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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. METHOD

    Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models

    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...

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

    Genome Biology 2016 17:59

    Published on: 31 March 2016

  2. Research

    Local compartment changes and regulatory landscape alterations in histone H1-depleted cells

    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...

    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

    Genome Biology 2015 16:289

    Published on: 23 December 2015

  3. Software

    HiC-Pro: an optimized and flexible pipeline for Hi-C data processing

    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...

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

    Genome Biology 2015 16:259

    Published on: 1 December 2015

  4. Research

    Glucocorticoid receptor and nuclear factor kappa-b affect three-dimensional chromatin organization

    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 ...

    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

    Genome Biology 2015 16:264

    Published on: 1 December 2015

  5. Research

    A transient ischemic environment induces reversible compaction of chromatin

    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...

    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

    Genome Biology 2015 16:246

    Published on: 5 November 2015

  6. Software

    HiFive: a tool suite for easy and efficient HiC and 5C data analysis

    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...

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

    Genome Biology 2015 16:237

    Published on: 24 October 2015

  7. Research

    Impact of flanking chromosomal sequences on localization and silencing by the human non-coding RNA XIST

    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...

    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

    Genome Biology 2015 16:208

    Published on: 2 October 2015

  8. Research

    Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells

    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...

    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

    Genome Biology 2015 16:214

    Published on: 28 September 2015

  9. Research

    Heterochromatin Protein 1β (HP1β) has distinct functions and distinct nuclear distribution in pluripotent versus differentiated cells

    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...

    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

    Genome Biology 2015 16:213

    Published on: 28 September 2015

  10. Research

    Deep sequencing and de novo assembly of the mouse oocyte transcriptome define the contribution of transcription to the DNA methylation landscape

    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...

    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

    Genome Biology 2015 16:209

    Published on: 25 September 2015

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

  11. Research

    Spatial reorganization of telomeres in long-lived quiescent cells

    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...

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

    Genome Biology 2015 16:206

    Published on: 23 September 2015

  12. Software

    HiCPlotter integrates genomic data with interaction matrices

    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...

    Kadir Caner Akdemir and Lynda Chin

    Genome Biology 2015 16:198

    Published on: 21 September 2015

  13. Review

    Analysis methods for studying the 3D architecture of the genome

    The rapidly increasing quantity of genome-wide chromosome conformation capture data presents great opportunities and challenges in the computational modeling and interpretation of the three-dimensional genome....

    Ferhat Ay and William S. Noble

    Genome Biology 2015 16:183

    Published on: 2 September 2015

  14. Research

    Comparison of Hi-C results using in-solution versus in-nucleus ligation

    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...

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

    Genome Biology 2015 16:175

    Published on: 26 August 2015

  15. Opinion

    Chromatin in 3D: progress and prospects for plants

    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...

    Chang Liu and Detlef Weigel

    Genome Biology 2015 16:170

    Published on: 21 August 2015

  16. Research highlight

    Single-cell ATAC-seq: strength in numbers

    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.

    Sebastian Pott and Jason D. Lieb

    Genome Biology 2015 16:172

    Published on: 21 August 2015

  17. Review

    Xist localization and function: new insights from multiple levels

    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 ...

    Andrea Cerase, Greta Pintacuda, Anna Tattermusch and Philip Avner

    Genome Biology 2015 16:166

    Published on: 15 August 2015

  18. Research

    Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions

    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.

    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

    Genome Biology 2015 16:161

    Published on: 14 August 2015

  19. Method

    Predicting chromatin organization using histone marks

    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...

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

    Genome Biology 2015 16:162

    Published on: 14 August 2015

  20. Research

    Bipartite structure of the inactive mouse X chromosome

    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...

    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

    Genome Biology 2015 16:152

    Published on: 7 August 2015

  21. Research

    Dynamics of gene silencing during X inactivation using allele-specific RNA-seq

    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 ...

    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

    Genome Biology 2015 16:149

    Published on: 3 August 2015

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

  22. Method

    Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution

    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 ...

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

    Genome Biology 2015 16:156

    Published on: 3 August 2015

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