Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
Genes (Basel). 2023 May 2;14(5):1036. doi: 10.3390/genes14051036.
Using a whole-genome assembly of , I applied my bioinformatics strategy to locate candidate imprinting control regions (ICRs) genome-wide. In mammals, genomic imprinting plays essential roles in embryogenesis. In my strategy, peaks in plots mark the locations of known, inferred, and candidate ICRs. Genes in the vicinity of candidate ICRs correspond to potential imprinted genes. By displaying my datasets on the UCSC genome browser, one could view peak positions with respect to genomic landmarks. I give two examples of candidate ICRs in loci that influence spermatogenesis in bulls: and . I also give examples of candidate ICRs in loci that influence muscle development: and . By examining the ENCODE data reported for mice, I deduced regulatory clues about cattle. I focused on DNase I hypersensitive sites (DHSs). Such sites reveal accessibility of chromatin to regulators of gene expression. For inspection, I chose DHSs in chromatin from mouse embryonic stem cells (ESCs) ES-E14, mesoderm, brain, heart, and skeletal muscle. The ENCODE data revealed that the promoter was accessible to the transcription initiation apparatus in mouse ESCs, mesoderm, and skeletal muscles. The data also revealed accessibility of locus to regulatory proteins in mouse ESCs and examined tissues.
利用 的全基因组组装，我应用我的生物信息学策略在全基因组范围内定位候选印记控制区域（ICRs）。在哺乳动物中，基因组印记在胚胎发生中起着至关重要的作用。在我的策略中，图中的峰标记了已知、推断和候选 ICR 的位置。候选 ICR 附近的基因对应于潜在的印记基因。通过在 UCSC 基因组浏览器上显示我的数据集，人们可以查看相对于基因组标记的峰位置。我给出了影响公牛精子发生的两个候选 ICR 所在基因座的例子： 和 。我还给出了影响肌肉发育的候选 ICR 所在基因座的例子： 和 。通过检查为小鼠报告的 ENCODE 数据，我推断了关于牛的调控线索。我专注于 DNase I 超敏位点（DHSs）。这些位点揭示了染色质对基因表达调控因子的可及性。供检查，我选择了来自小鼠胚胎干细胞（ESCs）ES-E14、中胚层、大脑、心脏和骨骼肌的染色质中的 DHSs。ENCODE 数据显示， 在小鼠 ESCs、中胚层和骨骼肌中，启动子对转录起始装置是可及的。该数据还揭示了 基因座在小鼠 ESCs 和检查组织中的调节蛋白的可及性。
