modify some headers and rebuild

01-intro.Rmd

@@ -158,7 +158,7 @@ Importantly, enhancer-promoter interactions seem to be mostly constrained within
 
 Altogether, there is accumulating evidence that TADs are fundamental units of chromosome organization [@Dixon2016]
 
-### Hierarchy of domain-like structures across genomic-length scales
+### Hierarchy of domain structures across genomic length scales
 
 Globally, higher-order interactions between different TADs leads to a tree-like hierarchy of TADs and meta-TADs across genomic scales up to the range of entire chromosomes [@Fraser2015].
 Similar to A/B-compartments, these tree structures correlate with epigenetic marks and expression changes during cell differentiation [@Fraser2015].
@@ -233,7 +233,7 @@ TADs form clusters by their epigenomic type into A/B compartments, and coalescen
 Proximity ligation experiments, like Hi-C, measure contact frequencies as average over millions of cells in the sample. Therefore, identified contacts might be present only in a subset of cells. Furthermore, specific contacts could be very dynamic over short time-scales in individual cells.
 While recent methodological advances allow studying of variation across individual cells (discussed in section \@ref(single-cell)), initial studies focused on the differences of genome folding across cell cycle and cell differentiation. 
 
-### Dynamics across cell cycle
+### Dynamics across the cell cycle
 
 It is important to keep in mind how chromosome folding changes during cell division. Spatial organization is generally studied in non-synchronous cells, of which interphase cells make up the biggest proportion [@Bouwman2015].
 In interphase, chromosomes are decondensed and hierarchically organized into territories, compartments, and TADs as described above. 

bib/PhDflt.bib

@@ -1041,23 +1041,6 @@ @article{Fullwood2009
 volume = {462},
 year = {2009}
 }
-@article{Hnisz2017,
-abstract = {Phase-separated multi-molecular assemblies provide a general regulatory mechanism to compartmentalize biochemical reactions within cells. We propose that a phase separation model explains established and recently described features of transcriptional control. These features include the formation of super-enhancers, the sensitivity of super-enhancers to perturbation, the transcriptional bursting patterns of enhancers, and the ability of an enhancer to produce simultaneous activation at multiple genes. This model provides a conceptual framework to further explore principles of gene control in mammals.},
-author = {Hnisz, Denes and Shrinivas, Krishna and Young, Richard A. and Chakraborty, Arup K. and Sharp, Phillip A.},
-doi = {10.1016/j.cell.2017.02.007},
-file = {:home/ibnsalem/Mendeley/Hnisz et al. - 2017 - A Phase Separation Model for Transcriptional Control.pdf:pdf},
-issn = {10974172},
-journal = {Cell},
-keywords = {bursting,co-operativity,enhancer,gene control,nuclear body,phase separation,super-enhancer,transcription,transcriptional burst},
-number = {1},
-pages = {13--23},
-pmid = {28340338},
-publisher = {Elsevier Inc.},
-title = {{A Phase Separation Model for Transcriptional Control}},
-url = {http://dx.doi.org/10.1016/j.cell.2017.02.007},
-volume = {169},
-year = {2017}
-}
 @article{Barrington2017,
 annote = {NULL},
 author = {Barrington, Christopher and Finn, Ronald and Hadjur, Suzana},
@@ -8260,22 +8243,6 @@ @article{Pevzner2003
 volume = {100},
 year = {2003}
 }
-@article{Aranda2015,
-abstract = {The Polycomb group (PcG) of proteins defines a subset of factors that physically associate and function to maintain the positional identity of cells from the embryo to adult stages. PcG has long been considered a paradigmatic model for epigenetic maintenance of gene transcription programs. Despite intensive research efforts to unveil the molecular mechanisms of action of PcG proteins, several fundamental questions remain unresolved: How many different PcG complexes exist in mammalian cells? How are PcG complexes targeted to specific loci? How does PcG regulate transcription? In this review, we discuss the diversity of PcG complexes in mammalian cells, examine newly identified modes of recruitment to chromatin, and highlight the latest insights into the molecular mechanisms underlying the function of PcGs in transcription regulation and three-dimensional chromatin conformation.},
-author = {Aranda, S. and Mas, G. and {Di Croce}, L.},
-doi = {10.1126/sciadv.1500737},
-file = {:home/ibnsalem/Mendeley/Aranda, Mas, Di Croce - 2015 - Regulation of gene transcription by Polycomb proteins.pdf:pdf},
-issn = {2375-2548},
-journal = {Science Advances},
-month = {dec},
-number = {11},
-pages = {e1500737--e1500737},
-publisher = {American Association for the Advancement of Science},
-title = {{Regulation of gene transcription by Polycomb proteins}},
-url = {http://advances.sciencemag.org/cgi/doi/10.1126/sciadv.1500737},
-volume = {1},
-year = {2015}
-}
 @article{Giorgio2015,
 author = {Giorgio, Elisa and Robyr, Daniel and Spielmann, Malte and Ferrero, Enza and {Di Gregorio}, Eleonora and Imperiale, Daniele and Vaula, Giovanna and Stamoulis, Georgios and Santoni, Federico and Atzori, Cristiana and Gasparini, Laura and Ferrera, Denise and Canale, Claudio and Guipponi, Michel and Pennacchio, Len A. and Antonarakis, Stylianos E. and Brussino, Alessandro and Brusco, Alfredo},
 doi = {10.1093/hmg/ddv065},
@@ -8595,20 +8562,6 @@ @article{Schreiber2017
 title = {{Nucleotide sequence and DNaseI sensitivity are predictive of 3D chromatin architecture}},
 year = {2017}
 }
-@article{Nagano2017,
-author = {Nagano, Takashi and Lubling, Yaniv and V{\'{a}}rnai, Csilla and Dudley, Carmel and Leung, Wing and Baran, Yael and Mendelson-cohen, Netta},
-doi = {10.1038/nature23001},
-file = {:home/ibnsalem/Mendeley/Nagano et al. - 2017 - Cell-cycle dynamics of chromosomal organization at single-cell resolution.pdf:pdf},
-issn = {0028-0836},
-journal = {Nature Publishing Group},
-number = {7661},
-pages = {61--67},
-publisher = {Nature Publishing Group},
-title = {{Cell-cycle dynamics of chromosomal organization at single-cell resolution}},
-url = {http://dx.doi.org/10.1038/nature23001},
-volume = {547},
-year = {2017}
-}
 @article{Hnisz2016a,
 author = {Hnisz, Denes and Day, Daniel S. and Young, Richard A.},
 doi = {10.1016/j.cell.2016.10.024},

bib/PhDfltClean.bib

@@ -63,18 +63,6 @@ @article{Anger2014
  year = {2014}
 }
 
-@article{Aranda2015,
- author = {Aranda, S. and Mas, G. and {Di Croce}, L.},
- doi = {10.1126/sciadv.1500737},
- journal = {Science Advances},
- number = {11},
- pages = {e1500737--e1500737},
- publisher = {American Association for the Advancement of Science},
- title = {Regulation of gene transcription by Polycomb proteins},
- volume = {1},
- year = {2015}
-}
-
 @article{GTExConsortium2015,
  author = {Ardlie, Kristin G. and DeLuca, David S. and Segr{\`{e}}, Ayellet V. and Sullivan, Timothy J. and Young, Taylor R. and Gelfand, Ellen T. and Trowbridge, Casandra A. and Maller, Julian B. and Tukiainen, Taru and Lek, Monkol and Ward, Lucas D. and Kheradpour, Pouya and Iriarte, Benjamin and Meng, Yan and Palmer, Cameron D. and Esko, T{\~{o}}nu and Winckler, Wendy and Hirschhorn, Joel N. and Kellis, Manolis and others},
  doi = {10.1126/science.1262110},
@@ -1500,18 +1488,6 @@ @article{Hnisz2016a
  year = {2016}
 }
 
-@article{Hnisz2017,
- author = {Hnisz, Denes and Shrinivas, Krishna and Young, Richard A. and Chakraborty, Arup K. and Sharp, Phillip A.},
- doi = {10.1016/j.cell.2017.02.007},
- journal = {Cell},
- number = {1},
- pages = {13--23},
- publisher = {Elsevier Inc.},
- title = {A Phase Separation Model for Transcriptional Control},
- volume = {169},
- year = {2017}
-}
-
 @article{Hnisz2016,
  author = {Hnisz, Denes and Weintraub, Abraham S and Day, Daniel S and Valton, Anne-laure and Bak, Rasmus O and Li, Charles H and Goldmann, Johanna and Lajoie, Bryan R and Fan, Zi Peng and Sigova, Alla A and Reddy, Jessica and Borges-Rivera, Diego and Lee, Tong Ihn and Jaenisch, Rudolf and Porteus, Matthew H and Dekker, Job and Young, Richard A},
  doi = {10.1126/science.aad9024},
@@ -2361,18 +2337,6 @@ @article{Nagano2013
  year = {2013}
 }
 
-@article{Nagano2017,
- author = {Nagano, Takashi and Lubling, Yaniv and V{\'{a}}rnai, Csilla and Dudley, Carmel and Leung, Wing and Baran, Yael and Mendelson-cohen, Netta},
- doi = {10.1038/nature23001},
- journal = {Nature Publishing Group},
- number = {7661},
- pages = {61--67},
- publisher = {Nature Publishing Group},
- title = {Cell-cycle dynamics of chromosomal organization at single-cell resolution},
- volume = {547},
- year = {2017}
-}
-
 @article{Nagy2016,
  author = {Nagy, Gergely and Czipa, Erik and Steiner, L{\'{a}}szl{\'{o}} and Nagy, Tibor and Pongor, S{\'{a}}ndor and Nagy, L{\'{a}}szl{\'{o}} and Barta, Endre},
  doi = {10.1186/s12864-016-2940-7},

docs/1-1-regulation-of-expression.html

@@ -78,12 +78,12 @@
 <li class="chapter" data-level="1.4.1" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#chromosomal-territories-and-inter-chromosomal-contacts"><i class="fa fa-check"></i><b>1.4.1</b> Chromosomal territories and inter-chromosomal contacts</a></li>
 <li class="chapter" data-level="1.4.2" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#ab-compartments"><i class="fa fa-check"></i><b>1.4.2</b> A/B compartments</a></li>
 <li class="chapter" data-level="1.4.3" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#topologically-associating-domains-tads"><i class="fa fa-check"></i><b>1.4.3</b> Topologically associating domains (TADs)</a></li>
-<li class="chapter" data-level="1.4.4" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#hierarchy-of-domain-like-structures-across-genomic-length-scales"><i class="fa fa-check"></i><b>1.4.4</b> Hierarchy of domain-like structures across genomic-length scales</a></li>
+<li class="chapter" data-level="1.4.4" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#hierarchy-of-domain-structures-across-genomic-length-scales"><i class="fa fa-check"></i><b>1.4.4</b> Hierarchy of domain structures across genomic length scales</a></li>
 <li class="chapter" data-level="1.4.5" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#chromatin-looping-interactions"><i class="fa fa-check"></i><b>1.4.5</b> Chromatin looping interactions</a></li>
 <li class="chapter" data-level="1.4.6" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#loop-mechanism"><i class="fa fa-check"></i><b>1.4.6</b> TAD and loop formation by architectural proteins</a></li>
 </ul></li>
 <li class="chapter" data-level="1.5" data-path="1-5-dynamics-of-chromatin-structure.html"><a href="1-5-dynamics-of-chromatin-structure.html"><i class="fa fa-check"></i><b>1.5</b> Dynamics of chromatin structure</a><ul>
-<li class="chapter" data-level="1.5.1" data-path="1-5-dynamics-of-chromatin-structure.html"><a href="1-5-dynamics-of-chromatin-structure.html#dynamics-across-cell-cycle"><i class="fa fa-check"></i><b>1.5.1</b> Dynamics across cell cycle</a></li>
+<li class="chapter" data-level="1.5.1" data-path="1-5-dynamics-of-chromatin-structure.html"><a href="1-5-dynamics-of-chromatin-structure.html#dynamics-across-the-cell-cycle"><i class="fa fa-check"></i><b>1.5.1</b> Dynamics across the cell cycle</a></li>
 <li class="chapter" data-level="1.5.2" data-path="1-5-dynamics-of-chromatin-structure.html"><a href="1-5-dynamics-of-chromatin-structure.html#dynamics-across-cell-types-and-differntiation"><i class="fa fa-check"></i><b>1.5.2</b> Dynamics across cell types and differntiation</a></li>
 </ul></li>
 <li class="chapter" data-level="1.6" data-path="1-6-evolution-of-chromatin-organization.html"><a href="1-6-evolution-of-chromatin-organization.html"><i class="fa fa-check"></i><b>1.6</b> Evolution of chromatin organization</a></li>

docs/1-2-distal-regulation-by-enhancers.html

@@ -78,12 +78,12 @@
 <li class="chapter" data-level="1.4.1" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#chromosomal-territories-and-inter-chromosomal-contacts"><i class="fa fa-check"></i><b>1.4.1</b> Chromosomal territories and inter-chromosomal contacts</a></li>
 <li class="chapter" data-level="1.4.2" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#ab-compartments"><i class="fa fa-check"></i><b>1.4.2</b> A/B compartments</a></li>
 <li class="chapter" data-level="1.4.3" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#topologically-associating-domains-tads"><i class="fa fa-check"></i><b>1.4.3</b> Topologically associating domains (TADs)</a></li>
-<li class="chapter" data-level="1.4.4" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#hierarchy-of-domain-like-structures-across-genomic-length-scales"><i class="fa fa-check"></i><b>1.4.4</b> Hierarchy of domain-like structures across genomic-length scales</a></li>
+<li class="chapter" data-level="1.4.4" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#hierarchy-of-domain-structures-across-genomic-length-scales"><i class="fa fa-check"></i><b>1.4.4</b> Hierarchy of domain structures across genomic length scales</a></li>
 <li class="chapter" data-level="1.4.5" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#chromatin-looping-interactions"><i class="fa fa-check"></i><b>1.4.5</b> Chromatin looping interactions</a></li>
 <li class="chapter" data-level="1.4.6" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#loop-mechanism"><i class="fa fa-check"></i><b>1.4.6</b> TAD and loop formation by architectural proteins</a></li>
 </ul></li>
 <li class="chapter" data-level="1.5" data-path="1-5-dynamics-of-chromatin-structure.html"><a href="1-5-dynamics-of-chromatin-structure.html"><i class="fa fa-check"></i><b>1.5</b> Dynamics of chromatin structure</a><ul>
-<li class="chapter" data-level="1.5.1" data-path="1-5-dynamics-of-chromatin-structure.html"><a href="1-5-dynamics-of-chromatin-structure.html#dynamics-across-cell-cycle"><i class="fa fa-check"></i><b>1.5.1</b> Dynamics across cell cycle</a></li>
+<li class="chapter" data-level="1.5.1" data-path="1-5-dynamics-of-chromatin-structure.html"><a href="1-5-dynamics-of-chromatin-structure.html#dynamics-across-the-cell-cycle"><i class="fa fa-check"></i><b>1.5.1</b> Dynamics across the cell cycle</a></li>
 <li class="chapter" data-level="1.5.2" data-path="1-5-dynamics-of-chromatin-structure.html"><a href="1-5-dynamics-of-chromatin-structure.html#dynamics-across-cell-types-and-differntiation"><i class="fa fa-check"></i><b>1.5.2</b> Dynamics across cell types and differntiation</a></li>
 </ul></li>
 <li class="chapter" data-level="1.6" data-path="1-6-evolution-of-chromatin-organization.html"><a href="1-6-evolution-of-chromatin-organization.html"><i class="fa fa-check"></i><b>1.6</b> Evolution of chromatin organization</a></li>

docs/1-3-methods-to-probe-the-3d-chromatin-architecture.html

@@ -78,12 +78,12 @@
 <li class="chapter" data-level="1.4.1" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#chromosomal-territories-and-inter-chromosomal-contacts"><i class="fa fa-check"></i><b>1.4.1</b> Chromosomal territories and inter-chromosomal contacts</a></li>
 <li class="chapter" data-level="1.4.2" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#ab-compartments"><i class="fa fa-check"></i><b>1.4.2</b> A/B compartments</a></li>
 <li class="chapter" data-level="1.4.3" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#topologically-associating-domains-tads"><i class="fa fa-check"></i><b>1.4.3</b> Topologically associating domains (TADs)</a></li>
-<li class="chapter" data-level="1.4.4" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#hierarchy-of-domain-like-structures-across-genomic-length-scales"><i class="fa fa-check"></i><b>1.4.4</b> Hierarchy of domain-like structures across genomic-length scales</a></li>
+<li class="chapter" data-level="1.4.4" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#hierarchy-of-domain-structures-across-genomic-length-scales"><i class="fa fa-check"></i><b>1.4.4</b> Hierarchy of domain structures across genomic length scales</a></li>
 <li class="chapter" data-level="1.4.5" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#chromatin-looping-interactions"><i class="fa fa-check"></i><b>1.4.5</b> Chromatin looping interactions</a></li>
 <li class="chapter" data-level="1.4.6" data-path="1-4-hierarchy-of-chromatin-3d-structure.html"><a href="1-4-hierarchy-of-chromatin-3d-structure.html#loop-mechanism"><i class="fa fa-check"></i><b>1.4.6</b> TAD and loop formation by architectural proteins</a></li>
 </ul></li>
 <li class="chapter" data-level="1.5" data-path="1-5-dynamics-of-chromatin-structure.html"><a href="1-5-dynamics-of-chromatin-structure.html"><i class="fa fa-check"></i><b>1.5</b> Dynamics of chromatin structure</a><ul>
-<li class="chapter" data-level="1.5.1" data-path="1-5-dynamics-of-chromatin-structure.html"><a href="1-5-dynamics-of-chromatin-structure.html#dynamics-across-cell-cycle"><i class="fa fa-check"></i><b>1.5.1</b> Dynamics across cell cycle</a></li>
+<li class="chapter" data-level="1.5.1" data-path="1-5-dynamics-of-chromatin-structure.html"><a href="1-5-dynamics-of-chromatin-structure.html#dynamics-across-the-cell-cycle"><i class="fa fa-check"></i><b>1.5.1</b> Dynamics across the cell cycle</a></li>
 <li class="chapter" data-level="1.5.2" data-path="1-5-dynamics-of-chromatin-structure.html"><a href="1-5-dynamics-of-chromatin-structure.html#dynamics-across-cell-types-and-differntiation"><i class="fa fa-check"></i><b>1.5.2</b> Dynamics across cell types and differntiation</a></li>
 </ul></li>
 <li class="chapter" data-level="1.6" data-path="1-6-evolution-of-chromatin-organization.html"><a href="1-6-evolution-of-chromatin-organization.html"><i class="fa fa-check"></i><b>1.6</b> Evolution of chromatin organization</a></li>