Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans.
Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans.
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DOI：
10.1101/gr.270082.120
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发表时间：
2021-07
期刊：
影响因子：
7
通讯作者：
Meyer BJ
中科院分区：
文献类型：
--
作者：
Krassovsky K;Ghosh RP;Meyer BJ
DNA拓扑结构和替代的DNA结构与调节不同的生物过程有关。虽然这些结构的生物力学特性在体外已经得到了广泛的研究，但在体内，特别是在多细胞生物体中的表征是有限的。我们设计了新的方法来定位线虫胚胎和滞育幼虫的DNA超螺旋和单链DNA。为了绘制超螺旋图谱，我们使用高通量测序对生物素化补骨脂素掺入DNA进行了量化。为了绘制单链DNA图谱，我们将高锰酸盐处理与诱导双链断裂的全基因组测序相结合。我们在胚胎的转录起始点(TSS)发现了高水平的负超卷曲。富含GC的区域两侧是从GC到AT的急剧转变，描绘了超级线圈传播的边界。与胚胎中的TSSS相比，滞育幼虫中的TSSS表现出显著的负超卷曲减少，而没有伴随转录的衰减，这表明发育阶段特有的调控。为了评估替代DNA结构是否控制染色体结构和基因表达，我们在X染色体剂量补偿的背景下检查了DNA超螺旋。我们发现凝聚素剂量补偿复合体在其最高占有率结合部位局部产生了负超螺旋，但没有发现沿X染色体存在大规模超螺旋结构域的证据。与转录偶联的负超螺旋不同，转录末端最明显的单链依赖于高AT含量和对称定位的核小体。我们认为，功能基因组元件上序列组成的急剧转变构成了一个共同的调控密码，而调控元件上的DNA结构和扭转应力的传播是形成重要发育事件的关键参数。
DNA topology and alternative DNA structures are implicated in regulating diverse biological processes. Although biomechanical properties of these structures have been studied extensively in vitro, characterization in vivo, particularly in multicellular organisms, is limited. We devised new methods to map DNA supercoiling and single-stranded DNA in Caenorhabditis elegans embryos and diapause larvae. To map supercoiling, we quantified the incorporation of biotinylated psoralen into DNA using high-throughput sequencing. To map single-stranded DNA, we combined permanganate treatment with genome-wide sequencing of induced double-stranded breaks. We found high levels of negative supercoiling at transcription start sites (TSSs) in embryos. GC-rich regions flanked by a sharp GC-to-AT transition delineate boundaries of supercoil propagation. In contrast to TSSs in embryos, TSSs in diapause larvae showed dramatic reductions in negative supercoiling without concomitant attenuation of transcription, suggesting developmental-stage-specific regulation. To assess whether alternative DNA structures control chromosome architecture and gene expression, we examined DNA supercoiling in the context of X-Chromosome dosage compensation. We showed that the condensin dosage compensation complex creates negative supercoils locally at its highest-occupancy binding sites but found no evidence for large-scale supercoiling domains along X Chromosomes. In contrast to transcription-coupled negative supercoiling, single-strandedness, which is most pronounced at transcript end sites, is dependent on high AT content and symmetrically positioned nucleosomes. We propose that sharp transitions in sequence composition at functional genomic elements constitute a common regulatory code and that DNA structure and propagation of torsional stress at regulatory elements are critical parameters in shaping important developmental events.
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DOI：
10.1126/science.aar7831
发表时间：
2018-04-06
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Ganji M;Shaltiel IA;Bisht S;Kim E;Kalichava A;Haering CH;Dekker C
通讯作者：
Dekker C
转录依赖性动态超串联是一种短距离基因组力。
影响因子：
16.8
作者：
Kouzine, Fedor;Gupta, Ashutosh;Baranello, Laura;Wojtowicz, Damian;Ben-Aissa, Khadija;Liu, Juhong;Przytycka, Teresa M.;Levens, David
通讯作者：
Levens, David
影响因子：
10.7
作者：
Kasinathan S;Henikoff S
通讯作者：
Henikoff S
DOI：
10.1016/0006-291x(84)90763-0
发表时间：
1984-01-01
影响因子：
3.1
作者：
JORDANO, J;MONTERO, F;PALACIAN, E
通讯作者：
PALACIAN, E
影响因子：
16.8
作者：
Kouzine, Fedor;Sanford, Suzanne;Levens, David
通讯作者：
Levens, David