How a genome with linear length over meters is compacted into the micrometer-sized nucleus of higher eukaryotic cells, and how this compaction affects and is affected by the genome functionalities have puzzled biologi...How a genome with linear length over meters is compacted into the micrometer-sized nucleus of higher eukaryotic cells, and how this compaction affects and is affected by the genome functionalities have puzzled biologists for decades. There are mainly two classes of technologies that are dedicated to the probing of genome spatial organization. Image-based analyses of three-dimensional （3D） fluorescence in situ hybridization （FISH） [1] have been widely used in genome spatial research. This technology family has contributed to many early land- mark discoveries of 3D genome （e.g., finding that chromo- somes occupy distinct non-overlapping territories in interphase [2]）, and continues to assist biologists in zooming into the genome spatial structure [3]. The other technology family is 3D genome mapping, which takes advantage of the next-generation sequencing （NGS） technology to sample the proximity ligated genome fragments [4,5] as chromatin interac- tions. Chromatin interaction analysis by paired-end tag sequencing （ChIA-PET） and high-throughput chromosome conformation capture （Hi-C） are two representative technolo- gies in this class [4,5]. ChIA-PET detects chromatin interac- tions mediated by specific protein factors, thus it is more specific and has higher resolution in comparison to Hi-C, which captures all chromatin contacts comprehensively. Since the introduction of ChIA-PET and Hi-C seven years ago [6,7], more detailed spatial genome architectures have been revealed,such as topologically associated domains （TAD） [8] and clus- tered gene promoters for transcription [9]. However, both Hi-C and ChlA-PET technologies face challenges including data noise stemming from complicated experimental protocols, exponential explosion in the sequencing depth required for higher resolution analysis, and large starting cell numbers. Some endeavors have been made to address one or some of such challenges. For instance, DNase I or micrococcal nucle- ase have been used to substitute restriction enzymes for chro- matin fragmentation, enabling higher resolution in chromatin contact mapping [10,11].展开更多
基金supported by grants from the National Natural Science Foundation of China(NSFC,Grant Nos.91540114,91131012,and 31271398)the National High-tech R&D Program of China(863 Program,Grant No.2014AA021103)+1 种基金the National Basic Research Program of China(the 973 Program,Grant No.2014CB542002)the"100-Talent Program"of the Chinese Academy of Sciences to ZZ.
文摘How a genome with linear length over meters is compacted into the micrometer-sized nucleus of higher eukaryotic cells, and how this compaction affects and is affected by the genome functionalities have puzzled biologists for decades. There are mainly two classes of technologies that are dedicated to the probing of genome spatial organization. Image-based analyses of three-dimensional （3D） fluorescence in situ hybridization （FISH） [1] have been widely used in genome spatial research. This technology family has contributed to many early land- mark discoveries of 3D genome （e.g., finding that chromo- somes occupy distinct non-overlapping territories in interphase [2]）, and continues to assist biologists in zooming into the genome spatial structure [3]. The other technology family is 3D genome mapping, which takes advantage of the next-generation sequencing （NGS） technology to sample the proximity ligated genome fragments [4,5] as chromatin interac- tions. Chromatin interaction analysis by paired-end tag sequencing （ChIA-PET） and high-throughput chromosome conformation capture （Hi-C） are two representative technolo- gies in this class [4,5]. ChIA-PET detects chromatin interac- tions mediated by specific protein factors, thus it is more specific and has higher resolution in comparison to Hi-C, which captures all chromatin contacts comprehensively. Since the introduction of ChIA-PET and Hi-C seven years ago [6,7], more detailed spatial genome architectures have been revealed,such as topologically associated domains （TAD） [8] and clus- tered gene promoters for transcription [9]. However, both Hi-C and ChlA-PET technologies face challenges including data noise stemming from complicated experimental protocols, exponential explosion in the sequencing depth required for higher resolution analysis, and large starting cell numbers. Some endeavors have been made to address one or some of such challenges. For instance, DNase I or micrococcal nucle- ase have been used to substitute restriction enzymes for chro- matin fragmentation, enabling higher resolution in chromatin contact mapping [10,11].
