Literature DB >> 32123395

Visualizing the genome in high resolution challenges our textbook understanding.

Melike Lakadamyali1,2, Maria Pia Cosma3,4,5,6,7.   

Abstract

The relationship between the 4D folding of the genome and its function is an outstanding question in biology. A range of methods that probe the folding of the genome in space and time with unprecedented resolution have been developed. These methods, including chromosome conformation capture and high-resolution light and electron microscopy, are shedding new light on genome architecture and function. Here, we review the emerging picture of genome organization revealed by super-resolution and live-cell imaging. We compare and contrast population-based chromosome conformation capture approaches and imaging-based approaches and highlight future challenges.

Mesh:

Substances:

Year:  2020        PMID: 32123395     DOI: 10.1038/s41592-020-0758-3

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  86 in total

1.  The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells.

Authors:  S Boyle; S Gilchrist; J M Bridger; N L Mahy; J A Ellis; W A Bickmore
Journal:  Hum Mol Genet       Date:  2001-02-01       Impact factor: 6.150

Review 2.  Chromatin higher-order structure and dynamics.

Authors:  Christopher L Woodcock; Rajarshi P Ghosh
Journal:  Cold Spring Harb Perspect Biol       Date:  2010-04-07       Impact factor: 10.005

Review 3.  Chromosome territories.

Authors:  Thomas Cremer; Marion Cremer
Journal:  Cold Spring Harb Perspect Biol       Date:  2010-03       Impact factor: 10.005

Review 4.  Regulation of chromatin by histone modifications.

Authors:  Andrew J Bannister; Tony Kouzarides
Journal:  Cell Res       Date:  2011-02-15       Impact factor: 25.617

Review 5.  Nucleolus and nuclear periphery: velcro for heterochromatin.

Authors:  Jan Padeken; Patrick Heun
Journal:  Curr Opin Cell Biol       Date:  2014-03-29       Impact factor: 8.382

6.  Spheroid chromatin units (v bodies).

Authors:  A L Olins; D E Olins
Journal:  Science       Date:  1974-01-25       Impact factor: 47.728

7.  General transcription factors bind promoters repressed by Polycomb group proteins.

Authors:  A Breiling; B M Turner; M E Bianchi; V Orlando
Journal:  Nature       Date:  2001-08-09       Impact factor: 49.962

8.  Systematic protein location mapping reveals five principal chromatin types in Drosophila cells.

Authors:  Guillaume J Filion; Joke G van Bemmel; Ulrich Braunschweig; Wendy Talhout; Jop Kind; Lucas D Ward; Wim Brugman; Inês J de Castro; Ron M Kerkhoven; Harmen J Bussemaker; Bas van Steensel
Journal:  Cell       Date:  2010-09-30       Impact factor: 41.582

9.  Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription.

Authors:  Séverine Chambeyron; Wendy A Bickmore
Journal:  Genes Dev       Date:  2004-05-15       Impact factor: 11.361

10.  Integrative analysis of 111 reference human epigenomes.

Authors:  Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi-Moussavi; Pouya Kheradpour; Zhizhuo Zhang; Jianrong Wang; Michael J Ziller; Viren Amin; John W Whitaker; Matthew D Schultz; Lucas D Ward; Abhishek Sarkar; Gerald Quon; Richard S Sandstrom; Matthew L Eaton; Yi-Chieh Wu; Andreas R Pfenning; Xinchen Wang; Melina Claussnitzer; Yaping Liu; Cristian Coarfa; R Alan Harris; Noam Shoresh; Charles B Epstein; Elizabeta Gjoneska; Danny Leung; Wei Xie; R David Hawkins; Ryan Lister; Chibo Hong; Philippe Gascard; Andrew J Mungall; Richard Moore; Eric Chuah; Angela Tam; Theresa K Canfield; R Scott Hansen; Rajinder Kaul; Peter J Sabo; Mukul S Bansal; Annaick Carles; Jesse R Dixon; Kai-How Farh; Soheil Feizi; Rosa Karlic; Ah-Ram Kim; Ashwinikumar Kulkarni; Daofeng Li; Rebecca Lowdon; GiNell Elliott; Tim R Mercer; Shane J Neph; Vitor Onuchic; Paz Polak; Nisha Rajagopal; Pradipta Ray; Richard C Sallari; Kyle T Siebenthall; Nicholas A Sinnott-Armstrong; Michael Stevens; Robert E Thurman; Jie Wu; Bo Zhang; Xin Zhou; Arthur E Beaudet; Laurie A Boyer; Philip L De Jager; Peggy J Farnham; Susan J Fisher; David Haussler; Steven J M Jones; Wei Li; Marco A Marra; Michael T McManus; Shamil Sunyaev; James A Thomson; Thea D Tlsty; Li-Huei Tsai; Wei Wang; Robert A Waterland; Michael Q Zhang; Lisa H Chadwick; Bradley E Bernstein; Joseph F Costello; Joseph R Ecker; Martin Hirst; Alexander Meissner; Aleksandar Milosavljevic; Bing Ren; John A Stamatoyannopoulos; Ting Wang; Manolis Kellis
Journal:  Nature       Date:  2015-02-19       Impact factor: 69.504

View more
  27 in total

Review 1.  Visualizing, quantifying and manipulating mitochondrial DNA in vivo.

Authors:  David L Prole; Patrick F Chinnery; Nick S Jones
Journal:  J Biol Chem       Date:  2020-10-15       Impact factor: 5.157

Review 2.  In search of lost time: Enhancers as modulators of timing in lymphocyte development and differentiation.

Authors:  Jonathan M Chu; Nicholas A Pease; Hao Yuan Kueh
Journal:  Immunol Rev       Date:  2021-03-18       Impact factor: 12.988

3.  Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localization Microscopy.

Authors:  Maike Steindel; Igor Orsine de Almeida; Stanley Strawbridge; Valentyna Chernova; David Holcman; Aleks Ponjavic; Srinjan Basu
Journal:  Methods Mol Biol       Date:  2022

4.  Differences in nanoscale organization of regulatory active and inactive human chromatin.

Authors:  Katharina Brandstetter; Tilo Zülske; Tobias Ragoczy; David Hörl; Miguel Guirao-Ortiz; Clemens Steinek; Toby Barnes; Gabriela Stumberger; Jonathan Schwach; Eric Haugen; Eric Rynes; Philipp Korber; John A Stamatoyannopoulos; Heinrich Leonhardt; Gero Wedemann; Hartmann Harz
Journal:  Biophys J       Date:  2022-02-10       Impact factor: 4.033

Review 5.  Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C.

Authors:  Ning Liu; Wai Yee Low; Hamid Alinejad-Rokny; Stephen Pederson; Timothy Sadlon; Simon Barry; James Breen
Journal:  Epigenetics Chromatin       Date:  2021-08-28       Impact factor: 4.954

6.  Genome oligopaint via local denaturation fluorescence in situ hybridization.

Authors:  Yanbo Wang; Wayne Taylor Cottle; Haobo Wang; Xinyu Ashlee Feng; John Mallon; Momcilo Gavrilov; Scott Bailey; Taekjip Ha
Journal:  Mol Cell       Date:  2021-03-02       Impact factor: 17.970

Review 7.  Close to the edge: Heterochromatin at the nucleolar and nuclear peripheries.

Authors:  Aizhan Bizhanova; Paul D Kaufman
Journal:  Biochim Biophys Acta Gene Regul Mech       Date:  2020-12-08       Impact factor: 4.490

8.  Nucleosome-induced homology recognition in chromatin.

Authors:  Jonathan G Hedley; Vladimir B Teif; Alexei A Kornyshev
Journal:  J R Soc Interface       Date:  2021-06-16       Impact factor: 4.293

9.  Live imaging of chromatin distribution reveals novel principles of nuclear architecture and chromatin compartmentalization.

Authors:  Daria Amiad-Pavlov; Dana Lorber; Gaurav Bajpai; Adriana Reuveny; Francesco Roncato; Ronen Alon; Samuel Safran; Talila Volk
Journal:  Sci Adv       Date:  2021-06-02       Impact factor: 14.136

Review 10.  The macro and micro of chromosome conformation capture.

Authors:  Viraat Y Goel; Anders S Hansen
Journal:  Wiley Interdiscip Rev Dev Biol       Date:  2020-09-28       Impact factor: 5.814

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.