Kc H2Av Knockdown 600 mM Salt Extracted Chromatin

modENCODE_submission_2759 This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes. Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions. Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and unbound intermediates in active processes, thus providing a simple, powerful strategy for mapping epigenome dynamics. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: tiling array analysis. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female; NUMBER OF REPLICATES: 2; EXPERIMENTAL FACTORS: Cell Line Kc167; biochemical fraction (extract) soluble fraction; sodium chloride concentration (Compound) 600 mM; extraction time (sampling_time_point) 1 to 2 hours

modENCODE_submission_2759 本提交源自Steven Henikoff牵头的modENCODE项目。如需获取modENCODE项目完整列表，请访问http://www.genome.gov/26524648。
项目目标：我们对经微球菌核酸酶(micrococcal nuclease)消化处理的果蝇染色质的连续盐抽提组分开展了全基因组谱型分析(genome-wide profiling)。经消化后采用80 mM或150 mM NaCl抽提的染色质组分以单核小体为主，对应经典的“活性”染色质。此类低盐可溶性组分的谱型显示，在局部组蛋白H3.3缺失的转录活性基因区域存在相位排布的核小体，且与组蛋白H2Av(H2A.Z)及RNA聚合酶II的谱型高度吻合。这种对应关系提示，转录过程可引发H3.3+H2Av核小体的解离，并生成低盐可溶性核小体。采用600 mM NaCl可实现染色质的近乎定量回收；但剩余的不溶性染色质在活跃转录区域存在富集。盐不溶性染色质大概率对应结合于大型蛋白质复合物的寡核小体。低盐抽提组分与不溶性染色质均富含全基因组范围内的表观遗传调控元件对应序列。活性染色质在盐溶解度两个极端区间的存在，表明此类盐抽提组分捕获了活性过程中结合态与游离态的中间产物，从而为表观基因组动态图谱的绘制提供了一种简便高效的策略。
如需了解数据使用条款与条件，请访问http://www.genome.gov/27528022 及 http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf。
实验类型：瓦片阵列分析(tiling array analysis)
生物来源：细胞系：Kc167；组织：胚胎来源细胞系；发育阶段：晚期胚胎阶段；基因型：se/e；性别：雌性
生物学重复数：2
实验因素：细胞系Kc167；生化组分（抽提物）：可溶性组分；氯化钠浓度（化合物）：600 mM；抽提时间（采样时间点）：1至2小时