Bacteria 3D genomics

被引:1
|
作者
Tian, Liu [1 ]
Wang, Xuting [1 ]
Hua, Kangjian [1 ]
Ma, Binguang [1 ]
机构
[1] Huazhong Agr Univ, Coll Informat, Hubei Key Lab Agr Bioinformat, State Key Lab Agr Microbiol, Wuhan 430070, Hubei, Peoples R China
来源
CHINESE SCIENCE BULLETIN-CHINESE | 2019年 / 64卷 / 17期
关键词
microorganisms; chromosome structure; super-resolution microscopy; Hi-C; systems biology; HI-C DATA; ESCHERICHIA-COLI; CHROMOSOME ORGANIZATION; SPATIAL-ORGANIZATION; TRANSCRIPTION; CONFORMATION; CAPTURE; CONDENSIN; REVEALS; REPLICATION;
D O I
10.1360/N972018-01016
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Bacteria, the most widely distributed species on Earth, play an important role in the biosphere and in human life. Unlike eukaryotes, bacteria do not have a nucleus, and most of the bacterial genetic materials are concentrated in a specific area of the cell, known as the nucleoid. Bacterial cells vary in morphology and are rich in genetic diversity. However, until now, little is known about the way in which bacterial chromosomes are organized. Are the chromosomes in the bacteria randomly distributed or are there specific organization patterns? With the rise of genome sequencing technology, more and more regulatory elements in bacteria have been resolved. The one-dimensional organization pattern of the bacterial genome has gradually become clear. There are several sets of evidence that the genome layout is not random. The chromosome conformation capture and super-resolution microscopy technology developed in recent years provide a powerful tool for the study of bacterial three-dimensional genomes; the former is often a high-throughput method using cell populations as experimental materials, while the latter is low-throughput method based on single-cell molecular markers; these two methods are usually used in conjunction with each other. The sequencing data obtained by 3C/Hi-C technology can be processed in common pipelines like eukaryotes. In recent years, some software tools for constructing the three-dimensional structures of chromosomes based on 3C/Hi-C data have appeared, but they are usually aimed at eukaryotic species, and tools for prokaryotes have yet to be developed. At present, five bacterial model species, namely, Caulobacter crescentus, Escherichia coli, Bacillus subtilis, Vibrio cholerae, Mycoplasma pneumoniae, have undergone preliminary three-dimensional genome research, and some knowledge about the spatial organization characteristics of bacterial chromosomes has been obtained, revealing the important roles of nucleoid-associated proteins in chromosomal spatial organization. It was found that bacterial chromosomal spatial organization is connected with gene transcription and cell cycles, which has greatly extended our knowledge on the three-dimensional genome of bacteria. However, compared with eukaryotes, the research on the three-dimensional genome of prokaryotes is still insufficient. In view of the complexity of biological processes, the spatial structure of bacterial chromosome is correlated with intracellular and external signal stimulation responses, gene expression regulation, protein interactions, and metabolic processes. Understanding the physiological functions of bacterial three-dimensional genomes from a systematic perspective will be the research focus in future.
引用
收藏
页码:1780 / 1790
页数:11
相关论文
共 68 条
  • [1] Chromosome3D: reconstructing three-dimensional chromosomal structures from Hi-C interaction frequency data using distance geometry simulated annealing
    Adhikari, Badri
    Tuan Trieu
    Cheng, Jianlin
    [J]. BMC GENOMICS, 2016, 17
  • [2] Hi-C: A comprehensive technique to capture the conformation of genomes
    Belton, Jon-Matthew
    McCord, Rachel Patton
    Gibcus, Johan Harmen
    Naumova, Natalia
    Zhan, Ye
    Dekker, Job
    [J]. METHODS, 2012, 58 (03) : 268 - 276
  • [3] Organization and function of the 3D genome
    Bonev, Boyan
    Cavalli, Giacomo
    [J]. NATURE REVIEWS GENETICS, 2016, 17 (11) : 661 - 678
  • [4] Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription
    Cagliero, Cedric
    Grand, Ralph S.
    Jones, M. Beatrix
    Jin, Ding J.
    O'Sullivan, Justin M.
    [J]. NUCLEIC ACIDS RESEARCH, 2013, 41 (12) : 6058 - 6071
  • [5] A Model for all Genomes: The Role of Transcription Factories
    Cook, Peter R.
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 2010, 395 (01) : 1 - 10
  • [6] Normalization of a chromosomal contact map
    Cournac, Axel
    Marie-Nelly, Herve
    Marbouty, Martial
    Koszul, Romain
    Mozziconacci, Julien
    [J]. BMC GENOMICS, 2012, 13
  • [7] Capturing chromosome conformation
    Dekker, J
    Rippe, K
    Dekker, M
    Kleckner, N
    [J]. SCIENCE, 2002, 295 (5558) : 1306 - 1311
  • [8] Bacterial nucleoid-associated proteins, nucleoid structure and gene expression
    Dillon, Shane C.
    Dorman, Charles J.
    [J]. NATURE REVIEWS MICROBIOLOGY, 2010, 8 (03) : 185 - 195
  • [9] Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements
    Dostie, Josee
    Richmond, Todd A.
    Arnaout, Ramy A.
    Selzer, Rebecca R.
    Lee, William L.
    Honan, Tracey A.
    Rubio, Eric D.
    Krumm, Anton
    Lamb, Justin
    Nusbaum, Chad
    Green, Roland D.
    Dekker, Job
    [J]. GENOME RESEARCH, 2006, 16 (10) : 1299 - 1309
  • [10] Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
    Durand, Neva C.
    Shamim, Muhammad S.
    Machol, Ido
    Rao, Suhas S. P.
    Huntley, Miriam H.
    Lander, Eric S.
    Aiden, Erez Lieberman
    [J]. CELL SYSTEMS, 2016, 3 (01) : 95 - 98