Single-base Resolution Nucleosome Mapping on DNA Sequences

被引：33
|
作者：
Gabdank, I. [1 ]
Barash, D. [1 ]
Trifonov, E. N. [2 ,3 ]
机构：
[1] Ben Gurion Univ Negev, Dept Comp Sci, IL-84105 Beer Sheva, Israel
[2] Univ Haifa, Genome Divers Ctr, Inst Evolut, IL-31905 Haifa, Israel
[3] Masaryk Univ, Dept Funct Genom & Prote, Inst Expt Biol, Fac Sci, CZ-62500 Brno, Czech Republic
来源：
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS | 2010年 / 28卷 / 01期
基金：
以色列科学基金会;
关键词：
Chromatin code; DNA hendability; Nucleosome DNA; Nucleosome positioning; Nucleosome structure; CORE PARTICLE; PAIR DNA; CHROMATIN; ALIGNMENT; CRYSTALS; POSITION; PATTERN; SITES; PITCH;
D O I：
10.1080/07391102.2010.10507347
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
Nucleosome DNA bendahility pattern extracted from large nucleosome DNA database of C. elegans is used for construction of full length (116 dinucleotide positions) nucleosome DNA bendahility matrix. The matrix can he used for sequence-directed mapping of the nucleosomes on the sequences. Several alternative positions for a given nucleosome are typically predicted. separated by multiples of nucleosome DNA period. The corresponding computer program is successfully tested on best known experimental examples of accurately positioned nucleosomes. The uncertainty of the computational mapping is +/- 1 base. The procedure is placed on publicly accessible server and can he applied to any DNA sequence of interest.
引用
收藏
页码：107 / 121
页数：15
相关论文
共 50 条
  • [31] Targeting single-base DNA mismatches with bulky metallointercalators
    Barton, JK
    Hart, JR
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2005, 230 : U2117 - U2117
  • [32] Mapping of Single-Base Differences between Two DNA Strands in a Single Molecule Using Holliday Junction Nanomechanics
    Breme, Camille
    Heslot, Francois
    PLOS ONE, 2013, 8 (02):
  • [33] Mapping Combinatorial Epigenetic Modifications at Single Nucleosome Resolution
    Chang, Jen-Chien
    Watanabe, Kazuhide
    Umehara, Takashi
    Taniguchi, Yuichi
    Sato, Yuko
    Kimura, Hiroshi
    Minoda, Akiko
    BIOPHYSICAL JOURNAL, 2018, 114 (03) : 254A - 254A
  • [34] The Transcriptome-Wide Mapping of 2-Methylthio-N6-isopentenyladenosine at Single-Base Resolution
    Fang, Zhentian
    Lu, Ziang
    Han, Shaoqing
    Zhou, Yuanyuan
    Yang, Wei
    Zhang, Xiaolian
    Zhou, Xiang
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2023, 145 (09) : 5467 - 5473
  • [35] Single-Base Resolution Mapping of 5-Hydroxymethylcytosine Modifications in Hippocampus of Alzheimer’s Disease Subjects
    Elizabeth M. Ellison
    Melissa A. Bradley-Whitman
    Mark A. Lovell
    Journal of Molecular Neuroscience, 2017, 63 : 185 - 197
  • [36] Single-Base Resolution Mapping of 5-Hydroxymethylcytosine Modifications in Hippocampus of Alzheimer's Disease Subjects
    Ellison, Elizabeth M.
    Bradley-Whitman, Melissa A.
    Lovell, Mark A.
    JOURNAL OF MOLECULAR NEUROSCIENCE, 2017, 63 (02) : 185 - 197
  • [37] High-throughput single-base resolution mapping of RNA 2′-O-methylated residues
    Incarnato, Danny
    Anselmi, Francesca
    Morandi, Edoardo
    Neri, Francesco
    Maldotti, Mara
    Rapelli, Stefania
    Parlato, Caterina
    Basile, Giulia
    Oliviero, Salvatore
    NUCLEIC ACIDS RESEARCH, 2017, 45 (03) : 1433 - 1441
  • [38] Detection of DNA sequences with a single-base mismatch on a gold-based and pyrene-assisted platform
    Lee, Mei-Hwa
    Lin, Hung-Yin
    Chang, Hsueh-Wen
    Yang, Chia-Ning
    SENSORS AND ACTUATORS B-CHEMICAL, 2018, 266 : 522 - 527
  • [39] Probing DNA single strands for single-base bulges with neocarzinostatin chromophore
    Kappen, LS
    Xi, Z
    Goldberg, IH
    BIOCHEMISTRY, 2001, 40 (50) : 15378 - 15383
  • [40] Highly integrated single-base resolution maps of the epigenome in Arabidopsis
    Lister, Ryan
    O'Malley, Ronan C.
    Tonti-Filippini, Julian
    Gregory, Brian D.
    Berry, Charles C.
    Millar, A. Harvey
    Ecker, Joseph R.
    CELL, 2008, 133 (03) : 523 - 536
12345