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\babel@toc {english}{}
\babel@toc {french}{}
\babel@toc {english}{}
\contentsline {chapter}{Acknowledgements}{i}{chapter*.1}
\contentsline {chapter}{Preface}{iii}{chapter*.2}
\contentsline {chapter}{Abstract (English/Fran\IeC {\c c}ais/Deutsch)}{v}{chapter*.3}
\babel@toc {german}{}
\babel@toc {english}{}
\babel@toc {french}{}
\babel@toc {english}{}
\contentsline {chapter}{\numberline {1}Introduction}{1}{chapter.1}
\contentsline {chapter}{Introduction}{1}{chapter.1}
\contentsline {section}{\numberline {1.1}About chromatin}{1}{section.1.1}
\contentsline {subsection}{\numberline {1.1.1}The chromatin structure}{1}{subsection.1.1.1}
\contentsline {subsection}{\numberline {1.1.2}The chromatin is dynamic}{3}{subsection.1.1.2}
\contentsline {subsection}{\numberline {1.1.3}Measuring nucleosome occupancy}{4}{subsection.1.1.3}
\contentsline {section}{\numberline {1.2}About transcription factors}{5}{section.1.2}
\contentsline {subsection}{\numberline {1.2.1}TF co-binding}{6}{subsection.1.2.1}
\contentsline {subsection}{\numberline {1.2.2}Modeling sequence specificity}{7}{subsection.1.2.2}
\contentsline {subsubsection}{Position weight matrix}{7}{subsection.1.2.2}
\contentsline {subsubsection}{Predicting binding sites}{9}{equation.1.2.4}
\contentsline {subsubsection}{Aligning binding sites}{10}{equation.1.2.6}
\contentsline {subsection}{\numberline {1.2.3}Measuring TF binding in vivo}{10}{subsection.1.2.3}
\contentsline {subsection}{\numberline {1.2.4}Measuring TF binding in vitro}{11}{subsection.1.2.4}
\contentsline {section}{\numberline {1.3}About nucleosome positioning}{11}{section.1.3}
\contentsline {section}{\numberline {1.4}Gene regulation in a nutshell}{14}{section.1.4}
\contentsline {subsection}{\numberline {1.4.1}The chromatin barrier}{14}{subsection.1.4.1}
\contentsline {subsection}{\numberline {1.4.2}TFs cooperative binding}{14}{subsection.1.4.2}
\contentsline {subsection}{\numberline {1.4.3}Pioneer TFs}{15}{subsection.1.4.3}
\contentsline {subsection}{\numberline {1.4.4}Regulatory elements}{15}{subsection.1.4.4}
\contentsline {subsection}{\numberline {1.4.5}The genome goes 3D}{16}{subsection.1.4.5}
\contentsline {subsection}{\numberline {1.4.6}Digital footprinting}{17}{subsection.1.4.6}
\contentsline {chapter}{\numberline {2}Laboratory resources}{21}{chapter.2}
\contentsline {chapter}{Laboratory resources}{21}{chapter.2}
\contentsline {section}{\numberline {2.1}Mass Genome Annotation repository}{21}{section.2.1}
\contentsline {subsection}{\numberline {2.1.1}MGA content and organization}{22}{subsection.2.1.1}
\contentsline {subsection}{\numberline {2.1.2}Conclusions}{24}{subsection.2.1.2}
\contentsline {section}{\numberline {2.2}Eukaryotic Promoter Database}{25}{section.2.2}
\contentsline {subsection}{\numberline {2.2.1}EPDnew now annotates (some of) your mushrooms and vegetables}{26}{subsection.2.2.1}
\contentsline {subsection}{\numberline {2.2.2}Increased mapping precision in human}{27}{subsection.2.2.2}
\contentsline {subsection}{\numberline {2.2.3}Integration of EPDnew with other resources}{27}{subsection.2.2.3}
\contentsline {subsection}{\numberline {2.2.4}Conclusions}{28}{subsection.2.2.4}
\contentsline {subsection}{\numberline {2.2.5}Methods}{28}{subsection.2.2.5}
\contentsline {subsubsection}{Motif occurrence profiles}{28}{subsection.2.2.5}
\contentsline {chapter}{\numberline {3}ENCODE peaks analysis}{29}{chapter.3}
\contentsline {chapter}{ENCODE peaks analysis}{29}{chapter.3}
\contentsline {section}{\numberline {3.1}Data}{29}{section.3.1}
\contentsline {section}{\numberline {3.2}ChIPPartitioning : an algorithm to identify chromatin architectures}{31}{section.3.2}
\contentsline {subsection}{\numberline {3.2.1}Data realignment}{32}{subsection.3.2.1}
\contentsline {section}{\numberline {3.3}Nucleosome organization around transcription factor binding sites}{33}{section.3.3}
\contentsline {section}{\numberline {3.4}The case of CTCF, RAD21, SMC3, YY1 and ZNF143}{35}{section.3.4}
\contentsline {section}{\numberline {3.5}CTCF and JunD interactomes}{39}{section.3.5}
\contentsline {section}{\numberline {3.6}EBF1 binds nucleosomes}{43}{section.3.6}
\contentsline {section}{\numberline {3.7}Discussion}{46}{section.3.7}
\contentsline {section}{\numberline {3.8}Methods}{46}{section.3.8}
\contentsline {subsection}{\numberline {3.8.1}Data and data processing}{46}{subsection.3.8.1}
\contentsline {subsection}{\numberline {3.8.2}Classification of MNase patterns}{47}{subsection.3.8.2}
\contentsline {subsection}{\numberline {3.8.3}Quantifying nucleosome array intensity from classification results}{48}{subsection.3.8.3}
\contentsline {subsection}{\numberline {3.8.4}Peak colocalization}{49}{subsection.3.8.4}
\contentsline {subsection}{\numberline {3.8.5}NDR detection}{50}{subsection.3.8.5}
\contentsline {subsection}{\numberline {3.8.6}CTCF and JunD interactors}{52}{subsection.3.8.6}
\contentsline {subsection}{\numberline {3.8.7}EBF1 and nucleosome}{53}{subsection.3.8.7}
\contentsline {chapter}{\numberline {4}SPar-K}{55}{chapter.4}
\contentsline {section}{\numberline {4.1}Algorithm}{55}{section.4.1}
\contentsline {subsection}{\numberline {4.1.1}Implementation}{56}{subsection.4.1.1}
\contentsline {section}{\numberline {4.2}Benchmarking}{57}{section.4.2}
\contentsline {subsection}{\numberline {4.2.1}K-means}{57}{subsection.4.2.1}
\contentsline {subsection}{\numberline {4.2.2}ChIPPartitioning}{60}{subsection.4.2.2}
\contentsline {subsection}{\numberline {4.2.3}Data}{60}{subsection.4.2.3}
\contentsline {subsection}{\numberline {4.2.4}Performances}{61}{subsection.4.2.4}
\contentsline {section}{\numberline {4.3}Partition of DNase and MNase data}{61}{section.4.3}
\contentsline {section}{\numberline {4.4}Conclusions}{61}{section.4.4}
\contentsline {chapter}{\numberline {5}SMiLE-seq data analysis}{65}{chapter.5}
\contentsline {chapter}{SMiLE-seq data analysis}{65}{chapter.5}
\contentsline {subsection}{\numberline {5.0.1}Introduction}{65}{subsection.5.0.1}
\contentsline {subsection}{\numberline {5.0.2}Hidden Markov Model Motif discovery}{67}{subsection.5.0.2}
\contentsline {subsection}{\numberline {5.0.3}Binding motif evaluation}{68}{subsection.5.0.3}
\contentsline {subsection}{\numberline {5.0.4}Results}{70}{subsection.5.0.4}
\contentsline {subsection}{\numberline {5.0.5}Conclusions}{72}{subsection.5.0.5}
\contentsline {chapter}{\numberline {6}PWMScan}{73}{chapter.6}
\contentsline {section}{\numberline {6.1}Algorithms}{73}{section.6.1}
\contentsline {subsection}{\numberline {6.1.1}Scanner algorithm}{74}{subsection.6.1.1}
\contentsline {subsection}{\numberline {6.1.2}Matches enumeration and mapping}{74}{subsection.6.1.2}
\contentsline {section}{\numberline {6.2}PMWScan architecture}{75}{section.6.2}
\contentsline {section}{\numberline {6.3}Benchmark}{77}{section.6.3}
\contentsline {section}{\numberline {6.4}Conclusions}{79}{section.6.4}
\contentsline {chapter}{\numberline {7}Chromatin accessibility of monocytes}{81}{chapter.7}
\contentsline {section}{\numberline {7.1}Monitoring TF binding}{81}{section.7.1}
\contentsline {section}{\numberline {7.2}The advent of single cell DGF}{82}{section.7.2}
\contentsline {section}{\numberline {7.3}Open issues}{82}{section.7.3}
\contentsline {section}{\numberline {7.4}Data}{82}{section.7.4}
\contentsline {section}{\numberline {7.5}Identifying over-represented signals}{83}{section.7.5}
\contentsline {subsection}{\numberline {7.5.1}ChIPPartitioning : an algorithm to identify over-represented read patterns}{83}{subsection.7.5.1}
\contentsline {subsection}{\numberline {7.5.2}EMSequence : an algorithm to identify over-represented sequences}{83}{subsection.7.5.2}
\contentsline {subsubsection}{without shift and flip}{85}{figure.caption.36}
\contentsline {subsubsection}{with shift and flip}{85}{equation.7.5.2}
\contentsline {subsection}{\numberline {7.5.3}EMJoint : an algorithm to identify over-represented sequences and chromatin architectures}{86}{subsection.7.5.3}
\contentsline {subsection}{\numberline {7.5.4}Data realignment}{87}{subsection.7.5.4}
\contentsline {section}{\numberline {7.6}Results}{88}{section.7.6}
\contentsline {subsection}{\numberline {7.6.1}Fragment size analysis}{90}{subsection.7.6.1}
\contentsline {subsection}{\numberline {7.6.2}Measuring open chromatin and nucleosome occupancy}{90}{subsection.7.6.2}
\contentsline {subsection}{\numberline {7.6.3}Evaluation of EMSequence and ChIPPartitioning}{92}{subsection.7.6.3}
\contentsline {subsubsection}{EMSequence}{93}{subsection.7.6.3}
\contentsline {subsubsection}{ChIPPartitioning}{95}{figure.caption.41}
\contentsline {section}{\numberline {7.7}Aligning the binding sites}{97}{section.7.7}
\contentsline {section}{\numberline {7.8}Exploring individual TF classes}{101}{section.7.8}
\contentsline {section}{\numberline {7.9}Discussions}{101}{section.7.9}
\contentsline {section}{\numberline {7.10}Perspectives}{102}{section.7.10}
\contentsline {section}{\numberline {7.11}Methods}{103}{section.7.11}
\contentsline {subsection}{\numberline {7.11.1}Partitioning programs}{103}{subsection.7.11.1}
\contentsline {subsection}{\numberline {7.11.2}Fragment classes}{103}{subsection.7.11.2}
\contentsline {subsection}{\numberline {7.11.3}Simulated sequences}{104}{subsection.7.11.3}
\contentsline {subsection}{\numberline {7.11.4}Realignment using JASPAR motifs}{104}{subsection.7.11.4}
\contentsline {subsection}{\numberline {7.11.5}Model extension}{106}{subsection.7.11.5}
\contentsline {subsection}{\numberline {7.11.6}Extracting data assigned to a class}{106}{subsection.7.11.6}
\contentsline {subsection}{\numberline {7.11.7}Peak processing}{109}{subsection.7.11.7}
\contentsline {subsection}{\numberline {7.11.8}Per TF classes}{109}{subsection.7.11.8}
\contentsline {subsection}{\numberline {7.11.9}Per TF sub-classes}{109}{subsection.7.11.9}
\contentsline {chapter}{\numberline {8}Discussion}{111}{chapter.8}
\contentsline {chapter}{Discussions}{111}{chapter.8}
\vspace {\normalbaselineskip }
\contentsline {chapter}{\numberline {A}An appendix}{115}{appendix.A}
\contentsline {section}{\numberline {A.1}Supplementary figures}{115}{section.A.1}
\contentsline {chapter}{Bibliography}{147}{section*.66}
\contentsline {chapter}{Bibliography}{159}{appendix*.67}
\contentsline {chapter}{Curriculum Vitae}{161}{section*.68}

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