Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations
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{"title"=>"Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations", "type"=>"journal", "authors"=>[{"first_name"=>"Toru", "last_name"=>"Niina", "scopus_author_id"=>"57200103765"}, {"first_name"=>"Giovanni B.", "last_name"=>"Brandani", "scopus_author_id"=>"57200103930"}, {"first_name"=>"Cheng", "last_name"=>"Tan", "scopus_author_id"=>"55190872100"}, {"first_name"=>"Shoji", "last_name"=>"Takada", "scopus_author_id"=>"7202611424"}], "year"=>2017, "source"=>"PLoS Computational Biology", "identifiers"=>{"issn"=>"15537358", "pui"=>"620067035", "doi"=>"10.1371/journal.pcbi.1005880", "sgr"=>"85039561545", "isbn"=>"1111111111", "scopus"=>"2-s2.0-85039561545"}, "id"=>"d99cee16-9b96-3b58-a6a5-d7f87c113707", "abstract"=>"While nucleosome positioning on eukaryotic genome play important roles for genetic regula-tion, molecular mechanisms of nucleosome positioning and sliding along DNA are not well understood. Here we investigated thermally-activated spontaneous nucleosome sliding mechanisms developing and applying a coarse-grained molecular simulation method that incorporates both long-range electrostatic and short-range hydrogen-bond interactions between histone octamer and DNA. The simulations revealed two distinct sliding modes depending on the nucleosomal DNA sequence. A uniform DNA sequence showed frequent sliding with one base pair step in a rotation-coupled manner, akin to screw-like motions. On the contrary, a strong positioning sequence, the so-called 601 sequence, exhibits rare, abrupt transitions of five and ten base pair steps without rotation. Moreover, we evaluated the importance of hydrogen bond interactions on the sliding mode, finding that strong and weak bonds favor respectively the rotation-coupled and -uncoupled sliding movements. Author summary Nucleosomes are fundamental units of chromatin folding consisting of double-stranded DNA wrapped ~1.7 times around a histone octamer. By densely populating the eukaryotic genome, nucleosomes enable efficient genome compaction inside the cellular nucleus. However, the portion of DNA occupied by a nucleosome can hardly be accessed by other DNA-binding proteins, obstructing fundamental cellular processes such as DNA replica-tion and transcription. DNA compaction and access by other proteins can simultaneously be achieved via the dynamical repositioning of nucleosomes, which can slide along the DNA sequence. In this study, we developed and used coarse-grained molecular dynamics simulations to reveal the molecular details of nucleosome sliding. We find that the sliding mode is highly dependent on the underlying DNA sequence. Specifically, a sequence with a strong nucleosome positioning signal slides via large jumps by five and ten base pairs, preserving the optimal DNA bending profile. On the other hand, uniform sequences with-out the positioning signal slide via a screw-like motion of DNA, one base pair at the time. Citation: Niina T, Brandani GB, Tan C, Takada S (2017) Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations. PLoS Comput Biol 13(12):", "link"=>"http://www.mendeley.com/research/sequencedependent-nucleosome-sliding-rotationcoupled-uncoupled-modes-revealed-molecular-simulations", "reader_count"=>10, "reader_count_by_academic_status"=>{"Researcher"=>1, "Student > Ph. D. Student"=>8, "Professor"=>1}, "reader_count_by_user_role"=>{"Researcher"=>1, "Student > Ph. D. Student"=>8, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Physics and Astronomy"=>3, "Chemistry"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Chemistry"=>{"Chemistry"=>2}, "Physics and Astronomy"=>{"Physics and Astronomy"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}}, "group_count"=>0}

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