Krawetz Stephen A, Draghici Sorin, Goodrich Robert, Liu Zhandong, Ostermeier G Charles
Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA.
Methods Mol Med. 2005;108:439-58. doi: 10.1385/1-59259-850-1:439.
Chromatin loops are tethered at discrete regions that are approx 100-1000 bp in length. These regions of attachment serve as specific sequence landmarks, anchoring the DNA to the fibers of the chromosomal scaffold. It has been estimated that our genome contains 70,000 nuclear matrix attachment sites that serve as a dynamic nuclear organizer in both the interphase and metaphase cell. Approximately 30,000-40,000 matrix attachment regions (MARs) serve as origins of replication. MARs can also be associated with chromosomal segments densely populated with transcription factor-binding sites. This may facilitate transcription that is initiated within the region of the chromosome coincident with the surface of the nuclear matrix. Assuming an average somatic loop size of 100 kb, it is reasonable to propose that each cell utilizes 30,000 MARs to anchor each of the approx 20,000 active genic domains. This is sufficient to encompass the 30,000 functional genes in our genome that exist as members of single or multigenic families, each constituting a single chromatin domain. With the sequencing phase of various genome projects complete, in silico tools are being developed to identify the long-range control elements that modulate gene expression. This information is necessary to specifically target the time-intensive wet-bench verification and expression experiments that will provide a unified understanding of gene regulation. In this chapter we review some of the in silico strategies that are currently available and a new in vivo method based on the real-time polymerase chain reaction, to assess regions of matrix association.
染色质环锚定在长度约为100 - 1000碱基对的离散区域。这些附着区域作为特定的序列标志，将DNA锚定到染色体支架纤维上。据估计，我们的基因组包含70,000个核基质附着位点，它们在间期和中期细胞中作为动态的核组织者。大约30,000 - 40,000个基质附着区域（MARs）作为复制起点。MARs也可与富含转录因子结合位点的染色体片段相关联。这可能有助于在与核基质表面重合的染色体区域内起始的转录。假设平均体细胞环大小为100 kb，提出每个细胞利用30,000个MARs来锚定大约20,000个活跃基因结构域中的每一个是合理的。这足以涵盖我们基因组中作为单基因或多基因家族成员存在的30,000个功能基因，每个基因构成一个单一的染色质结构域。随着各种基因组计划测序阶段的完成，正在开发计算机工具来识别调节基因表达的远程控制元件。这些信息对于专门针对耗时费力且能统一理解基因调控的湿实验台验证和表达实验至关重要。在本章中，我们将回顾一些目前可用的计算机策略以及一种基于实时聚合酶链反应的新体内方法，以评估基质关联区域。
