Herein we describe a sensitive immunochemical method for mapping the spatial distribution of 5mC oxidation derivatives based on the use of peroxidase-conjugated secondary antibodies and tyramide signal amplification.
Methylation of cytosine bases (5-methylcytosine, 5mC) occurring in vertebrate genomes is usually associated with transcriptional silencing. 5-hydroxylmethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) are the recently discovered modified cytosine bases produced by enzymatic oxidation of 5mC, whose biological functions remain relatively obscure. A number of approaches ranging from biochemical to antibody based techniques have been employed to study the genomic distribution and global content of these modifications in various biological systems. Although some of these approaches can be useful for quantitative assessment of these modified forms of 5mC, most of these methods do not provide any spatial information regarding the distribution of these DNA modifications in different cell types, required for correct understanding of their functional roles. Here we present a highly sensitive method for immunochemical detection of the modified forms of cytosine. This method permits co-detection of these epigenetic marks with protein lineage markers and can be employed to study their nuclear localization, thus, contributing to deciphering their potential biological roles in different experimental contexts.
在DNA(5MC)胞嘧啶碱基甲基化代表与转录沉默1个相关基因脊椎动物中发现了一个重要的表观遗传标记。 5MC被引入并通过DNA甲基2-5保持,并已被证明在许多生物过程中起重要作用,包括基因组印记,X染色体失活,细胞分化,发育3,6。因此,破坏5MC基因组的图案与许多疾病7,8-11相关联。尽管在理解发育和疾病5MC作用的进展,但仍仍是未知如何标记在发展中国家和成人组织中被删除。 DNA去甲基化的几个潜在的机制近来已经提出包括主动和被动去甲基化机构12,13,14,15。发现5MC连续氧化由一零一一年易位enzym介导的产品ES(TET1 / 2/3),例如5- hydroxylmethylcytosine(5hmC),5- formylcytosine(5FC),和在真核生物DNA 16,17,18,19提示猜测5- carboxylcytosine(5caC)是否可作为中间体在自己的权利13 DNA去甲基化的过程,或者作为稳定表观遗传标记。而碱基切除修复的组件,胸腺嘧啶DNA糖基化酶(TDG)可结合和从DNA的19删除这两个5FC和5caC示范,20表明了改性5MC衍生物在活性DNA去甲基化的作用。最近的证据表明5FC / 5caC可以调节的RNA II延伸能力点率转录调控29这些标记可能参与。由于5MC的氧化形式这个潜在的生物重要性,一系列的生物化学和基于抗体的技术已被用于研究其基因组分布和全球内容16,19-24。
鉴于大多数的t他脊椎动物的器官由不同类型的细胞和的修饰的胞嘧啶碱基的分布是组织和细胞类型特异性16-18,20,23,25-27,在确定在不同组织中的氧化5MC衍生物的空间分布成为一个重要的实验为揭开它们的生物学功能任务必需的。大部分的生物化学和基于抗体的方法并不提供关于5MC的不同组织和细胞类型的修饰形式的分布的任何空间信息。相反,基于免疫化学技术可以提供用于评估5MC 28及其氧化衍生物20的空间分布和核定位一个快速的工具。即表示,所报告的丰富度很低5FC(20中每10 6个胞嘧啶)和5caC(3中每10 6个胞嘧啶)在小鼠基因组18代表用于标准免疫化学一个显著挑战。
这里,我们描述提供了强大的一个高度敏感的免疫化学方法和在哺乳动物脑组织胞嘧啶氧化形式的快速检测。通过将加上信号放大步骤过氧化物酶缀合的第二抗体,这种方法绕过了检测非常低量的5FC和5caC的挑战。此外,这种技术可用于与谱系特异性标记胞嘧啶的共同检测修饰形式,有效地补充在阐明这些表观遗传标记的生物学功能的其他方法。
虽然报告的低丰度5MC氧化衍生物,5FC和5caC在一些组织的将提出显著限制为一个标准免疫化学协议,过氧化物酶缀合的二抗的掺入允许这些胞嘧啶修饰在固定组织和细胞的检测( 图2) 。然而,最适孵育时间与酪酰胺溶液应当通过实验为每个单独的批次,其中信号强度与酪胺根据信号放大的持续时间之间的线性关系被观察到的,对于细节酪酰胺信号放大试剂盒的优化参阅Almeida 等人。2012 26 。另外,信号/背景比,可以显著通过携带在一个科普林缸中洗涤,以允许有效地除去多余的抗体的提高。在与酪胺液孵化,它立即停止利用水洗PBT解决方案到D的反应是非常重要的ecrease背景染色。关键是不要让部分在操作过程中的任何点干燥。
DNA脱嘌呤的效率可以通过进行在37℃的脱嘌呤反应加以改进。在使用4当量盐酸代替2 N增强了使用4当量盐酸进行DNA脱嘌呤将不允许共染色用DAPI 5MC的修饰形式的染色,因为它与双链DNA完全相互作用。
尽管这种技术可以提供的胞嘧啶碱基,其中可检测的修饰形式健壮半定量评估,它不能被用于评估5MC或其氧化衍生物的绝对水平。因此,我们建议使用其他补充的,但定量方法16,19 -24。因为在哺乳动物基因组5MC氧化衍生物的发现,几种方法已经被开发,以研究它们的生物作用16,19-24。虽然这些approaCHES可以是在确定5MC氧化衍生物的绝对水平有价值的,它们不提供有关的信息的空间分布20,26,我们已成功地使用这里所描述的方法来映射5MC氧化衍生物在不同的细胞类型的空间分布和定位发展中国家和成人大脑20
通过揭示它们的空间分布20中 ,该技术可以是对理解生物影响,并在不同的生物的上下文5MC的氧化衍生物,其中5MC的这些修饰的衍生物可包括细胞分化,发育和疾病进行检测的命运至关重要。此外,我们在这里描述的方法可以通过在含有tyrami不同的孵育时间评估过氧化物酶反应的动力学(其正比于染色强度)得到5MC的在不同组织中的氧化衍生物的半定量评估德26。
The authors have nothing to disclose.
We thank the Advanced Microscopy Unit (School of Life Sciences, University of Nottingham) and the Histology team of MRC Human Reproductive Sciences Unit (Edinburgh), the Institute of Neuroscience at the ULB and the FNRS for help and support. This work was supported by MRC (MR/L001047/1 to A.D.J.).
Coplin jar | Cole-Parmer | UY-48585-30 | Glass made |
Xylene | Use only in Class II safety cabinet | ||
Phosphate buffer saline (PBS) | Fisher Scientific | 12821680 | pPH 7.5, filtered before use |
4% paraformaldehyde (PFA) | Sigma Aldrich | P6148 | Once made can be stored at -20°C in aliquotes for several months |
4% formaldehyde (FA) | Sigma Aldrich | F8775 | Once made can be stored at -20°C in aliquotes for several months |
Ethanol, anhydrous denatured, histological grade | Sigma Aldrich | 64-17-5 | 95, 75, 50 % in PBS |
0.01 % Tween 20 in PBS | Sigma Aldrich | P9416 | PBT |
0.5% Triton X-100 in PBS | Sigma Aldrich | X100 | PBX |
2 N HCl | Sigma Aldrich | 71826 | caution extremely toxic |
100 mM Tris-HCl | Promega | H5121 | PH adjusted to 8.5 |
hydrophobic barrier pen | Abcam | ab2601 | for immunohistochemistry |
Slide moisture chamber | Scientific Device Laboratory | 197-BL | |
anti-5mC mouse antibody | Diagenode | C15200081 | monoclonal primary antibody |
Anti-5hmC antibody | Active Motif | 39791 | rabbit polyclonal primary antibody |
Anti-5caC antibody | Active Motif | 61225 | rabbit polyclonal primary antibody |
Peroxidase-conjugated anti-rabbit seconday antibody | Dako | K1497 | |
555-congjuated goat anti-mouse antibody | Molecular probes | A-11005 | secondary antibody |
10% BSA | Sigma Aldrich | A9418 | Blocking solution |
22x32mm Glass cover slips | BDH | 406/0188/24 | |
Tyramide Signal Amplification System | Perkin Elmer | NEL741001KT | Other fluorochome conjugated seconday antibodies can be used for co-detection of oxi-5mC |
Mounting Medium with DAPI | Vector Labs | H-1200 | |
Colourless nail polish | |||
chicken polyclonal anti-GFAP polyclonal antibody | Thermo Scientific | PA5-18598 | 1:400 dilution |
anti-NeuN mouse monoclonal antibody | Merck milipore | MAB377B | 1:400 dilution |