Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland.
Genome Res. 2012 Apr;22(4):666-80. doi: 10.1101/gr.130286.111. Epub 2012 Jan 27.
The genomic loci occupied by RNA polymerase (RNAP) III have been characterized in human culture cells by genome-wide chromatin immunoprecipitations, followed by deep sequencing (ChIP-seq). These studies have shown that only ∼40% of the annotated 622 human tRNA genes and pseudogenes are occupied by RNAP-III, and that these genes are often in open chromatin regions rich in active RNAP-II transcription units. We have used ChIP-seq to characterize RNAP-III-occupied loci in a differentiated tissue, the mouse liver. Our studies define the mouse liver RNAP-III-occupied loci including a conserved mammalian interspersed repeat (MIR) as a potential regulator of an RNAP-III subunit-encoding gene. They reveal that synteny relationships can be established between a number of human and mouse RNAP-III genes, and that the expression levels of these genes are significantly linked. They establish that variations within the A and B promoter boxes, as well as the strength of the terminator sequence, can strongly affect RNAP-III occupancy of tRNA genes. They reveal correlations with various genomic features that explain the observed variation of 81% of tRNA scores. In mouse liver, loci represented in the NCBI37/mm9 genome assembly that are clearly occupied by RNAP-III comprise 50 Rn5s (5S RNA) genes, 14 known non-tRNA RNAP-III genes, nine Rn4.5s (4.5S RNA) genes, and 29 SINEs. Moreover, out of the 433 annotated tRNA genes, half are occupied by RNAP-III. Transfer RNA gene expression levels reflect both an underlying genomic organization conserved in dividing human culture cells and resting mouse liver cells, and the particular promoter and terminator strengths of individual genes.
通过全基因组染色质免疫沉淀结合深度测序（ChIP-seq），研究人员已经鉴定了人培养细胞中 RNA 聚合酶（RNAP）III 占据的基因组位置。这些研究表明，仅有约 40%注释的 622 个人 tRNA 基因和假基因被 RNAP-III 占据，这些基因通常位于富含活跃的 RNAP-II 转录单元的开放染色质区域。我们使用 ChIP-seq 来研究分化组织（即小鼠肝脏）中的 RNAP-III 占据的位置。我们的研究定义了包括保守的哺乳动物散布重复序列（MIR）在内的小鼠肝脏 RNAP-III 占据的位置，该重复序列可能是一个 RNAP-III 亚基编码基因的调节剂。它们揭示了许多人类和小鼠 RNAP-III 基因之间可以建立同线性关系，并且这些基因的表达水平显著相关。它们确定了 A 和 B 启动子盒内的变异以及终止子序列的强度可以强烈影响 tRNA 基因的 RNAP-III 占据。它们揭示了与各种基因组特征的相关性，这些特征解释了观察到的 81%的 tRNA 分数的变化。在小鼠肝脏中，在 NCBI37/mm9 基因组组装中明确被 RNAP-III 占据的位置包括 50 个 Rn5s（5S RNA）基因、14 个已知的非 tRNA RNAP-III 基因、9 个 Rn4.5s（4.5S RNA）基因和 29 个 SINEs。此外，在 433 个注释的 tRNA 基因中，有一半被 RNAP-III 占据。转移 RNA 基因的表达水平反映了在分裂的人培养细胞和静止的小鼠肝脏细胞中保守的基本基因组组织，以及各个基因的特定启动子和终止子强度。
