report.bib

@article{mccord_chromosome_2020,
	title = {Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function},
	volume = {77},
	issn = {10972765},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1097276519309517},
	doi = {10.1016/j.molcel.2019.12.021},
	shorttitle = {Chromosome Conformation Capture and Beyond},
	pages = {688--708},
	number = {4},
	journaltitle = {Molecular Cell},
	author = {{McCord}, Rachel Patton and Kaplan, Noam and Giorgetti, Luca},
	urldate = {2023-01-13},
	date = {2020-02},
	langid = {english},
	file = {S1097-2765(19)30951-7.pdf:C\:\\Users\\Match\\Zotero\\storage\\R6KHZZ7M\\S1097-2765(19)30951-7.pdf:application/pdf},
}

@article{fudenberg_formation_2016,
	title = {Formation of Chromosomal Domains by Loop Extrusion},
	volume = {15},
	issn = {2211-1247},
	url = {https://www.sciencedirect.com/science/article/pii/S2211124716305307},
	doi = {10.1016/j.celrep.2016.04.085},
	abstract = {Topologically associating domains ({TADs}) are fundamental structural and functional building blocks of human interphase chromosomes, yet the mechanisms of {TAD} formation remain unclear. Here, we propose that loop extrusion underlies {TAD} formation. In this process, cis-acting loop-extruding factors, likely cohesins, form progressively larger loops but stall at {TAD} boundaries due to interactions with boundary proteins, including {CTCF}. Using polymer simulations, we show that this model produces {TADs} and finer-scale features of Hi-C data. Each {TAD} emerges from multiple loops dynamically formed through extrusion, contrary to typical illustrations of single static loops. Loop extrusion both explains diverse experimental observations—including the preferential orientation of {CTCF} motifs, enrichments of architectural proteins at {TAD} boundaries, and boundary deletion experiments—and makes specific predictions for the depletion of {CTCF} versus cohesin. Finally, loop extrusion has potentially far-ranging consequences for processes such as enhancer-promoter interactions, orientation-specific chromosomal looping, and compaction of mitotic chromosomes.},
	pages = {2038--2049},
	number = {9},
	journaltitle = {Cell Reports},
	author = {Fudenberg, Geoffrey and Imakaev, Maxim and Lu, Carolyn and Goloborodko, Anton and Abdennur, Nezar and Mirny, Leonid A.},
	urldate = {2023-01-13},
	date = {2016-05-31},
	langid = {english},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\Match\\Zotero\\storage\\GX42TYJF\\Fudenberg et al. - 2016 - Formation of Chromosomal Domains by Loop Extrusion.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Match\\Zotero\\storage\\I5KCRSG6\\S2211124716305307.html:text/html},
}

@article{mirny_two_2019,
	title = {Two major mechanisms of chromosome organization},
	volume = {58},
	issn = {0955-0674},
	url = {https://www.sciencedirect.com/science/article/pii/S0955067418301601},
	doi = {10.1016/j.ceb.2019.05.001},
	series = {Cell Nucleus},
	abstract = {The spatial organization of chromosomes has long been connected to their polymeric nature and is believed to be important for their biological functions, including the control of interactions between genomic elements, the maintenance of genetic information, and the compaction and safe transfer of chromosomes to cellular progeny. chromosome conformation capture techniques, particularly Hi-C, have provided a comprehensive picture of spatial chromosome organization and revealed new features and elements of chromosome folding. Furthermore, recent advances in microscopy have made it possible to obtain distance maps for extensive regions of chromosomes (Bintu et al., 2018; Nir et al., 2018 [2••,3]), providing information complementary to, and in excellent agreement with, Hi-C maps. Not only has the resolution of both techniques advanced significantly, but new perturbation data generated in the last two years have led to the identification of molecular mechanisms behind large-scale genome organization. Two major mechanisms that have been proposed to govern chromosome organization are (i) the active ({ATP}-dependent) process of loop extrusion by Structural Maintenance of Chromosomes ({SMC}) complexes, and (ii) the spatial compartmentalization of the genome, which is likely mediated by affinity interactions between heterochromatic regions (Falk et al., 2019 [76••]) rather than by {ATP}-dependent processes. Here, we review existing evidence that these two processes operate together to fold chromosomes in interphase and that loop extrusion alone drives mitotic compaction. We discuss possible implications of these mechanisms for chromosome function.},
	pages = {142--152},
	journaltitle = {Current Opinion in Cell Biology},
	author = {Mirny, Leonid A and Imakaev, Maxim and Abdennur, Nezar},
	urldate = {2023-01-13},
	date = {2019-06-01},
	langid = {english},
	file = {Accepted Version:C\:\\Users\\Match\\Zotero\\storage\\VVB54H42\\Mirny et al. - 2019 - Two major mechanisms of chromosome organization.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Match\\Zotero\\storage\\HVEY2T3U\\S0955067418301601.html:text/html},
}

@article{denker_second_2016,
	title = {The second decade of 3C technologies: detailed insights into nuclear organization},
	volume = {30},
	issn = {0890-9369, 1549-5477},
	url = {http://genesdev.cshlp.org/content/30/12/1357},
	doi = {10.1101/gad.281964.116},
	shorttitle = {The second decade of 3C technologies},
	abstract = {The relevance of three-dimensional (3D) genome organization for transcriptional regulation and thereby for cellular fate at large is now widely accepted. Our understanding of the fascinating architecture underlying this function is based on microscopy studies as well as the chromosome conformation capture (3C) methods, which entered the stage at the beginning of the millennium. The first decade of 3C methods rendered unprecedented insights into genome topology. Here, we provide an update of developments and discoveries made over the more recent years. As we discuss, established and newly developed experimental and computational methods enabled identification of novel, functionally important chromosome structures. Regulatory and architectural chromatin loops throughout the genome are being cataloged and compared between cell types, revealing tissue invariant and developmentally dynamic loops. Architectural proteins shaping the genome were disclosed, and their mode of action is being uncovered. We explain how more detailed insights into the 3D genome increase our understanding of transcriptional regulation in development and misregulation in disease. Finally, to help researchers in choosing the approach best tailored for their specific research question, we explain the differences and commonalities between the various 3C-derived methods.},
	pages = {1357--1382},
	number = {12},
	journaltitle = {Genes Dev.},
	author = {Denker, Annette and Laat, Wouter de},
	urldate = {2023-01-13},
	date = {2016-06-15},
	langid = {english},
	pmid = {27340173},
	note = {Company: Cold Spring Harbor Laboratory Press
Distributor: Cold Spring Harbor Laboratory Press
Institution: Cold Spring Harbor Laboratory Press
Label: Cold Spring Harbor Laboratory Press
Publisher: Cold Spring Harbor Lab},
	keywords = {3C technology, 3D genome, chromatin loops, {CTCF}, long-range gene regulation, transcription},
	file = {Full Text PDF:C\:\\Users\\Match\\Zotero\\storage\\UHCBWY59\\Denker and Laat - 2016 - The second decade of 3C technologies detailed ins.pdf:application/pdf},
}

@article{dekker_capturing_2002,
	title = {Capturing Chromosome Conformation},
	volume = {295},
	url = {https://www.science.org/doi/abs/10.1126/science.1067799},
	doi = {10.1126/science.1067799},
	abstract = {We describe an approach to detect the frequency of interaction between any two genomic loci. Generation of a matrix of interaction frequencies between sites on the same or different chromosomes reveals their relative spatial disposition and provides information about the physical properties of the chromatin fiber. This methodology can be applied to the spatial organization of entire genomes in organisms from bacteria to human. Using the yeast Saccharomyces cerevisiae, we could confirm known qualitative features of chromosome organization within the nucleus and dynamic changes in that organization during meiosis. We also analyzed yeast chromosome {III} at the G1stage of the cell cycle. We found that chromatin is highly flexible throughout. Furthermore, functionally distinct {AT}- and {GC}-rich domains were found to exhibit different conformations, and a population-average 3D model of chromosome {III} could be determined. Chromosome {III} emerges as a contorted ring.},
	pages = {1306--1311},
	number = {5558},
	journaltitle = {Science},
	author = {Dekker, Job and Rippe, Karsten and Dekker, Martijn and Kleckner, Nancy},
	urldate = {2023-01-13},
	date = {2002-02-15},
	note = {Publisher: American Association for the Advancement of Science},
}

@article{wit_decade_2012,
	title = {A decade of 3C technologies: insights into nuclear organization},
	volume = {26},
	issn = {0890-9369, 1549-5477},
	url = {http://genesdev.cshlp.org/content/26/1/11},
	doi = {10.1101/gad.179804.111},
	shorttitle = {A decade of 3C technologies},
	abstract = {Over the past 10 years, the development of chromosome conformation capture (3C) technology and the subsequent genomic variants thereof have enabled the analysis of nuclear organization at an unprecedented resolution and throughput. The technology relies on the original and, in hindsight, remarkably simple idea that digestion and religation of fixed chromatin in cells, followed by the quantification of ligation junctions, allows for the determination of {DNA} contact frequencies and insight into chromosome topology. Here we evaluate and compare the current 3C-based methods (including 4C [chromosome conformation capture-on-chip], 5C [chromosome conformation capture carbon copy], {HiC}, and {ChIA}-{PET}), summarize their contribution to our current understanding of genome structure, and discuss how shape influences genome function.},
	pages = {11--24},
	number = {1},
	journaltitle = {Genes Dev.},
	author = {Wit, Elzo de and Laat, Wouter de},
	urldate = {2023-01-13},
	date = {2012-01-01},
	langid = {english},
	pmid = {22215806},
	note = {Company: Cold Spring Harbor Laboratory Press
Distributor: Cold Spring Harbor Laboratory Press
Institution: Cold Spring Harbor Laboratory Press
Label: Cold Spring Harbor Laboratory Press
Publisher: Cold Spring Harbor Lab},
	keywords = {chromosome conformation capture, functional genomics, genome structure, nuclear organization},
	file = {Full Text PDF:C\:\\Users\\Match\\Zotero\\storage\\N9I3I866\\Wit and Laat - 2012 - A decade of 3C technologies insights into nuclear.pdf:application/pdf},
}

@article{li_chromatin_2014,
	title = {Chromatin Interaction Analysis with Paired-End Tag ({ChIA}-{PET}) sequencing technology and application},
	volume = {15},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/1471-2164-15-S12-S11},
	doi = {10.1186/1471-2164-15-S12-S11},
	abstract = {Long-range chromatin interactions play an important role in transcription regulation. Chromatin Interaction Analysis with Paired-End-Tag sequencing ({ChIA}-{PET}) is an emerging technology that has unique advantages in chromatin interaction analysis, and thus provides insight into the study of transcription regulation.},
	pages = {S11},
	number = {12},
	journaltitle = {{BMC} Genomics},
	author = {Li, Guoliang and Cai, Liuyang and Chang, Huidan and Hong, Ping and Zhou, Qiangwei and Kulakova, Ekaterina V. and Kolchanov, Nikolay A. and Ruan, Yijun},
	urldate = {2023-01-13},
	date = {2014-12-19},
	keywords = {Chromatin Interaction, Distal Regulatory Element, Luciferase Reporter Gene Assay, Nonlinear Optimization Model, Transcription Regulation},
	file = {Full Text PDF:C\:\\Users\\Match\\Zotero\\storage\\N5BZZKIC\\Li et al. - 2014 - Chromatin Interaction Analysis with Paired-End Tag.pdf:application/pdf;Snapshot:C\:\\Users\\Match\\Zotero\\storage\\Q9MMINPC\\1471-2164-15-S12-S11.html:text/html},
}

@article{rao_3d_2014,
	title = {A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping},
	volume = {159},
	issn = {0092-8674, 1097-4172},
	url = {https://www.cell.com/cell/abstract/S0092-8674(14)01497-4},
	doi = {10.1016/j.cell.2014.11.021},
	pages = {1665--1680},
	number = {7},
	journaltitle = {Cell},
	author = {Rao, Suhas S. P. and Huntley, Miriam H. and Durand, Neva C. and Stamenova, Elena K. and Bochkov, Ivan D. and Robinson, James T. and Sanborn, Adrian L. and Machol, Ido and Omer, Arina D. and Lander, Eric S. and Aiden, Erez Lieberman},
	urldate = {2023-01-13},
	date = {2014-12-18},
	pmid = {25497547},
	note = {Publisher: Elsevier},
	file = {Full Text PDF:C\:\\Users\\Match\\Zotero\\storage\\ZY5KVN7N\\Rao et al. - 2014 - A 3D Map of the Human Genome at Kilobase Resolutio.pdf:application/pdf},
}

@article{jost_modeling_2014,
	title = {Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains},
	volume = {42},
	issn = {0305-1048},
	url = {https://doi.org/10.1093/nar/gku698},
	doi = {10.1093/nar/gku698},
	shorttitle = {Modeling epigenome folding},
	abstract = {Genomes of eukaryotes are partitioned into domains of functionally distinct chromatin states. These domains are stably inherited across many cell generations and can be remodeled in response to developmental and external cues, hence contributing to the robustness and plasticity of expression patterns and cell phenotypes. Remarkably, recent studies indicate that these 1D epigenomic domains tend to fold into 3D topologically associated domains forming specialized nuclear chromatin compartments. However, the general mechanisms behind such compartmentalization including the contribution of epigenetic regulation remain unclear. Here, we address the question of the coupling between chromatin folding and epigenome. Using polymer physics, we analyze the properties of a block copolymer model that accounts for local epigenomic information. Considering copolymers build from the epigenomic landscape of Drosophila, we observe a very good agreement with the folding patterns observed in chromosome conformation capture experiments. Moreover, this model provides a physical basis for the existence of multistability in epigenome folding at sub-chromosomal scale. We show how experiments are fully consistent with multistable conformations where topologically associated domains of the same epigenomic state interact dynamically with each other. Our approach provides a general framework to improve our understanding of chromatin folding during cell cycle and differentiation and its relation to epigenetics.},
	pages = {9553--9561},
	number = {15},
	journaltitle = {Nucleic Acids Research},
	author = {Jost, Daniel and Carrivain, Pascal and Cavalli, Giacomo and Vaillant, Cédric},
	urldate = {2023-01-13},
	date = {2014-09-02},
	file = {Full Text PDF:C\:\\Users\\Match\\Zotero\\storage\\LEE98DGN\\Jost et al. - 2014 - Modeling epigenome folding formation and dynamics.pdf:application/pdf},
}

@article{benedetti_models_2014,
	title = {Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes},
	volume = {42},
	issn = {0305-1048},
	url = {https://doi.org/10.1093/nar/gkt1353},
	doi = {10.1093/nar/gkt1353},
	abstract = {Understanding the structure of interphase chromosomes is essential to elucidate regulatory mechanisms of gene expression. During recent years, high-throughput {DNA} sequencing expanded the power of chromosome conformation capture (3C) methods that provide information about reciprocal spatial proximity of chromosomal loci. Since 2012, it is known that entire chromatin in interphase chromosomes is organized into regions with strongly increased frequency of internal contacts. These regions, with the average size of ∼1 Mb, were named topological domains. More recent studies demonstrated presence of unconstrained supercoiling in interphase chromosomes. Using Brownian dynamics simulations, we show here that by including supercoiling into models of topological domains one can reproduce and thus provide possible explanations of several experimentally observed characteristics of interphase chromosomes, such as their complex contact maps.},
	pages = {2848--2855},
	number = {5},
	journaltitle = {Nucleic Acids Research},
	author = {Benedetti, Fabrizio and Dorier, Julien and Burnier, Yannis and Stasiak, Andrzej},
	urldate = {2023-01-13},
	date = {2014-03-01},
	file = {Full Text PDF:C\:\\Users\\Match\\Zotero\\storage\\DKGQBPFC\\Benedetti et al. - 2014 - Models that include supercoiling of topological do.pdf:application/pdf},
}

@article{kim_human_2019,
	title = {Human cohesin compacts {DNA} by loop extrusion},
	volume = {366},
	url = {https://www.science.org/doi/10.1126/science.aaz4475},
	doi = {10.1126/science.aaz4475},
	abstract = {Cohesin is a chromosome-bound, multisubunit adenosine triphosphatase complex. After loading onto chromosomes, it generates loops to regulate chromosome functions. It has been suggested that cohesin organizes the genome through loop extrusion, but direct evidence is lacking. Here, we used single-molecule imaging to show that the recombinant human cohesin-{NIPBL} complex compacts both naked and nucleosome-bound {DNA} by extruding {DNA} loops. {DNA} compaction by cohesin requires adenosine triphosphate ({ATP}) hydrolysis and is force sensitive. This compaction is processive over tens of kilobases at an average rate of 0.5 kilobases per second. Compaction of double-tethered {DNA} suggests that a cohesin dimer extrudes {DNA} loops bidirectionally. Our results establish cohesin-{NIPBL} as an {ATP}-driven molecular machine capable of loop extrusion.},
	pages = {1345--1349},
	number = {6471},
	journaltitle = {Science},
	author = {Kim, Yoori and Shi, Zhubing and Zhang, Hongshan and Finkelstein, Ilya J. and Yu, Hongtao},
	urldate = {2023-01-13},
	date = {2019-12-13},
	note = {Publisher: American Association for the Advancement of Science},
	file = {Accepted Version:C\:\\Users\\Match\\Zotero\\storage\\DE25YEYR\\Kim et al. - 2019 - Human cohesin compacts DNA by loop extrusion.pdf:application/pdf},
}