The long-range interaction map of ribosomal DNA arrays.
The long-range interaction map of ribosomal DNA arrays.
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DOI：
10.1371/journal.pgen.1007258
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发表时间：
2018-03
期刊：
影响因子：
4.5
通讯作者：
Lemos B
中科院分区：
文献类型：
--
作者：
Yu S;Lemos B
重复的 rDNA 阵列产生了核仁，这是一种对于应激反应、细胞周期调节、RNA 修饰、细胞代谢和基因组稳定性等细胞过程至关重要的细胞器。 rDNA 阵列还负责产生 70% 以上的所有细胞 RNA（核糖体 RNA）。 rRNA 由两组基因座产生：5S rDNA 阵列仅位于人类 1 号染色体上，而 45S rDNA 阵列则位于人类 5 条近端着丝粒染色体的短臂上。这些关键基因组元件仍未组装，并且已被排除在迄今为止的所有 Hi-C 分析之外。在这里，我们结合了来自多个实验的超过 150 亿个 Hi-C 读数，构建了第一个 5S 和 45S rDNA 阵列与基因组其余部分接触的高分辨率图谱。这些数据具有足够高的覆盖率，能够以 1MB 分辨率绘制 rDNA-基因组相互作用图并识别 rDNA-基因接触。该图谱显示，5S 和 45S 阵列在基因组的共同位点上显示出优先接触，但其本身距离不够近，无法产生 5S-45S Hi-C 接触。核糖体 DNA 接触点富含封闭、抑制和晚期复制染色质片段以及 CTCF 结合位点。最后，我们确定了功能类别，其分散的基因在 rDNA 阵列附近聚结或避免与 rDNA 阵列接近。这些观察进一步加深了我们对 rDNA 阵列的空间定位及其对细胞核结构的贡献的理解。重复的核糖体 DNA (rDNA) 阵列产生核仁，这是一种参与关键细胞过程的细胞器，例如应激反应、细胞周期调节、RNA 修饰以及 70% 以上的细胞 RNA（核糖体 RNA）的产生。这一关键基因组元件仍未组装，并且已被排除在迄今为止的所有 Hi-C 分析之外。在这里，我们构建了第一个 5S 和 45S rDNA 与基因组其余部分接触的图谱。该图产生了许多新颖的结果，挑战了 5S 和 45S 阵列在细胞核中靠近的预期。 rDNA 阵列在整个基因组中共享共同的接触位点，偏向于封闭、抑制和晚期复制染色质的片段，并且表现出更接近或避开功能相干的基因集。这些结果进一步加深了我们对 rDNA 阵列及其在核环境中定位的理解。
The repeated rDNA array gives rise to the nucleolus, an organelle that is central to cellular processes as varied as stress response, cell cycle regulation, RNA modification, cell metabolism, and genome stability. The rDNA array is also responsible for the production of more than 70% of all cellular RNAs (the ribosomal RNAs). The rRNAs are produced from two sets of loci: the 5S rDNA array resides exclusively on human chromosome 1 while the 45S rDNA arrays reside on the short arm of five human acrocentric chromosomes. These critical genome elements have remained unassembled and have been excluded from all Hi-C analyses to date. Here we built the first high resolution map of 5S and 45S rDNA array contacts with the rest of the genome combining over 15 billion Hi-C reads from several experiments. The data enabled sufficiently high coverage to map rDNA-genome interactions with 1MB resolution and identify rDNA-gene contacts. The map showed that the 5S and 45S arrays display preferential contact at common sites along the genome but are not themselves sufficiently close to yield 5S-45S Hi-C contacts. Ribosomal DNA contacts are enriched in segments of closed, repressed, and late replicating chromatin, as well as CTCF binding sites. Finally, we identified functional categories whose dispersed genes coalesced in proximity to the rDNA arrays or instead avoided proximity with the rDNA arrays. The observations further our understanding of the spatial localization of rDNA arrays and their contribution to the architecture of the cell nucleus. The repeated ribosomal DNA (rDNA) array gives rise to the nucleolus, an organelle that is involved in key cellular processes such as stress response, cell cycle regulation, RNA modification, and production of more than 70% of all cellular RNAs (the ribosomal RNAs). This critical genome element has remained unassembled and has been excluded from all Hi-C analyses to date. Here we built the first map of 5S and 45S rDNA contacts with the rest of the genome. The map yielded a number of novel results and challenge the expectation that 5S and 45S arrays are close together in the nucleus. The rDNA arrays share common sites of contact across the genome, are biased towards segments of closed, repressed, and late replicating chromatin, and display greater proximity or avoidance to functionally coherent gene sets. The results further our understanding of the rDNA arrays and their localization in the nuclear environment.
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影响因子：
12.3
作者：
Fortin JP;Hansen KD
通讯作者：
Hansen KD
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
64.8
作者：
Dixon JR;Jung I;Selvaraj S;Shen Y;Antosiewicz-Bourget JE;Lee AY;Ye Z;Kim A;Rajagopal N;Xie W;Diao Y;Liang J;Zhao H;Lobanenkov VV;Ecker JR;Thomson JA;Ren B
通讯作者：
Ren B
影响因子：
7
作者：
Ganley, Austen R. D.;Kobayashi, Takehiko
通讯作者：
Kobayashi, Takehiko
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y