Literature DB >> 32152365

Three-dimensional genome: developmental technologies and applications in precision medicine.

Yingqi Li1, Tao Tao2, Likun Du3, Xiao Zhu4.   

Abstract

In the 20th century, our familiar structure of DNA was the double helix. Due to technical limitations, we do not have a good way to understand the finer structure of the genome, let alone its transcriptional regulation. Until the advent of 3C technologies, we were no longer blind to this one. Three-dimensional (3D) genomics is a new subject, which mainly studies the 3D structure and transcriptional regulation of eukaryotic genomes. Now, this field mainly has Hi-C series and CHIA-PET series technologies. Through 3D genomics, we can understand the basic structure of DNA, understand the growth and development of organisms and the occurrence of diseases, so as to promote human medical and health undertakings. The review introduces the main research techniques of 3D genomics and their characteristics, the latest development of 3D genome structure, the relationship between diseases and 3D genome structure, the applications of 3D genome in precision medicine, and the development of the 4D nucleome project.

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Year:  2020        PMID: 32152365     DOI: 10.1038/s10038-020-0737-7

Source DB:  PubMed          Journal:  J Hum Genet        ISSN: 1434-5161            Impact factor:   3.172


  132 in total

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2.  Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements.

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Journal:  Genome Res       Date:  2006-09-05       Impact factor: 9.043

3.  Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C).

Authors:  Marieke Simonis; Petra Klous; Erik Splinter; Yuri Moshkin; Rob Willemsen; Elzo de Wit; Bas van Steensel; Wouter de Laat
Journal:  Nat Genet       Date:  2006-10-08       Impact factor: 38.330

4.  Capturing chromosome conformation.

Authors:  Job Dekker; Karsten Rippe; Martijn Dekker; Nancy Kleckner
Journal:  Science       Date:  2002-02-15       Impact factor: 47.728

5.  ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells.

Authors:  Horng D Ou; Sébastien Phan; Thomas J Deerinck; Andrea Thor; Mark H Ellisman; Clodagh C O'Shea
Journal:  Science       Date:  2017-07-28       Impact factor: 47.728

6.  Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture.

Authors:  Da Lin; Ping Hong; Siheng Zhang; Weize Xu; Muhammad Jamal; Keji Yan; Yingying Lei; Liang Li; Yijun Ruan; Zhen F Fu; Guoliang Li; Gang Cao
Journal:  Nat Genet       Date:  2018-04-26       Impact factor: 38.330

7.  A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

Authors:  Suhas S P Rao; Miriam H Huntley; Neva C Durand; Elena K Stamenova; Ivan D Bochkov; James T Robinson; Adrian L Sanborn; Ido Machol; Arina D Omer; Eric S Lander; Erez Lieberman Aiden
Journal:  Cell       Date:  2014-12-11       Impact factor: 41.582

8.  Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Authors:  Erez Lieberman-Aiden; Nynke L van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R Lajoie; Peter J Sabo; Michael O Dorschner; Richard Sandstrom; Bradley Bernstein; M A Bender; Mark Groudine; Andreas Gnirke; John Stamatoyannopoulos; Leonid A Mirny; Eric S Lander; Job Dekker
Journal:  Science       Date:  2009-10-09       Impact factor: 47.728

9.  Cell-cycle dynamics of chromosomal organization at single-cell resolution.

Authors:  Takashi Nagano; Yaniv Lubling; Csilla Várnai; Carmel Dudley; Wing Leung; Yael Baran; Netta Mendelson Cohen; Steven Wingett; Peter Fraser; Amos Tanay
Journal:  Nature       Date:  2017-07-05       Impact factor: 49.962

10.  Single-cell Hi-C reveals cell-to-cell variability in chromosome structure.

Authors:  Takashi Nagano; Yaniv Lubling; Tim J Stevens; Stefan Schoenfelder; Eitan Yaffe; Wendy Dean; Ernest D Laue; Amos Tanay; Peter Fraser
Journal:  Nature       Date:  2013-09-25       Impact factor: 49.962

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  4 in total

1.  Hi-C Identifies Complex Genomic Rearrangements and TAD-Shuffling in Developmental Diseases.

Authors:  Uirá Souto Melo; Robert Schöpflin; Rocio Acuna-Hidalgo; Martin Atta Mensah; Björn Fischer-Zirnsak; Manuel Holtgrewe; Marius-Konstantin Klever; Seval Türkmen; Verena Heinrich; Ilina Datkhaeva Pluym; Eunice Matoso; Sérgio Bernardo de Sousa; Pedro Louro; Wiebke Hülsemann; Monika Cohen; Andreas Dufke; Anna Latos-Bieleńska; Martin Vingron; Vera Kalscheuer; Fabiola Quintero-Rivera; Malte Spielmann; Stefan Mundlos
Journal:  Am J Hum Genet       Date:  2020-05-28       Impact factor: 11.025

2.  Clinical and Prognostic Pan-Cancer Analysis of N6-Methyladenosine Regulators in Two Types of Hematological Malignancies: A Retrospective Study Based on TCGA and GTEx Databases.

Authors:  Xiangsheng Zhang; Liye Zhong; Zhilin Zou; Guosheng Liang; Zhenye Tang; Kai Li; Shuzhen Tan; Yongmei Huang; Xiao Zhu
Journal:  Front Oncol       Date:  2021-03-18       Impact factor: 6.244

3.  Systems Cytogenomics: Are We Ready Yet?

Authors:  Ivan Y Iourov; Svetlana G Vorsanova; Yuri B Yurov
Journal:  Curr Genomics       Date:  2021-02       Impact factor: 2.236

Review 4.  The Prospective Study of Epigenetic Regulatory Profiles in Sport and Exercise Monitored Through Chromosome Conformation Signatures.

Authors:  Elliott C R Hall; Christopher Murgatroyd; Georgina K Stebbings; Brian Cunniffe; Lee Harle; Matthew Salter; Aroul Ramadass; Jurjen W Westra; Ewan Hunter; Alexandre Akoulitchev; Alun G Williams
Journal:  Genes (Basel)       Date:  2020-08-07       Impact factor: 4.096

  4 in total

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