CHROMATIN ========= 1) structure, histones, nucleosomes, genome compaction Venkatesh and Workman 2015 (nucleosome structure, histone variants, histone turnover and effect of histone turnover/echange on gene expression) Henikoff and Smith 2015 (nucleosome structure, histones, histone variants, DNA compaction by histones) Jolman and Taipale book 2011 chapter 11.5 (nucleosome act as regulator for gene expression) 2) nucleosome positioning, statistical positioning, sequence positioning Jiang and Pugh 2009 (nucleosome positioning, statistical positioning, rotational positioning, structure and function of NDR, nucleosome and TF binding site / control of DNA access) Trifonov 2011 (nucleosome DNA sequence preferences) 3) measuring nucleosome occupancy (MNase-seq) Voong et al 2017 (review about MNase-seq, speak of the assay and its limitations) Schones et al 2008 (original description of MNase-seq) Gaffney et al 2012 (paired-end MNase-seq) briefly say that ATAC-seq can also map nucleosome (Buenrostro et al 2013 (paired-ended ATAC-seq can unravel nucleosomes)) but leave more precise description for DGF part Tsompana et al 2014 (chromatin accessibility assay (MNase-seq), DNase-seq, ATAC-seq, MNase-seq experimentally difficult) 4) histone PTMs, euchromatin, heterochromatin, TAD, transcription Kouzarides 2007 (histone PTM, functional consequences, readers, writters, etc) Hyun et al 2017 (histone PTMs, reader/writer/erasers, functions) Längst and Manelyte 2015 (chromatin readers only) Losada 2014 (cohesin complex functions, DNA looping, effect on gene expression) Ong and Corces 2014 (about CTCF, its functions in TAD, effect on gene expression) Ghirlando and Felsenfeld 2016 (functions of CTCF and cohesin in looping and how loops are made) Voss and Hager 2014 (interaction chromatin/nucleosomes with TF and impact on gene expression) Bart and Imhof 2010 (histone code, where are PTMs) Bonev and Cavalli 2016 (TAD / 3D genome structure, how TAD are formed, impact on gene expression) 5) regulatory regions (TF binding, NDR, open chromatin) Zhou et al 2001 (histone PTMs, their link with expression, TSS/enhaner/insulator PTMs, link with gene expression, chromatin domains, etc) Van Loo and Marynen 2009 (computational CRM prediction method, can use PWMs) Jiang and Pugh 2009 (nucleosome positioning, statistical positioning, rotational positioning, structure and function of NDR, nucleosome and TF binding site / control of DNA access) Cairn 2009 (about nucleosome organization at promoters, constitutive promoters and inducible promoters architecture) Heinz et al 2015 (enhancers classe features (silence, poised, active), how enhancers are selected during development by lineage determinant TF (pioneer), how enhancers are selected by signal dependent TF, enhancer function for gene expression, 3D chromatin looping) Shlyueva et al 2014 (list the features of enhancers by discussing enhancer prediction from sequence/histone PTM/chromatin accessibility/interaction with promoters) 7) DGF / DNase-seq / ATAC-seq, footprint Tsompana et al 2014 (chromatin accessibility assay (MNase-seq), DNase-seq, ATAC-seq) 8) pioneering TF Zaret and Carroll 2011 (pioneer TF, nucleosome binding and chromatin to establish gene expression) Iwafuchi-Doi and Zaret 2014 (pioneer TF, nucleosome binding and chromatin opening, direct cell conversions, pioneer at enhancers) Heinz et al 2015 (enhancers classe features (silence, poised, active), how enhancers are selected during development/pioneer TF) Jolma and Taipale book 2011 chapter 11.4 (some TFs such as FoxA1 can bind nucleosomal DNA and open chromatin alone) TRANSCRIPTION FACTOR ==================== 1) About transcription factors Jolman and Taipale book 2011 chapter 3 2) The chromatin affects TF binding 3) Pioneer TF Already done 3) Modelling sequence specificity Stormo and Fields 1998 () Stormo 2000 () Stormo and Zhao 2010 () specificity and affinity definitions probability matrix, PWM (positional independance assomption) constructing a matrix from aligned sequences constructing a matrix from unaligned sequences (lawrence and reilly, Hertz et al 1990, Stormo and Hartzell 1989) identifying binding sites in the genome (scanner) TF may have several TF specificites : Badis et al 2009 long lived controversy about independent contribution : Man and Stormo 2001, Bulyk et al 2002, Benos et al 2002, Zhao and Stormo 2011 references to HOCOMOCO and JASPAR databases that offers collections of models 4) TF co-binding 5) Measuring TF binding in vivo 6) Measuring TF binding in vitro