Genome-wide mapping reveals conserved and diverged R-loop activities in the unusual genetic landscape of the African trypanosome genome
Genome-wide mapping reveals conserved and diverged R-loop activities in the unusual genetic landscape of the African trypanosome genome
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DOI：
10.1101/357020
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发表时间：
2018-06
影响因子：
14.9
通讯作者：
E. Briggs;G. Hamilton;K. Crouch;C. Lapsley;R. McCulloch
中科院分区：
文献类型：
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作者：
E. Briggs;G. Hamilton;K. Crouch;C. Lapsley;R. McCulloch
R-环是一种稳定的RNA-DNA杂交体，参与转录的启动和终止，以及端粒的稳态、染色质的形成以及基因组的复制和不稳定。在布氏锥虫原虫中，RNA聚合酶(Pol)II的转录是非常不寻常的：几乎所有的基因都是由多基因转录单位共转录的，mRNAs是通过连接的反式剪接和聚腺苷作用产生的，并且转录起始点没有显示保守的启动子基序。在这里，我们描述了R-环在野生型哺乳动物感染的布氏锥虫和缺乏RNaseH1的突变体中的全基因组分布，揭示了保守和分歧的功能。在着丝粒、rRNA基因和反转录转座子相关基因上发现了保守的定位。RNA Pol II转录起始点也显示R-环，表明尽管缺乏启动子保守或转录起始调控，但仍具有广泛保守的作用。然而，最丰富的R-loop富集区位于多基因转录单元的基因间区，杂交体与多聚腺苷化和核小体耗竭的位置重合。因此，大多数布鲁氏锥虫R-环不是在转录终止中发挥作用，而是在一个新的角色中发挥作用，促进RNA POL II运动或mRNA处理。最后，我们发现R-环的定位与DNA复制起始的定位之间几乎没有相关性的证据。
R-loops are stable RNA-DNA hybrids that have been implicated in transcription initiation and termination, as well as in telomere homeostasis, chromatin formation, and genome replication and instability. RNA Polymerase (Pol) II transcription in the protozoan parasite Trypanosoma brucei is highly unusual: virtually all genes are co-transcribed from multigene transcription units, with mRNAs generated by linked trans-splicing and polyadenylation, and transcription initiation sites display no conserved promoter motifs. Here, we describe the genome-wide distribution of R-loops in wild type mammal-infective T. brucei and in mutants lacking RNase H1, revealing both conserved and diverged functions. Conserved localisation was found at centromeres, rRNA genes and retrotransposon-associated genes. RNA Pol II transcription initiation sites also displayed R-loops, suggesting a broadly conserved role despite the lack of promoter conservation or transcription initiation regulation. However, the most abundant sites of R-loop enrichment were within the intergenic regions of the multigene transcription units, where the hybrids coincide with sites of polyadenylation and nucleosome-depletion. Thus, instead of functioning in transcription termination, most T. brucei R-loops act in a novel role, promoting RNA Pol II movement or mRNA processing. Finally, we show there is little evidence for correlation between R-loop localisation and mapped sites of DNA replication initiation.