Controls of nucleosome positioning in the human genome.
Controls of nucleosome positioning in the human genome.
复制标题
人类基因组中核小体定位的控制。
DOI：
10.1371/journal.pgen.1003036
复制
发表时间：
2012
期刊：
影响因子：
4.5
通讯作者：
Pritchard JK
中科院分区：
文献类型：
--
作者：
Gaffney DJ;McVicker G;Pai AA;Fondufe-Mittendorf YN;Lewellen N;Michelini K;Widom J;Gilad Y;Pritchard JK
核小体对于基因调控很重要，因为它们在基因组上的排列可以控制哪些蛋白质与 DNA 结合。目前，很少有人类核小体被认为在细胞中的位置一致。然而，由于现有数据的分辨率有限，这一点很难评估。我们对来自 7 个类淋巴母细胞系的微球菌核酸酶消化的染色质 (MNase–seq) 进行了配对末端测序，并将超过 36 亿个 MNase–seq 片段映射到人类基因组，以创建迄今为止人类细胞类型中最高分辨率的核小体占据图谱。与之前的结果相比，我们发现大多数核小体的定位比偶然预期的更加一致，并且相当一部分（8.7％）的核小体具有中等到强的定位。总的来说，核小体序列在二核苷酸频率和 DNase I 敏感性方面具有 10 bp 周期性模式；而且，在细胞中，核小体经常具有 10 bp 倍数的翻译偏移。我们估计，几乎一半的基因组包含规则间隔的核小体阵列，这些核小体富含活性染色质结构域。降低 DNase I 敏感性的单核苷酸多态性会破坏核小体阵列的定相，这表明它们通常是由于定位于其他蛋白质形成的屏障而产生的。然而，核小体阵列也可以仅通过 DNA 序列创建。最引人注目的例子是 12 号染色体上超过 400 个核小体的阵列，它是通过具有强定位特性的序列串联重复而创建的。总之，很大一部分核小体的位置是一致的——在某些区域是因为它们采用了有利的序列位置，而在其他区域是因为它们通过染色质重塑或 DNA 结合蛋白被迫进行特定的排列。在细胞核内，真核生物的基因组被紧密包装到染色质中。染色质由一系列重复的珠状核小体组成，每个核小体被一串 DNA 环绕 1.7 圈。核小体在基因组上的组织至关重要，因为它们可以阻止其他蛋白质接触 DNA。先前对人类核小体的研究得出的结论是，大多数核小体的定位模糊，并且往往在不同细胞中占据不同的位置。然而，这种解释可能是现有数据分辨率低的结果。在这里，我们通过生成迄今为止为人类细胞系创建的最精确的核小体位置图来重新审视核小体定位问题。我们发现 8.7% 的核小体具有非常一致的定位，并且大多数核小体的定位比偶然预期的更加一致。此外，我们估计几乎一半的基因组包含规则间隔的核小体阵列。这种定位很大程度上是由于核小体对某些 DNA 序列的内在偏好超过其他序列。但在基因组的某些区域，核小体的序列偏好被蛋白质所取代，这些蛋白质在结合竞争中胜出或利用 ATP 的能量取代它们。
Nucleosomes are important for gene regulation because their arrangement on the genome can control which proteins bind to DNA. Currently, few human nucleosomes are thought to be consistently positioned across cells; however, this has been difficult to assess due to the limited resolution of existing data. We performed paired-end sequencing of micrococcal nuclease-digested chromatin (MNase–seq) from seven lymphoblastoid cell lines and mapped over 3.6 billion MNase–seq fragments to the human genome to create the highest-resolution map of nucleosome occupancy to date in a human cell type. In contrast to previous results, we find that most nucleosomes have more consistent positioning than expected by chance and a substantial fraction (8.7%) of nucleosomes have moderate to strong positioning. In aggregate, nucleosome sequences have 10 bp periodic patterns in dinucleotide frequency and DNase I sensitivity; and, across cells, nucleosomes frequently have translational offsets that are multiples of 10 bp. We estimate that almost half of the genome contains regularly spaced arrays of nucleosomes, which are enriched in active chromatin domains. Single nucleotide polymorphisms that reduce DNase I sensitivity can disrupt the phasing of nucleosome arrays, which indicates that they often result from positioning against a barrier formed by other proteins. However, nucleosome arrays can also be created by DNA sequence alone. The most striking example is an array of over 400 nucleosomes on chromosome 12 that is created by tandem repetition of sequences with strong positioning properties. In summary, a large fraction of nucleosomes are consistently positioned—in some regions because they adopt favored sequence positions, and in other regions because they are forced into specific arrangements by chromatin remodeling or DNA binding proteins. Within the nucleus of the cell, the genome of eukaryotic organisms is tightly packaged into chromatin. Chromatin is composed of a repeating series of bead-like nucleosomes, each of which is encircled 1.7 times by a string of DNA. The organization of nucleosomes on the genome is fundamentally important because they can prevent other proteins from accessing the DNA. Previous studies of human nucleosomes concluded that most nucleosomes have fuzzy positioning and tend to occupy different locations in different cells. This interpretation, however, may be a consequence of the low resolution of existing data. Here we revisit the question of nucleosome positioning by generating the most precise map of nucleosome positions that has ever been created for a human cell line. We find that 8.7% of nucleosomes have very consistent positioning, and most nucleosomes are more consistently positioned than expected by chance. Additionally, we estimate that almost half of the genome contains regularly spaced arrays of nucleosomes. Much of this positioning is due to the intrinsic preference of nucleosomes for some DNA sequences over others; but in some regions of the genome, the sequence preferences of nucleosomes are overridden by proteins that out-compete them for binding or displace them using energy from ATP.
登录
查看更多内容
影响因子：
64.8
作者：
Ernst, Jason;Kheradpour, Pouya;Mikkelsen, Tarjei S.;Shoresh, Noam;Ward, Lucas D.;Epstein, Charles B.;Zhang, Xiaolan;Wang, Li;Issner, Robbyn;Coyne, Michael;Ku, Manching;Durham, Timothy;Kellis, Manolis;Bernstein, Bradley E.
通讯作者：
Bernstein, Bradley E.
影响因子：
4.5
作者：
Guan, Yongtao;Stephens, Matthew
通讯作者：
Stephens, Matthew
影响因子：
64.8
作者：
Brogaard, Kristin;Xi, Liqun;Wang, Ji-Ping;Widom, Jonathan
通讯作者：
Widom, Jonathan
影响因子：
12.3
作者：
Lai WK;Buck MJ
通讯作者：
Buck MJ
影响因子：
12.3
作者：
Kaplan N;Hughes TR;Lieb JD;Widom J;Segal E
通讯作者：
Segal E