\@writefile{lof}{\contentsline {figure}{\numberline {1.1}{\ignorespaces \textbf {A} Top view of a nucleosome core particle (NCP) displayed as a ribbon representation on the left and space filling representation on the left. The NCP is made of a four hetero-dimers histone octamer around which 146-148 DNA bp wraps. The histone tails protrude out of the nucleosome core particle and are accessible to other factors, unlike the inner part of the histone octamer. Taken and modified from \cite {mcginty_robert_k._and_tan_song_fundamentals_2014}. \textbf {B} The chromatin structure. Inside eukaryotes, DNA is wrapped around histones cores forming nucleosomes. Nucleosomes can then be organized into higher-level helical-like structure, compacting the DNA. The ultimate compaction state is reached at mitosis meta-phase, when the mitotic chromosomes are visible.\relax }}{2}{figure.caption.7}}
\newlabel{intro_chromatin}{{1.1}{2}{\textbf {A} Top view of a nucleosome core particle (NCP) displayed as a ribbon representation on the left and space filling representation on the left. The NCP is made of a four hetero-dimers histone octamer around which 146-148 DNA bp wraps. The histone tails protrude out of the nucleosome core particle and are accessible to other factors, unlike the inner part of the histone octamer. Taken and modified from \cite {mcginty_robert_k._and_tan_song_fundamentals_2014}. \textbf {B} The chromatin structure. Inside eukaryotes, DNA is wrapped around histones cores forming nucleosomes. Nucleosomes can then be organized into higher-level helical-like structure, compacting the DNA. The ultimate compaction state is reached at mitosis meta-phase, when the mitotic chromosomes are visible.\relax }{figure.caption.7}{}}
\@writefile{lof}{\contentsline {figure}{\numberline {1.2}{\ignorespaces \textbf {Nucleosome positioning} \textbf {A} Activated gene transcription start site (TSS) region. The nucleosomes located immediately downstream of the TSS show a strong positioning. The positioning of the first nucleosome can be influence by sequence preferences. Eventually the phasing is propagated to neighboring nucleosomes through statistical positioning. The nucleosome array is not anymore visible as the nucleosomes become fuzzily positioned among the cells. \textbf {B} Influence of the rotational positioning on the sequence accessibility. Left, a sequence (indicated by the black \IeC {\textquoteleft }rungs\IeC {\textquoteright } on the DNA helix) has its major groove facing toward the nucleosome outside and is accessible. Center, a 5bp rotation of the nucleosome hides the sequence as its major groove is not facing the histone octamer. Right, another 5bp rotation makes the sequence accessible again. Both images are taken and adapted from \citep {jiang_nucleosome_2009}.\relax }}{5}{figure.caption.8}}
\newlabel{intro_nucleosome_positioning}{{1.2}{5}{\textbf {Nucleosome positioning} \textbf {A} Activated gene transcription start site (TSS) region. The nucleosomes located immediately downstream of the TSS show a strong positioning. The positioning of the first nucleosome can be influence by sequence preferences. Eventually the phasing is propagated to neighboring nucleosomes through statistical positioning. The nucleosome array is not anymore visible as the nucleosomes become fuzzily positioned among the cells. \textbf {B} Influence of the rotational positioning on the sequence accessibility. Left, a sequence (indicated by the black ‘rungs’ on the DNA helix) has its major groove facing toward the nucleosome outside and is accessible. Center, a 5bp rotation of the nucleosome hides the sequence as its major groove is not facing the histone octamer. Right, another 5bp rotation makes the sequence accessible again. Both images are taken and adapted from \citep {jiang_nucleosome_2009}.\relax }{figure.caption.8}{}}