答：染色質(zhì)免疫沉淀技術(shù)（Chromatin Immunoprecipitation，簡(jiǎn)稱ChIP）是研究體內(nèi)蛋白質(zhì)與DNA相互作用的一種技術(shù)。它利用抗原抗體反應(yīng)的特異性，可以真實(shí)地反映體內(nèi)蛋白因子與基因組DNA結(jié)合的狀況。

答：近年來由于該技術(shù)不斷的發(fā)展和完善，其應(yīng)用范圍已經(jīng)從研究目的蛋白與已知靶序列間的相互作用，發(fā)展到研究目的蛋白與整個(gè)基因組的未知序列的相互作用；從研究一個(gè)目的蛋白與DNA的相互作用，發(fā)展到研究?jī)蓚€(gè)蛋白與DNA共同結(jié)合的相互作用；從研究啟動(dòng)子區(qū)域的組蛋白的修飾，發(fā)展到研究結(jié)合在DNA序列上的蛋白復(fù)合物。

答：生理狀態(tài)下把細(xì)胞內(nèi)的DNA與蛋白質(zhì)交聯(lián)在一起，通過超聲或酶處理將染色質(zhì)切為小片段后，利用抗原抗體的特異性識(shí)別反應(yīng)，將與目的蛋白相結(jié)合的DNA片段沉淀下來。染色質(zhì)免疫沉淀技術(shù)一般包括細(xì)胞固定，染色質(zhì)斷裂，染色質(zhì)免疫沉淀，交聯(lián)反應(yīng)的逆轉(zhuǎn)，DNA的純化，以及DNA的鑒定。因?yàn)镃hIP實(shí)驗(yàn)涉及的步驟多，結(jié)果的重復(fù)性較低，所以對(duì)ChIP實(shí)驗(yàn)過程的每一步都應(yīng)設(shè)計(jì)相應(yīng)的對(duì)照，而且對(duì)結(jié)果的分析也需要有一定的經(jīng)驗(yàn)。

答：不一定，視樣品及試驗(yàn)方案而定。做甲醛固定的為X-ChIP，而不需要固定的為N-ChIP。甲醛能有效的使蛋白質(zhì)-蛋白質(zhì)，蛋白質(zhì)-DNA，蛋白質(zhì)-RNA交聯(lián)，形成生物復(fù)合體，防止細(xì)胞內(nèi)組分的重新分布。甲醛的交聯(lián)反應(yīng)是完全可逆的，便于在后續(xù)步驟中對(duì)DNA和蛋白質(zhì)進(jìn)行分析。甲醛的交聯(lián)反應(yīng)可被加入的甘氨酸終止。

答：為確保ChIP實(shí)驗(yàn)有良好精度。若您的平均片段長(zhǎng)度大于1000bp，您將會(huì)分離獲得包含您目標(biāo)序列的DNA，但所要研究的蛋白會(huì)離您目標(biāo)序列有700個(gè)核苷酸的距離。

答：鮭魚精子用于降低降低染色質(zhì)DNA與瓊脂糖珠子的非特異性結(jié)合。實(shí)驗(yàn)者不太可能對(duì)鮭魚組織做ChIP實(shí)驗(yàn)，所以此DNA不會(huì)因交叉雜交而被PCR引物擴(kuò)增。

答：引物長(zhǎng)度應(yīng)為24個(gè)核苷酸，應(yīng)含有50%GC堿基對(duì)，Tm值為60°C。不要擴(kuò)增大于600-800個(gè)核苷酸的序列。不必考慮基因組內(nèi)不獨(dú)一序列。

答：在ChIP分析試劑盒內(nèi)可找到洗脫緩沖液，用它洗脫復(fù)合物。對(duì)于re-ChIP，有必要添加蛋白酶抑制劑到免疫沉淀洗液和洗脫緩沖液，及第二輪實(shí)驗(yàn)用的稀釋緩沖液。請(qǐng)確定所有溶液處于低溫，蛋白質(zhì)不會(huì)因此而在收集第一次免疫沉淀的復(fù)合物或第二次免疫沉淀時(shí)降解。

答: 蛋白質(zhì)A不能與小鼠IgM結(jié)合?？梢钥紤]用一個(gè)橋接抗體連接。

答: 在細(xì)胞與甲醛交聯(lián)后，細(xì)胞核可通過“溶脹緩沖液”培育及剪刀細(xì)胞均質(zhì)器（dounce homogenization）制備（至少10倍體積）。

溶脹緩沖液：

25M Hepes, pH 7.8

1.5mM MgCl2

10mM KCl

0.1% NP-40

1mM DTT

0.5mM PMSF

蛋白酶抑制劑混合劑

然后按照protocol在SDS裂解液中裂解

答: 1. 確定裂解物在冰上放置了至少10分鐘。不要震蕩或者搖晃裂解物，避免有氣飽（氣泡產(chǎn)生）。超聲波儀會(huì)替你做這些。

2．脈沖應(yīng)在~10秒（與體積一致）。

3. 樣品量小于400 uL間隔應(yīng)大于1分鐘，在EP管中的更大體積間隔大于3分鐘。

4. 避免泡沫。請(qǐng)確定超聲探頭靠近液體底部（不能讓探頭碰到管壁）。

5．若發(fā)現(xiàn)泡沫，立即停止超聲，置于冰上。旋轉(zhuǎn)EP管以去除泡沫，繼續(xù)超聲。

6. 在按“開始”鍵之前將探頭置于液體中。

答: 是，實(shí)際上比起全細(xì)胞，細(xì)胞核更好。我們用全細(xì)胞裂解物，因?yàn)樗?jiǎn)便，通常也能得到好結(jié)果。此頁有一些相關(guān)信息：

http://www./researchtools/protocol.php?protid=10

答：并不推薦少于4個(gè)小時(shí)的逆轉(zhuǎn)交聯(lián). 但是, 可以將樣本在65度過夜逆轉(zhuǎn)交聯(lián).需要注意的是,樣品不能干掉。

答：native ChIP中, Histone H3 and Histone H4 都不需要交聯(lián)反應(yīng), 因?yàn)樗鼈儽旧韥碚f和DNA結(jié)合的非常緊密. 組蛋白H2A和H2B并不是緊密聯(lián)接,但是在native ChIP中依然可以不需要交聯(lián)反應(yīng).

請(qǐng)ChIP初學(xué)者尤其注意此條！

答：從染色質(zhì)上獲得的未做過IP的已經(jīng)被逆轉(zhuǎn)交聯(lián)的DNA. 它是檢查PCR是否有效的對(duì)照。Output DNA是來自每次IP實(shí)驗(yàn)的DNA.其實(shí)就是genomic DNA. 在ChIP實(shí)驗(yàn)中, sonication 或酶解后, 樣本取部分不做IP, 直接逆轉(zhuǎn)交聯(lián). 它的最主要的作用就是檢查PCR系統(tǒng)是否work. 通常情況下, 在該條道中,都可以看到條帶的.如果沒有,說明PCR系統(tǒng)不work.

答：Not likely. 

Formaldehyde is a very reactive dipolar compound in which the carbon atom acts as a nucleophilic center for amino and imino groups of amino acids (Lys, Arg, and His) and of DNA (primarily A and C), leading to the formation of a Schiff base. This intermediate can further react with a second amino group, resulting in the final DNA–protein complex 1-3. Your protein, or the protein-DNA complex, also crosslink with other proteins and lipids, via the same mechanism,. Increasing formaldehyde concentration and/or the incubation time may adversely affect immunoprecipitation. It is recommended that you optimize other parts of the protocol for improvement.

答：DNA purified from ChIP experiments can be quantitated by PCR, providing the amplifying oligos meet specific criteria. Oligos should be 24 mers, with a GC content of 50% (+/- 4) and a Tm of 60.0C (+/- 2.0). You must be certain that the PCR reactions are within the linear range of amplification. Generally it takes time to achieve this. Too much input DNA will affect your results, so set up several tubes for each experiment to optimize the input DNA. Generally, this is about 1/25th to 1/100th for yeast, approximately 1/10 for mammalian cells, but depends on the amount of antibody and input chromatin. Also, do not use more than 20 cycles, making sure that dNTP's always remain in excess. Also, include each reaction a control primer (to compare your experimental band against-make sure the sizes are sufficiently different to allow proper separation-75 base pairs is usually OK) set to a region of the genome that should not change throughout your experimental conditions. Also PCR from purified input DNA (no ChIP) and include no antibody control PCR's as well. PCR products should be no more than 500 base pairs and should span the area of interest (where you think you will see changes in acetylation or methylation of histones). All PCR products should be run on 7-8% acrylamide gels and stained with SYBR Green 1 (Molecular Probes) at a dilution of 1:10,000 (in 1X Tris-borate-EDTA buffer, pH 7.5) for 30 minutes-no destaining is required. Quantitation is carried out subsequent to scanning of the gel on a Molecular Dynamics Storm 840 or 860 in Blue fluorescence mode with PMT voltage at 900 with ImageQuant software. This has distinct advantages over ethidium bromide staining. SYBR Green is much more sensitive, and illumination of ethidium stained gels can vary across the gel based on the quality of UV bulbs in your in your light box. For further info, see Strahl-Bolsinger et al. (1997) Genes Dev. 11: 83-93. A radioactive quantitation method is described in Suka et al (2001) Molec. Cell, 8: 473-479.

答：抗原抗體之間的結(jié)合是通過抗體特異性的識(shí)別抗原表位并結(jié)合的，有的抗體識(shí)別的抗原表位比較小，不容易暴露，在ChIP實(shí)驗(yàn)中容易被DNA包裹，從而使抗體無法結(jié)合，因此用來做ChIP的抗體一般是需要經(jīng)過chip實(shí)驗(yàn)驗(yàn)證的，商業(yè)化的抗體都應(yīng)該是驗(yàn)證過的。

1. Use the volume of SDS lysis buffer you choose, cool on ice 

2. Start sonication with increasing power until foaming occurs. 

3. Lower the power a little. This is the power you can use (for instance, if it starts foaming at 40%, then 35% should be OK). 

4. Cool the above vial and sonicate for one pulse. Touch the vial without glove and it should not be hot (warm is OK), otherwise shorten the time (10-15 seconds are generally used). 

5. Prepare cells in lysis buffer and sonicate for 3, 6, 9 (or whatever you prefer) pulses and check DNA on gel. 

Other things to watch out: 

Load ~1 x 10^5 cell equivalent (This is <0.7 ug DNA)/Lane. 

Make sure you digested all the RNA (The big smiley band) 

Load non-sonicated DNA in one lane.

ChIP reChIP是在第一次ChIP的基礎(chǔ)上不解交聯(lián)，而繼續(xù)進(jìn)行另一個(gè)目的蛋白的免疫沉淀，從而得到與兩種目的蛋白都結(jié)合的DNA序列。值得注意的是，因?yàn)?通過兩次免疫沉淀富集的DNA量比較少，所以在分析時(shí)通常要把多次免疫沉淀的DNA濃縮后再進(jìn)行操作。

答：Protein L is an immunoglobulin-binding protein that originates from the bacteria Peptostreptococcus magnus. Unlike Protein A and Protein G, which bind primarily through Fc regions (i.e., heavy chain) of immunoglobilins, Protein L binds Igs through interactions with the light chains. Since no part of the heavy chain is involved in the binding interaction, Protein L binds a wider range of Ig classes than Protein A or G. Protein L binds to representatives of all classes of Ig, including IgG, IgM, IgA, IgE and IgD. Single chain variable fragments (ScFv) and Fab fragments also bind to Protein L. From http://www./Objects/View.cfm?type=ProductFamilyID=01010323

Despite this wide-ranging binding capability with respect to Ig classes, Protein L is not a universal immunoglobilin-binding protein. Binding of Protein L to immunoglobulins is restricted to those containing kappa light chains (i.e., k chain of the VL domain).1 In humans and mice, kappa (k) light chains predominate. The remaining immunoglobulins have lambda (l) light chains. Furthermore, Protein L is effective in binding only certain subtypes of kappa light chains. For example, it binds human VkI, VkIII and VkIV subtypes but does not bind the VkII subtype. Binding of mouse immunoglobulins is restricted to those having VkI light chains.

It preferentially digests single-stranded DNA and AT or AU-rich regions but is also active against RNA and double-stranded DNA (all sequences are ultimately cleavable). Products of digestion are nucleic acid fragments containing 3' phosphate termini. Exhaustive digestion with excess enzyme yields mono- and dinucleotides. The enzyme requires calcium ions for activity and is easily inactivated by EDTA or EGTA. 

Application. 1. Removal of nucleic acids, especially single-stranded DNA or RNA. 2. Preparation of mRNA-free protein synthesis system from rabbit reticulocyte lysates. 3. Study of chromatin structure.

細(xì)菌應(yīng)該也能用。之前有兩篇論文可以做參考：

Molecular basis for the exploitation of spore formation as survival mechanism by virulent

phage phi29.

WJ Meijer, V Castilla-Llorente, L Villar, H Murray, J Errington, and M Salas

EMBO J, October 19, 2005; 24(20): 3647-57.

http://highwire./cgi/medline/pmid;16193065?maxtoshow=&HITS=&hits=&RESUL

TFORMAT=1&author1=Meijer&andorexacttitle=and&fulltext=molecular+basis+for+the+exploit

ation+of+spore+formation+&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=r

elevance&resourcetype=HWCIT

Identification of TonB homologs in the family Enterobacteriaceae and evidence for

conservation of TonB-dependent energy transduction complexes

RA Larsen, PS Myers, JT Skare, CL Seachord, RP Darveau, and K Postle

J. Bacteriol., Mar 1996; 178: 1363 - 1373.

http://highwire./cgi/searchresults?fulltext=Identification+of+TonB+Homologs&and

orexactfulltext=and&searchsubmit=redo&resourcetype=1&search=Search&author1=Larsen&

pubdate_year=1996&volume=&firstpage=&src=ml

可以。ChIP試劑盒已被成功用于肝臟、脾臟、結(jié)腸和全鼠胚胎。

答: 關(guān)鍵區(qū)別在于DNA的純化方式，EZ ChIP用純化柱純化DNA。

答: 蛋白質(zhì)A結(jié)合到IgG的Fc部分。蛋白質(zhì)G選擇性結(jié)合到IgG的Fc部分，但也能結(jié)合到Fab區(qū)域，因此可用于純化IgG1的Fab片段。

通常情況下，單個(gè)的人細(xì)胞中可得到6.6pg DNA，百萬細(xì)胞可得到7 ug. 4 mg肝組織相當(dāng)于~1.0 x 10^6 liver cells (K562). 有經(jīng)驗(yàn)的用戶往往可以從3 x 10^6 個(gè)細(xì)胞or 11 mg 肝組織中獲取15-30 mg DNA (使用RNase A). 因?yàn)槲覀兺ǔＴ贑hIP實(shí)驗(yàn)中使用約20 ug染色質(zhì)，您可以用2-5百萬個(gè)細(xì)胞。如果您使用染色質(zhì)來標(biāo)準(zhǔn)化ChIP實(shí)驗(yàn)，您就只需要最少的量. 如果您的PCR系統(tǒng)正常，就不會(huì)出現(xiàn)問題，因?yàn)镃hIP只需少量染色質(zhì)，實(shí)驗(yàn)標(biāo)準(zhǔn)化更加重要.

完全可以做，只要保證轉(zhuǎn)染效率。

但是轉(zhuǎn)染的質(zhì)粒在體內(nèi)的行為和染色體基因是不一樣的，因此用這種方法可能得到不同的結(jié)果。

答: 在ChIP分析試劑盒內(nèi)可找到洗脫緩沖液，用它洗脫復(fù)合物。對(duì)于re-ChIP，有必要添加蛋白酶抑制劑到免疫沉淀洗液和洗脫緩沖液，及第二輪實(shí)驗(yàn)用的稀釋緩沖液。請(qǐng)確定所有溶液處于低溫，蛋白質(zhì)不會(huì)因此而在收集第一次免疫沉淀的復(fù)合物或第二次免疫沉淀時(shí)降解。

答: 鮭魚精子用于降低降低染色質(zhì)DNA與瓊脂糖珠子的非特異性結(jié)合。實(shí)驗(yàn)者不太可能對(duì)鮭魚組織做ChIP實(shí)驗(yàn)，所以此DNA不會(huì)因交叉雜交而被PCR引物擴(kuò)增。

答: 是的，該抗體100%在大鼠中100%保守。

答: 關(guān)鍵區(qū)別在于DNA的純化方式，EZ ChIP用純化柱純化DNA。