Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components, Nature Cell Biology, vol.16, pp.281-291, 2014. ,
Genome-wide rules of nucleosome phasing in Drosophila, Molecular Cell, vol.72, pp.661-672, 2018. ,
Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors, Nature, vol.569, pp.136-140, 2019. ,
Nucleosome remodeling and epigenetics, Cold Spring Harbor Perspectives in Biology, vol.5, p.17905, 2013. ,
Julia: a fresh approach to numerical computing, SIAM Review, vol.59, pp.65-98, 2017. ,
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position, Nature Methods, vol.10, pp.1213-1218, 2013. ,
CTCF binding and higher order chromatin structure of the H19 locus are maintained in Mitotic chromatin, The EMBO Journal, vol.24, pp.3291-3300, 2005. ,
Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes, Genes & Development, vol.27, pp.251-260, 2013. ,
Binding of the winged-helix transcription factor HNF3 to a linker histone site on the nucleosome, The EMBO Journal, vol.17, pp.244-254, 1998. ,
The encyclopedia of DNA elements (ENCODE): data portal update, Nucleic Acids Research, vol.46, pp.794-801, 2018. ,
STAR: ultrafast universal RNA-seq aligner, Bioinformatics, vol.29, pp.15-21, 2013. ,
A common mechanism for mitotic inactivation of C2H2 zinc finger DNA-binding domains, Genes & Development, vol.16, pp.2985-2990, 2002. ,
Temporal control of gene expression by the pioneer factor zelda through transient interactions in hubs, Nature Communications, vol.9, p.5194, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02323402
Mediators of reprogramming: transcription factors and transitions through mitosis, Nature Reviews Molecular Cell Biology, vol.9, pp.505-516, 2008. ,
, An integrated encyclopedia of DNA elements in the human genome, ENCODE Project Consortium, vol.489, pp.57-74, 2012.
ChromHMM: automating chromatin-state discovery and characterization, Nature Methods, vol.9, pp.215-216, 2012. ,
Identifying ChIP-seq enrichment using MACS, Nature Protocols, vol.7, pp.1728-1740, 2012. ,
Mitotic binding of esrrb marks key regulatory regions of the pluripotency network, Nature Cell Biology, vol.18, pp.1139-1148, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01972743
Mitotic bookmarking in development and stem cells, Development, vol.144, pp.3633-3645, 2017. ,
URL : https://hal.archives-ouvertes.fr/pasteur-02024822
The epigenetic paradox of pluripotent ES cells, Journal of Molecular Biology, vol.429, pp.1476-1503, 2017. ,
URL : https://hal.archives-ouvertes.fr/pasteur-02024847
Transcription factor activity and nucleosome organization in mitosis, Genome Research, vol.29, pp.250-260, 2019. ,
The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome, PLOS Genetics, vol.4, p.1000138, 2008. ,
Monomeric complex of human orphan estrogen related receptor-2 with DNA: a pseudo-dimer interface mediates extended half-site recognition, Journal of Molecular Biology, vol.327, pp.819-832, 2003. ,
FIMO: scanning for occurrences of a given motif, Bioinformatics, vol.27, pp.1017-1018, 2011. ,
Chromatin challenges during DNA replication and repair, Cell, vol.128, pp.721-733, 2007. ,
Nucleosome dynamics define transcriptional enhancers, Nature Genetics, vol.42, pp.343-347, 2010. ,
Epigenome characterization at single base-pair resolution, PNAS, vol.108, pp.18318-18323, 2011. ,
The molecular logic of Nanog-induced self-renewal in mouse embryonic stem cells, Nature Communications, vol.10, p.1109, 2019. ,
URL : https://hal.archives-ouvertes.fr/pasteur-02083187
Speed-stability paradox in DNA-scanning by zinc-finger proteins, Transcription, vol.4, pp.58-61, 2013. ,
Chromatin particle spectrum analysis: a method for comparative chromatin structure analysis using paired-end mode next-generation DNA sequencing, Nucleic Acids Research, vol.39, p.26, 2011. ,
CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms, Molecular and Cellular Biology, vol.13, pp.7612-7624, 1993. ,
DNA mediated chromatin pull-down for the study of chromatin replication, Scientific Reports, vol.1, p.95, 2011. ,
Fast gapped-read alignment with bowtie 2, Nature Methods, vol.9, pp.357-359, 2012. ,
The sequence alignment/Map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 1000. ,
Dynamic regulation of transcription factors by nucleosome remodeling, Biophysical Journal, vol.106, p.76, 2014. ,
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome, BMC Bioinformatics, vol.12, p.323, 2011. ,
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biology, vol.15, p.550, 2014. ,
Crystal structure of the nucleosome core particle at 2.8 Å resolution, Nature, vol.389, pp.251-260, 1997. ,
Universal correction of enzymatic sequence Bias reveals molecular signatures of protein/DNA interactions, Nucleic Acids Research, vol.46, p.9, 2018. ,
Continued activity of the pioneer factor Zelda is required to drive zygotic genome activation, Molecular Cell, vol.74, pp.185-195, 2019. ,
CTCF and cohesin in genome folding and transcriptional gene regulation, Annual Review of Genomics and Human Genetics, vol.17, pp.17-43, 2016. ,
Collaborative competition mechanism for gene activation in vivo, Molecular and Cellular Biology, vol.23, pp.1623-1632, 2003. ,
Nucleosome-mediated cooperativity between transcription factors, PNAS, vol.107, pp.22534-22539, 2010. ,
Aurora B and Cdk1 mediate wapl activation and release of acetylated cohesin from chromosomes by phosphorylating sororin, PNAS, vol.110, pp.13404-13409, 2013. ,
Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization, Cell, vol.169, pp.930-944, 2017. ,
CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning, Genome Research, vol.29, pp.236-249, 2019. ,
Measuring absolute RNA copy numbers at high temporal resolution reveals transcriptome kinetics in development, Cell Reports, vol.14, pp.632-647, 2016. ,
Gain of CTCF-Anchored chromatin loops marks the exit from naive pluripotency, Cell Systems, vol.7, pp.482-495, 2018. ,
2017. hnRNPK recruits PCGF3/5-PRC1 to the xist RNA B-Repeat to establish Polycomb-Mediated chromosomal silencing, Molecular Cell, vol.68, pp.955-969 ,
Copper-Catalyzed Azide-Alkyne click chemistry for bioconjugation, Current Protocols in Chemical Biology, vol.3, pp.153-162, 2011. ,
Transcriptional regulators compete with nucleosomes Post-replication, Cell, vol.165, pp.580-592, 2016. ,
Objective criteria for the evaluation of clustering methods, Journal of the American Statistical Association, vol.66, pp.846-850, 1971. ,
Gaussian Processes for Machine Learning, 2006. ,
Lagging-strand replication shapes the mutational landscape of the genome, Nature, vol.518, pp.502-506, 2015. ,
Chromatin domains rich in inheritance, Science, vol.361, pp.33-34, 2018. ,
Global mitotic phosphorylation of C 2 H 2 zinc finger protein Linker peptides, Cell Cycle, vol.10, pp.3327-3336, 2011. ,
Mitotic phosphorylation of CCCTC-binding factor (CTCF) reduces its DNA binding activity, FEBS Open Bio, vol.7, pp.397-404, 2017. ,
A possible role of Drosophila CTCF in Mitotic bookmarking and maintaining chromatin domains during the cell cycle, Biological Research, vol.48, p.27, 2015. ,
Analysis of protein dynamics at active, stalled, and collapsed replication forks, Genes & Development, vol.25, pp.1320-1327, 2011. ,
Intrinsic coupling of lagging-strand synthesis to chromatin assembly, Nature, vol.483, pp.434-438, 2012. ,
Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming, Cell, vol.161, pp.555-568, 2015. ,
Cycling through developmental decisions: how cell cycle dynamics control pluripotency, differentiation and reprogramming, Development, vol.143, pp.4301-4311, 2016. ,
Transcription factors: from enhancer binding to developmental control, Nature Reviews Genetics, vol.13, pp.613-626, 2012. ,
Transcription restart establishes chromatin accessibility after DNA replication, Molecular Cell, vol.75, pp.408-414, 2019. ,
Genome-wide nucleosome positioning during embryonic stem cell development, Nature Structural & Molecular Biology, vol.19, pp.1185-1192, 2012. ,
Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development, Genome Research, vol.24, pp.1285-1295, 2014. ,
A stable mode of bookmarking by TBP recruits RNA polymerase II to mitotic chromosomes, vol.7, p.35621, 2018. ,
Variational learning of inducing variables in sparse gaussian processes, Proceedings of Machine Learning Research, vol.5, pp.567-574, 2009. ,
NucTools: analysis of chromatin feature occupancy profiles from highthroughput sequencing data, BMC Genomics, vol.18, p.158, 2017. ,
Determinants of nucleosome organization in primary human cells, Nature, vol.474, pp.516-520, 2011. ,
Dynamic regulation of transcriptional states by chromatin and transcription factors, Nature Reviews Genetics, vol.15, pp.69-81, 2014. ,
Two distinct pathways remove mammalian cohesin from chromosome arms in Prophase and from centromeres in anaphase, Cell, vol.103, pp.399-410, 2000. ,
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors, Genome Research, vol.22, pp.1798-1812, 2012. ,
The Drosophila RAD21 cohesin persists at the centromere region in mitosis, Current Biology, vol.10, pp.1463-1466, 2000. ,
The chromatin remodelling enzymes SNF2H and SNF2L position nucleosomes adjacent to CTCF and other transcription factors, PLOS Genetics, vol.12, p.1005940, 2016. ,
Pioneer transcription factors: establishing competence for gene expression, Genes & Development, vol.25, pp.2227-2241, 2011. ,
, Nucleic Acids Research, vol.46, pp.754-761, 2018.
Re-configuration of chromatin structure during the Mitosis-G1 phase transition, 2019. ,
VERSE: a versatile and efficient RNA-Seq read counting tool, 2016. ,