.1    Golding, A.2    Schlissel, M.S.3    Boeke, J.D.4
  • 33
    • 12244264820 scopus 로고    scopus 로고
    • R2 retrotransposition on assembled nucleosomes depends on the translational position of the target site
    • Ye,J., Yang,Z.Y., Hayes,J.J. and Eickbush,T.H. (2002) R2 retrotransposition on assembled nucleosomes depends on the translational position of the target site. EMBO J., 21, 6853-6864.
    • (2002) EMBO J. , vol.21 , pp. 6853-6864
    • Ye, J.1    Yang, Z.Y.2    Hayes, J.J.3    Eickbush, T.H.4
  • 34
    • 0036706170 scopus 로고    scopus 로고
    • Mobile genetic elements in protozoan parasites
    • Bhattacharya,S., Bakre,A. and Bhattacharya,A. (2002) Mobile genetic elements in protozoan parasites. J. Genet., 81, 73-86.
    • (2002) J. Genet. , vol.81 , pp. 73-86
    • Bhattacharya, S.1    Bakre, A.2    Bhattacharya, A.3
  • 35
    • 0035865136 scopus 로고    scopus 로고
    • Target DNA structure plays a critical role in Tn7 transposition
    • Kuduvalli,P.N., Rao,J.E. and Craig,N.L. (2001) Target DNA structure plays a critical role in Tn7 transposition. EMBO J., 20, 924-932.
    • (2001) EMBO J. , vol.20 , pp. 924-932
    • Kuduvalli, P.N.1    Rao, J.E.2    Craig, N.L.3
  • 36
    • 0029058441 scopus 로고
    • RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element
    • Luan,D.D. and Eickbush,T.H. (1995) RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element. Mol. Cell. Biol., 15, 3882-3981.
    • (1995) Mol. Cell. Biol. , vol.15 , pp. 3882-3981
    • Luan, D.D.1    Eickbush, T.H.2
  • 39
    • 0030331832 scopus 로고    scopus 로고
    • Integration of retroposable elements in mammals: Selection of target sites
    • Jurka,J. and Klonowski,P. (1996) Integration of retroposable elements in mammals: Selection of target sites. J. Mol. Evol., 43, 685-689.
    • (1996) J. Mol. Evol. , vol.43 , pp. 685-689
    • Jurka, J.1    Klonowski, P.2
  • 40
  • 41
    • 0031697371 scopus 로고    scopus 로고
    • Similar target site selection occurs in integration of plant and mammalian retroposons
    • Tatout,C., Lavie,L. and Deragon,J.M. (1998) Similar target site selection occurs in integration of plant and mammalian retroposons. J. Mol. Evol., 47, 463-470.
    • (1998) J. Mol. Evol. , vol.47 , pp. 463-470
    • Tatout, C.1    Lavie, L.2    Deragon, J.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.