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The relationship between transcription initiation RNAs and CCCTC-binding factor (CTCF) localization

机译：转录起始RNA与CCCTC结合因子（CTCF）定位之间的关系

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Background Transcription initiation RNAs (tiRNAs) are nuclear localized 18 nucleotide RNAs derived from sequences immediately downstream of RNA polymerase II (RNAPII) transcription start sites. Previous reports have shown that tiRNAs are intimately correlated with gene expression, RNA polymerase II binding and behaviors, and epigenetic marks associated with transcription initiation, but not elongation. Results In the present work, we show that tiRNAs are commonly found at genomic CCCTC-binding factor (CTCF) binding sites in human and mouse, and that CTCF sites that colocalize with RNAPII are highly enriched for tiRNAs. To directly investigate the relationship between tiRNAs and CTCF we examined tiRNAs originating near the intronic CTCF binding site in the human tumor suppressor gene, p21 (cyclin-dependent kinase inhibitor 1A gene, also known as CDKN1A). Inhibition of CTCF-proximal tiRNAs resulted in increased CTCF localization and increased p21 expression, while overexpression of CTCF-proximal tiRNA mimics decreased CTCF localization and p21 expression. We also found that tiRNA-regulated CTCF binding influences the levels of trimethylated H3K27 at the alternate upstream p21 promoter, and affects the levels of alternate p21 (p21alt) transcripts. Extending these studies to another randomly selected locus with conserved CTCF binding we found that depletion of tiRNA alters nucleosome density proximal to sites of tiRNA biogenesis. Conclusions Taken together, these data suggest that tiRNAs modulate local epigenetic structure, which in turn regulates CTCF localization.
机译：背景技术转录起始RNA（tiRNA）是位于RNA聚合酶II（RNAPII）转录起始位点紧下游的序列的核定位18核苷酸RNA。以前的报道表明，tiRNA与基因表达，RNA聚合酶II的结合和行为以及与转录起始相关但与延伸无关的表观遗传标记密切相关。结果在目前的工作中，我们显示tiRNA通常在人和小鼠的基因组CCCTC结合因子（CTCF）结合位点发现，并且与RNAPII共定位的CTCF位点富含tiRNA。为了直接研究tiRNA与CTCF之间的关系，我们检查了人类肿瘤抑制基因p21（细胞周期蛋白依赖性激酶抑制剂1A基因，也称为CDKN1A）内含CTCF结合位点附近的tiRNA。抑制CTCF近端tiRNA导致CTCF定位增加和p21表达增加，而CTCF近端tiRNA模拟物的过表达降低CTCF定位和p21表达。我们还发现，tiRNA调节的CTCF结合会影响备用p21启动子上三甲基化H3K27的水平，并影响备用p21（p21 alt ）转录本的水平。将这些研究扩展到另一个具有保守CTCF结合的随机选择的基因座，我们发现tiRNA的消耗会改变tiRNA生物发生位点附近的核小体密度。结论综上所述，这些数据表明tiRNA可以调节局部表观遗传结构，进而调节CTCF的定位。

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