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The three dimensional organization of the nucleus

Guest Editors: Peter Fraser and David Gilbert

Recent advances in microscopy and the chromosome conformation capture technology are improving our knowledge of how spatial arrangement in the nucleus affects genome function.

Genome Biology highlights these advances with a range of Research, Method and Review articles presenting methods for detecting and analyzing 3D interactions, and discussing insights derived from Hi-C, fluorescence microscopy and other methods.

  1. Content type: METHOD

    Chromosome conformation capture methods are being increasingly used to study three-dimensional genome architecture in multiple cell types and species. An important challenge is to examine changes in three-dime...

    Authors: Alireza Fotuhi Siahpirani, Ferhat Ay and Sushmita Roy

    Citation: Genome Biology 2016 17:114

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  2. Content type: METHOD

    The three-dimensional (3D) organization of chromosomes can be probed using methods like Capture-C. However, it is unclear how such population-level data relate to the organization within a single cell, and the...

    Authors: Chris A. Brackley, Jill M. Brown, Dominic Waithe, Christian Babbs, James Davies, Jim R. Hughes, Veronica J. Buckle and Davide Marenduzzo

    Citation: Genome Biology 2016 17:59

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  3. Content type: Research

    Linker histone H1 is a core chromatin component that binds to nucleosome core particles and the linker DNA between nucleosomes. It has been implicated in chromatin compaction and gene regulation and is anticip...

    Authors: Geert Geeven, Yun Zhu, Byung Ju Kim, Boris A. Bartholdy, Seung-Min Yang, Todd S. Macfarlan, Wesley D. Gifford, Samuel L. Pfaff, Marjon J. A. M. Verstegen, Hugo Pinto, Marit W. Vermunt, Menno P. Creyghton, Patrick J. Wijchers, John A. Stamatoyannopoulos, Arthur I. Skoultchi and Wouter de Laat

    Citation: Genome Biology 2015 16:289

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  4. Content type: Method

    Various efforts have been made to elucidate the cooperating proteins involved in maintaining chromatin interactions; however, many are still unknown. Here, we present 3CPET, a tool based on a non-parametric Ba...

    Authors: Mohamed Nadhir Djekidel, Zhengyu Liang, Qi Wang, Zhirui Hu, Guipeng Li, Yang Chen and Michael Q. Zhang

    Citation: Genome Biology 2015 16:288

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  5. Content type: Software

    HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs quality controls and generates in...

    Authors: Nicolas Servant, Nelle Varoquaux, Bryan R. Lajoie, Eric Viara, Chong-Jian Chen, Jean-Philippe Vert, Edith Heard, Job Dekker and Emmanuel Barillot

    Citation: Genome Biology 2015 16:259

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  6. Content type: Research

    The impact of signal-dependent transcription factors, such as glucocorticoid receptor and nuclear factor kappa-b, on the three-dimensional organization of chromatin remains a topic of discussion. The possible ...

    Authors: Tatyana Kuznetsova, Shuang-Yin Wang, Nagesha A. Rao, Amit Mandoli, Joost H. A. Martens, Nils Rother, Aafke Aartse, Laszlo Groh, Eva M. Janssen-Megens, Guoliang Li, Yijun Ruan, Colin Logie and Hendrik G. Stunnenberg

    Citation: Genome Biology 2015 16:264

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  7. Content type: Research

    Cells detect and adapt to hypoxic and nutritional stress through immediate transcriptional, translational and metabolic responses. The environmental effects of ischemia on chromatin nanostructure were investig...

    Authors: Ina Kirmes, Aleksander Szczurek, Kirti Prakash, Iryna Charapitsa, Christina Heiser, Michael Musheev, Florian Schock, Karolina Fornalczyk, Dongyu Ma, Udo Birk, Christoph Cremer and George Reid

    Citation: Genome Biology 2015 16:246

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  8. Content type: Software

    The chromatin interaction assays 5C and HiC have advanced our understanding of genomic spatial organization, but analysis approaches for these data are limited by usability and flexibility. The HiFive tool sui...

    Authors: Michael EG Sauria, Jennifer E. Phillips-Cremins, Victor G. Corces and James Taylor

    Citation: Genome Biology 2015 16:237

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  9. Content type: Research

    X-chromosome inactivation is a striking example of epigenetic silencing in which expression of the long non-coding RNA XIST initiates the heterochromatinization and silencing of one of the pair of X chromosome...

    Authors: Angela D. Kelsey, Christine Yang, Danny Leung, Jakub Minks, Thomas Dixon-McDougall, Sarah E.L. Baldry, Aaron B. Bogutz, Louis Lefebvre and Carolyn J. Brown

    Citation: Genome Biology 2015 16:208

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  10. Content type: Research

    Higher-order chromatin structure is often perturbed in cancer and other pathological states. Although several genetic and epigenetic differences have been charted between normal and breast cancer tissues, chan...

    Authors: A. Rasim Barutcu, Bryan R. Lajoie, Rachel P. McCord, Coralee E. Tye, Deli Hong, Terri L. Messier, Gillian Browne, Andre J. van Wijnen, Jane B. Lian, Janet L. Stein, Job Dekker, Anthony N. Imbalzano and Gary S. Stein

    Citation: Genome Biology 2015 16:214

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  11. Content type: Research

    Pluripotent embryonic stem cells (ESCs) have the unique ability to differentiate into every cell type and to self-renew. These characteristics correlate with a distinct nuclear architecture, epigenetic signatu...

    Authors: Anna Mattout, Yair Aaronson, Badi Sri Sailaja, Edupuganti V. Raghu Ram, Arigela Harikumar, Jan-Philipp Mallm, Kae Hwan Sim, Malka Nissim-Rafinia, Emmanuelle Supper, Prim B. Singh, Siu Kwan Sze, Susan M. Gasser, Karsten Rippe and Eran Meshorer

    Citation: Genome Biology 2015 16:213

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  12. Content type: Research

    Previously, a role was demonstrated for transcription in the acquisition of DNA methylation at imprinted control regions in oocytes. Definition of the oocyte DNA methylome by whole genome approaches revealed t...

    Authors: Lenka Veselovska, Sebastien A. Smallwood, Heba Saadeh, Kathleen R. Stewart, Felix Krueger, Stéphanie Maupetit-Méhouas, Philippe Arnaud, Shin-ichi Tomizawa, Simon Andrews and Gavin Kelsey

    Citation: Genome Biology 2015 16:209

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    The Erratum to this article has been published in Genome Biology 2015 16:271

  13. Content type: Research

    The spatiotemporal behavior of chromatin is an important control mechanism of genomic function. Studies in Saccharomyces cerevisiae have broadly contributed to demonstrate the functional importance of nuclear org...

    Authors: Micol Guidi, Myriam Ruault, Martial Marbouty, Isabelle Loïodice, Axel Cournac, Cyrille Billaudeau, Antoine Hocher, Julien Mozziconacci, Romain Koszul and Angela Taddei

    Citation: Genome Biology 2015 16:206

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  14. Content type: Software

    Metazoan genomic material is folded into stable non-randomly arranged chromosomal structures that are tightly associated with transcriptional regulation and DNA replication. Various factors including regulator...

    Authors: Kadir Caner Akdemir and Lynda Chin

    Citation: Genome Biology 2015 16:198

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  15. Content type: Research

    Chromosome conformation capture and various derivative methods such as 4C, 5C and Hi-C have emerged as standard tools to analyze the three-dimensional organization of the genome in the nucleus. These methods e...

    Authors: Takashi Nagano, Csilla Várnai, Stefan Schoenfelder, Biola-Maria Javierre, Steven W. Wingett and Peter Fraser

    Citation: Genome Biology 2015 16:175

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  16. Content type: Opinion

    Methods that use high-throughput sequencing have begun to reveal features of the three-dimensional structure of genomes at a resolution that goes far beyond that of traditional microscopy. Integration of these...

    Authors: Chang Liu and Detlef Weigel

    Citation: Genome Biology 2015 16:170

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  17. Content type: Research highlight

    Single-cell ATAC-seq detects open chromatin in individual cells. Currently data are sparse, but combining information from many single cells can identify determinants of cell-to-cell chromatin variation.

    Authors: Sebastian Pott and Jason D. Lieb

    Citation: Genome Biology 2015 16:172

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  18. Content type: Review

    In female mammals, one of the two X chromosomes in each cell is transcriptionally silenced in order to achieve dosage compensation between the genders in a process called X chromosome inactivation. The master ...

    Authors: Andrea Cerase, Greta Pintacuda, Anna Tattermusch and Philip Avner

    Citation: Genome Biology 2015 16:166

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  19. Content type: Research

    CTCF and BORIS (CTCFL), two paralogous mammalian proteins sharing nearly identical DNA binding domains, are thought to function in a mutually exclusive manner in DNA binding and transcriptional regulation.

    Authors: Elena M. Pugacheva, Samuel Rivero-Hinojosa, Celso A. Espinoza, Claudia Fabiola Méndez-Catalá, Sungyun Kang, Teruhiko Suzuki, Natsuki Kosaka-Suzuki, Susan Robinson, Vijayaraj Nagarajan, Zhen Ye, Abdelhalim Boukaba, John E. J. Rasko, Alexander V. Strunnikov, Dmitri Loukinov, Bing Ren and Victor V. Lobanenkov

    Citation: Genome Biology 2015 16:161

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  20. Content type: Method

    Genome-wide mapping of three dimensional chromatin organization is an important yet technically challenging task. To aid experimental effort and to understand the determinants of long-range chromatin interacti...

    Authors: Jialiang Huang, Eugenio Marco, Luca Pinello and Guo-Cheng Yuan

    Citation: Genome Biology 2015 16:162

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  21. Content type: Research

    In mammals, one of the female X chromosomes and all imprinted genes are expressed exclusively from a single allele in somatic cells. To evaluate structural changes associated with allelic silencing, we have ap...

    Authors: Xinxian Deng, Wenxiu Ma, Vijay Ramani, Andrew Hill, Fan Yang, Ferhat Ay, Joel B. Berletch, Carl Anthony Blau, Jay Shendure, Zhijun Duan, William S. Noble and Christine M. Disteche

    Citation: Genome Biology 2015 16:152

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  22. Content type: Research

    Epigenetic changes are being increasingly recognized as a prominent feature of cancer. This occurs not only at individual genes, but also over larger chromosomal domains. To investigate this, we set out to ide...

    Authors: Sehrish Rafique, Jeremy S. Thomas, Duncan Sproul and Wendy A. Bickmore

    Citation: Genome Biology 2015 16:145

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  23. Content type: Research

    During early embryonic development, one of the two X chromosomes in mammalian female cells is inactivated to compensate for a potential imbalance in transcript levels with male cells, which contain a single X ...

    Authors: Hendrik Marks, Hindrik H. D. Kerstens, Tahsin Stefan Barakat, Erik Splinter, René A. M. Dirks, Guido van Mierlo, Onkar Joshi, Shuang-Yin Wang, Tomas Babak, Cornelis A. Albers, Tüzer Kalkan, Austin Smith, Alice Jouneau, Wouter de Laat, Joost Gribnau and Hendrik G. Stunnenberg

    Citation: Genome Biology 2015 16:149

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    The Erratum to this article has been published in Genome Biology 2016 17:22

  24. Content type: Method

    Although the locations of promoters and enhancers have been identified in several cell types, we still have limited information on their connectivity. We developed HiCap, which combines a 4-cutter restriction ...

    Authors: Pelin Sahlén, Ilgar Abdullayev, Daniel Ramsköld, Liudmila Matskova, Nemanja Rilakovic, Britta Lötstedt, Thomas J. Albert, Joakim Lundeberg and Rickard Sandberg

    Citation: Genome Biology 2015 16:156

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