著者は、このプロトコルの確立の間に彼の優秀なテクニカル サポート 1 月アペルをありがとうございます。Rada イグレシアス研究室で作業に支えられて CMMC 学内資金、DFG 研究助成 (RA 2547/1-1、RA 2547/2-1、および TE 1007/3-1)、カタルーニャ ・ オープン大学上級研究員グループ Grant、および CECAD グラント。

<ol>
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D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Histone+modifications+at+human+enhancers+reflect+global+cell-type-specific+gene+expression.">Histone modifications at human enhancers reflect global cell-type-specific gene expression.</a> Nature. 459 (7243), 108-112 (2009).</li><li>Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S. A., Flynn, R. A., Wysocka, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+unique+chromatin+signature+uncovers+early+developmental+enhancers+in+humans.">A unique chromatin signature uncovers early developmental enhancers in humans.</a> Nature. 470 (7333), 279-283 (2011).</li><li>Creyghton, M. P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Histone+H3K27ac+separates+active+from+poised+enhancers+and+predicts+developmental+state.">Histone H3K27ac separates active from poised enhancers and predicts developmental state.</a> Proc Nat Acad Sci USA. 107 (50), 21931-21936 (2010).</li><li>Benayoun, B. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=H3K4me3+breadth+is+linked+to+cell+identity+and+transcriptional+consistency.">H3K4me3 breadth is linked to cell identity and transcriptional consistency.</a> Cell. 158 (3), 673-688 (2014).</li><li>Rehimi, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Epigenomics-Based+Identification+of+Major+Cell+Identity+Regulators+within+Heterogeneous+Cell+Populations.">Epigenomics-Based Identification of Major Cell Identity Regulators within Heterogeneous Cell Populations.</a> Cell Rep. 17 (11), 3062-3076 (2016).</li><li>Whyte, W. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Master+transcription+factors+and+mediator+establish+super-enhancers+at+key+cell+identity+genes.">Master transcription factors and mediator establish super-enhancers at key cell identity genes.</a> Cell. 153 (2), 307-319 (2013).</li><li>Valouev, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genome-wide+analysis+of+transcription+factor+binding+sites+based+on+ChIP-Seq+data.">Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.</a> Nat Methods. 5 (9), 829-834 (2008).</li><li>Dahl, J. 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著者には、開示すること、競合する金銭的な利益はありません。

エピゲノム チップ seq を使用してヒストン修飾のプロファイリングは、異なる携帯電話4,5,18で脊椎動物のゲノムの機能アノテーションを改善するために使用できます。これらエピゲノム プロファイルは使用できます、他のものの間でエンハンサー エンハンサー (すなわち、アクティブ、プライミング、または構え)?...

ヒストン翻訳後修飾は、転写、複製 DNA 修理1,2,3など、さまざまなクロマチンに依存するプロセスに直接関与しています。さらに、異なるヒストン修飾を示す正 (などH3K4me3 と H3K27ac) または負 (例えばH3K9me3 と H3K27me3) 遺伝子の発現との相関と広く定義することができます活性化または抑圧的なヒストンをマークしたようそれぞれ2,3。その結果、全体的なヒストン修飾マップ、エピゲノム マップとも呼ばれますが、機能的脊椎動物のゲノム4、5の注釈に強力で普遍的なツールとして浮上しています。たとえば、遠位規制エンハンサーを識別できるように基づく系列クロマチンの特定の存在 (例えば、アクティブなエンハンサー: H3K4me1 と H3K27ac)、近位プロモーター領域からそれらを区別する (など活性プロモーター: H3K4me3)6,7,8。その一方で、主要な細胞アイデンティティの規定する機能を持つ遺伝子、通常、広範なクロマチン ドメインそれぞれ根本的な遺伝子の転写活性アクティブまたは非アクティブの状態に応じて H3K4me3 と H3K27me3、マーク9 で発見します。 ,10。同様に、主要な細胞アイデンティティ遺伝子発現クラスター化エンハンサー (すなわち、超エンハンサー) 広範な H3K27ac マーク ドメイン11として識別することができます複数のと空間的に制御する頻繁にようであります。
現在、ヒストン修正図を生成する技術を使用してチップ seq チップ (チップ マイクロ アレイに結合) などの従来のアプローチと比較して高い解像度、ノイズ、大きい範囲、および下位以下の少ないアーティファクトを提供しますコスト12。それにもかかわらず、エピゲノム マップ チップ seq 技術を使用しての世代が関心のサンプル チップを正常に実行する能力と大抵関連付けられるその固有の限界あります。伝統的なチップ プロトコルは通常細胞の培養系にこの法の適用性線またはセル範囲が制限簡単に分離できます生体内で(例えば、血液細胞) 細胞の数百万を必要です。ここ数年で低細胞数と互換性のあるチップ プロトコルの修正の数は説明13,14,15,16をされています。ただし、これらのプロトコルを次世代シーケンス (すなわち、チップ seq) と結合される設計、彼らは通常アドホック図書館準備方法13,14,を使用15,16。
ここでは、我々 は中間に低細胞数 (5 × 104 - 5 x 10 の5セル) を使用して、ヒストン変更プロファイルを調査するためチップ プロトコルを記述した (すなわち、チップ qPCR) いずれかの選択した軌跡またはグローバル (すなわち、チップ seq) (図 1)。チップ seq 技術を組み合わせることで、当社のチップ プロトコルは標準ライブラリの製法をできるようになり、多くの研究所10に幅広くアクセスと共に使用できます。このプロトコルは、いくつかのヒストンを調査に使用されている(例えば、 H3K4me3、H3K27me3、および H3K27ac) 異なる鶏胚組織 (例えば、脊髄神経管 (SNT)、成人プロミネンスと胚盤葉上層) で。ただし、少量で、生物学的および臨床的に関連するサンプルをだけ得ることが他の生物に広く適用されると見込んでください。

<table><tbody><tr><td>&lt;strong&gt;Reagent&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>BSA powder</td><td>Carl Roth</td><td>3737.3</td><td></td></tr><tr><td>Phosphate Saline buffer (PBS)</td><td>Sigma Aldrich</td><td>D8537</td><td></td></tr><tr><td>Tris-HCL pH 8.0</td><td>Sigma Aldrich</td><td>T1503</td><td></td></tr><tr><td>NaCl</td><td>Carl Roth</td><td>3957.2</td><td></td></tr><tr><td>EDTA</td><td>Carl Roth</td><td>8043.2</td><td></td></tr><tr><td>EGTA</td><td>Carl Roth</td><td>3054.2</td><td></td></tr><tr><td>Na-Deoxycholate</td><td>Sigma Aldrich</td><td>D6750-24</td><td></td></tr><tr><td>N-lauroylsarcosine</td><td>Sigma Aldrich</td><td>61743-25G</td><td></td></tr><tr><td>Hepes</td><td>Applichem</td><td>A3724,0250</td><td></td></tr><tr><td>LiCl</td><td>Carl Roth</td><td>3739.2</td><td></td></tr><tr><td>NP-40</td><td>Sigma Aldrich</td><td>I3021-100ml</td><td></td></tr><tr><td>SDS</td><td>Carl Roth</td><td>1833</td><td></td></tr><tr><td>Protein G/magnetic beads</td><td>Invitrogen</td><td>1004D</td><td></td></tr><tr><td>37% Formaldehyde</td><td>Sigma Aldrich</td><td>252549-1L</td><td></td></tr><tr><td>Glycine</td><td></td><td></td><td></td></tr><tr><td>RNase</td><td>Peqlab</td><td>12-RA-03</td><td></td></tr><tr><td>Proteinase K</td><td>Sigma Aldrich</td><td>46.35 E</td><td></td></tr><tr><td>Na-butyrate</td><td>Sigma Aldrich</td><td>SLB2659V</td><td></td></tr><tr><td>Proteinase inhibitor</td><td>Roche</td><td>5892791001</td><td></td></tr><tr><td>SYBRgreen Mix</td><td>biozym</td><td>617004</td><td></td></tr><tr><td>dH&lt;sub&gt;2&lt;/sub&gt;O</td><td>Sigma Aldrich</td><td>W4502</td><td></td></tr><tr><td>1 Kb ladder</td><td>Thermofisher</td><td>SM1333</td><td></td></tr><tr><td>Orange G</td><td>Sigma Alrich</td><td>03756-25</td><td></td></tr><tr><td>Agarose</td><td>Invitrogen</td><td>16500-500</td><td></td></tr><tr><td>0.25% Trypsin-EDTA (1x)</td><td>Gibco</td><td>25200-072</td><td></td></tr><tr><td>Octylphenol Ethoxylate (Triton X 100)</td><td>Roth</td><td>3051.4</td><td></td></tr><tr><td>DMEM (Dulbecco&amp;acute;s Modified Eagle Medium)</td><td>Gibco</td><td>31331-028</td><td></td></tr><tr><td>Gel loading tips Multiflex</td><td>A.Hartenstein</td><td>GS21</td><td></td></tr><tr><td>qPCR Plates</td><td>Sarstedt</td><td>721,985,202</td><td></td></tr><tr><td>384 well</td><td>Sarstedt</td><td>721,985,202</td><td></td></tr><tr><td>1.5 mL tubes</td><td>Sarstedt</td><td>72,706</td><td></td></tr><tr><td>100 - 1,000 &amp;micro;L Filter tips</td><td>Sarstedt</td><td>70,762,211</td><td></td></tr><tr><td>2 - 20 &amp;micro;L Filter tips</td><td>Sarstedt</td><td>70,760,213</td><td></td></tr><tr><td>2 - 200 &amp;micro;L Filter tips</td><td>Sarstedt</td><td>70,760,211</td><td></td></tr><tr><td>0.5 - 10 &amp;micro;L Filter tips</td><td>Sarstedt</td><td>701,116,210</td><td></td></tr><tr><td>H3K27me3 antibody</td><td>Active Motif</td><td>39155</td><td></td></tr><tr><td>H3K27ac antibody</td><td>Active Motif</td><td>39133</td><td></td></tr><tr><td>H3K4me3 antibody</td><td>Active Motif</td><td>39159</td><td></td></tr><tr><td>H3K4me2 antibody</td><td>Active Motif</td><td>39141</td><td></td></tr><tr><td>End Repair Mix</td><td>Illumina</td><td>FC-121-4001</td><td></td></tr><tr><td>Paramagnetic beads</td><td>Beckman Coulter</td><td>A63881</td><td></td></tr><tr><td>Resuspension buffer</td><td>Illumina</td><td>FC-121-4001</td><td></td></tr><tr><td>A-Tailing Mix</td><td>Illumina</td><td>FC-121-4001</td><td></td></tr><tr><td>Ligation Mix</td><td>Illumina</td><td>FC-121-4001</td><td></td></tr><tr><td>RNA Adapter Indexes</td><td>Illumina</td><td>RS-122-2101</td><td></td></tr><tr><td>Stop Ligation Buffer</td><td>Illumina</td><td>FC-121-4001</td><td></td></tr><tr><td>PCR Primer Cocktail</td><td>Illumina</td><td>FC-121-4001</td><td></td></tr><tr><td>Enhanced PCR Mix</td><td>Illumina</td><td>FC-121-4001</td><td></td></tr><tr><td>Genomic DNA ladder</td><td>Agilent</td><td>5067-5582</td><td></td></tr><tr><td>Elution Buffer</td><td>Agilent</td><td>19086</td><td></td></tr><tr><td>Sample Buffer</td><td>Agilent</td><td>5067-5582</td><td></td></tr><tr><td>Library Quantification Kit</td><td>Kapa Biosystems</td><td>KK4835 &amp;ndash; 07960204001</td><td></td></tr><tr><td>Fertile chicken white eggs</td><td>LSL Rhein Main</td><td>KN: 15968</td><td></td></tr><tr><td>Needle (Neoject)</td><td>A.Hartenstein</td><td>10001</td><td></td></tr><tr><td>Syringe (Ecoject 10 mL)</td><td>Dispomed witt oHG</td><td>21010</td><td></td></tr><tr><td>&lt;strong&gt;Name&lt;/strong&gt;</td><td>&lt;strong&gt;Company&lt;/strong&gt;</td><td>&lt;strong&gt;Catalog Number&lt;/strong&gt;</td><td>&lt;strong&gt;Comments&lt;/strong&gt;</td></tr><tr><td>&lt;strong&gt;Equipment&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Centrifuge</td><td>Hermle</td><td>Z 216 MK</td><td></td></tr><tr><td>Thermoshaker</td><td>ITABIS</td><td>MKR13</td><td></td></tr><tr><td>Sonicator</td><td>Active Motive</td><td>EpiShear probe sonicator</td><td></td></tr><tr><td>Sonicator</td><td>Diagenode</td><td>Bioruptor Plus</td><td></td></tr><tr><td>Rotator</td><td>Stuart</td><td>SB3</td><td></td></tr><tr><td>Variable volume (5 &amp;ndash;1,000 &amp;mu;L) pipettes</td><td>Eppendorf</td><td>N/A</td><td></td></tr><tr><td>Timer</td><td>Sigma</td><td>N/A</td><td></td></tr><tr><td>Magnetic holder</td><td>Thermo Fisher</td><td>DynaMag-2 12321D</td><td></td></tr><tr><td>Table spinner</td><td>Heathrow Scientific</td><td>Sprout</td><td></td></tr><tr><td>Mixer</td><td>LMS</td><td>VTX 3000L</td><td></td></tr><tr><td>Real-Time PCR Cycler</td><td>Roche</td><td>Light Cycler; Serial Nr.5662</td><td></td></tr><tr><td>PCR Cycler</td><td>Applied Biosystems</td><td>Gene Amp PCR System 9700</td><td></td></tr><tr><td>DNA and RNA quality control system</td><td>Agilent</td><td>Agilent 4200 TapeStation System</td><td></td></tr><tr><td>Forceps</td><td>Dumont</td><td>5-Inox-H</td><td></td></tr><tr><td>Perforated spoon</td><td>World precision instruments</td><td>501997</td><td></td></tr></tbody></table>

chromatin immunoprecipitation (chip) protocol for low-abundance embryonic samples

クロマチン免疫沈降 (チップ) は、クロマチン修飾酵素特定の軌跡やゲノム規模で、転写因子やヒストン ファーストクリーニング変更されたヒストンのローカリゼーションをマッピングするための広く使われている手法です。次世代シーケンス (すなわち、チップ Seq) とチップ試金の組み合わせは、遺伝子制御ネットワークを世界的に明らかにして特に規制の非コーディング シーケンスのゲノムの機能アノテーションを改善する強力なアプローチです。チップ プロトコルは通常多量の細胞材料、従ってまれなセルタイプまたは小さい組織生検の調査にこの法の適用性を排除を必要です。チップ試金を初期脊椎動物胚体内で通常得られる生物学的材料の量に対応するために、するために述べるここでチップの簡易プロトコルを完了するために必要なステップ数、アッセイは、サンプルの損失を最小限に抑えるために減少しました。このチップ プロトコルは様々 なニワトリ胚および成体組織中細胞数 (5 × 104 - 5 x 10 の5セル) に低の異なるヒストン修飾を調査するため正常に使用されています。重要なは、このプロトコルは標準ライブラリの作製法を用いたチップ seq 技術と互換性のある、関連性の高い萌芽期ティッシュのマップ グローバル エピゲノムを提供します。

チップ seq 実験 HH19 鶏の胚からプールの SNT セクションを使用して、HH22 の上顎突起鶏胚との結合プロファイルを調査する段階 HH3 鶏胚を行ったチップ プロトコルのパフォーマンスを示すためには、各種のヒストンの修正は (すなわちH3K4me2、H3K27ac、H3K4me3、および H3K27me3)。チップ Dna が得られた後、超音波処理効率は対応する入力 Dna (図 3) ?...

Watch this Scientific Journal Video about Chromatin Immunoprecipitation ChIP Protocol for Low-abundance Embryonic Samples at JoVE.com

Chromatin Immunoprecipitation ChIP Protocol for Low-abundance Embryonic Samples

ここでは、クロマチン免疫沈降 (チップ) と低豊富な鶏胚サンプルからグローバル エピゲノム プロファイルを生成するチップ seq ライブラリの準備のプロトコルについて述べる。

クロマチン免疫沈降 (チップ) プロトコル低豊富な胚サンプル

Chromatin immunoprecipitation (ChIP) is a widely-used technique for mapping the localization of post-translationally modified histones, histone variants, ...

chromatin-immunoprecipitation-chip-protocol-for-low-abundance

Universidad de Cartagena UDEC

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Genetics

Chromatin Immunoprecipitation (ChIP) Protocol for Low-abundance Embryonic Samples

15.6K ビュー.  University of Cologne. ここでは、クロマチン免疫沈降 (チップ) と低豊富な鶏胚サンプルからグローバル エピゲノム プロファイルを生成するチップ seq ライブラリの準備のプロトコルについて述べる。

ビデオ: Chromatin Immunoprecipitation ChIP Protocol for Low-abundance Embryonic Samples

Genome-wide Snapshot of Chromatin Regulators and States in Xenopus Embryos by ChIP-Seq

The recruitment of chromatin regulators and the assignment of chromatin states to specific genomic loci are pivotal to cell fate decisions and tissue and organ formation during development. Determining the locations and levels of such chromatin features in vivo will provide valuable information about the spatio-temporal regulation of genomic elements, and will support aspirations to mimic embryonic tissue development in vitro. The most commonly used method for genome-wide and high-resolution profiling is chromatin immunoprecipitation followed by next-generation sequencing (ChIP-Seq). This protocol outlines how yolk-rich embryos such as those of the frog Xenopus can be processed for ChIP-Seq experiments, and it offers simple command lines for post-sequencing analysis. Because of the high efficiency with which the protocol extracts nuclei from formaldehyde-fixed tissue, the method allows easy upscaling to obtain enough ChIP material for genome-wide profiling. Our protocol has been used successfully to map various DNA-binding proteins such as transcription factors, signaling mediators, components of the transcription machinery, chromatin modifiers and post-translational histone modifications, and for this to be done at various stages of embryogenesis. Lastly, this protocol should be widely applicable to other model and non-model organisms as more and more genome assemblies become available.

Genome-wide Snapshot of Chromatin Regulators and States in Xenopus Embryos by ChIP-Seq

The question of how chromatin regulators and chromatin states affect the genome in vivo is key to our understanding of how early cell fate decisions are made in the developing embryo. ChIP-Seq&#8212;the most popular approach to investigate chromatin features at a global level&#8212;is outlined here for Xenopus embryos.

クロマチンレギュレータと米国でのゲノムワイドスナップショット<em&gt;アフリカツメガエル</emChIPの-配列によって&gt;胚

The recruitment of chromatin regulators and the assignment of chromatin states to specific genomic loci are pivotal to cell fate decisions and tissue and ...

発生生物学

Epigenetic Regulation of Cardiac Differentiation of Embryonic Stem Cells and Tissues

Specific gene transcription is a key biological process that underlies cell fate decision during embryonic development. The biological process is mediated by transcription factors which bind genomic regulatory regions including enhancers and promoters of cardiac constitutive genes. DNA is wrapped around histones that are subjected to chemical modifications. Modifications of histones further lead to repressed, activated or poised gene transcription, thus bringing another level of fine tuning regulation of gene transcription. Embryonic Stem cells (ES cells) recapitulate within embryoid bodies (i.e., cell aggregates) or in 2D culture the early steps of cardiac development. They provide in principle enough material for chromatin immunoprecipitation (ChIP), a technology broadly used to identify gene regulatory regions. Furthermore, human ES cells represent a human cell model of cardiogenesis. At later stages of development, mouse embryonic tissues allow for investigating specific epigenetic landscapes required for determination of cell identity. Herein, we describe protocols of ChIP, sequential ChIP followed by PCR or ChIP-sequencing using ES cells, embryoid bodies and cardiac specific embryonic regions. These protocols allow to investigating the epigenetic regulation of cardiac gene transcription.

A fine tuning regulation of gene transcription underlies embryonic cell fate decision. Herein, we describe chromatin immunoprecipitation assays used to investigate epigenetic regulation of both cardiac differentiation of stem cells and cardiac development of mouse embryos.

胚性幹細胞や組織の心臓分化のエピジェネティック制御

Specific gene transcription is a key biological process that underlies cell fate decision during embryonic development. The biological process is mediated ...

Chromatin Immunoprecipitation of Murine Brown Adipose Tissue

Most cellular processes are regulated by transcriptional modulation of specific gene programs. Such modulation is achieved through the combined actions of a wide range of transcription factors (TFs) and cofactors mediating transcriptional activation or repression via changes in chromatin structure. Chromatin immunoprecipitation (ChIP) is a useful molecular biology approach for mapping histone modifications and profiling transcription factors/cofactors binding to DNA, thus providing a snapshot of the dynamic nuclear changes occurring during different biological processes.
To study transcriptional regulation in adipose tissue, samples derived from in vitro cell cultures of immortalized or primary cell lines are often favored in ChIP assays because of the abundance of starting material and reduced biological variability. However, these models represent a limited snapshot of the actual chromatin state in living organisms. Thus, there is a critical need for optimized protocols to perform ChIP on adipose tissue samples derived from animal models.
Here we describe a protocol for efficient ChIP-seq of both histone modifications and non-histone proteins in brown adipose tissue (BAT) isolated from a mouse. The protocol is optimized for investigating genome-wide localization of proteins of interest and epigenetic markers in the BAT, which is a morphologically and physiologically distinct tissue amongst fat depots.

Here we describe a protocol for efficient chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) of brown adipose tissue (BAT) isolated from a mouse. This protocol is suitable for both mapping histone modifications and investigating genome-wide localization of non-histone proteins of interest in vivo.

マウスの褐色脂肪組織のクロマチン免疫沈降

Most cellular processes are regulated by transcriptional modulation of specific gene programs. Such modulation is achieved through the combined actions of ...

遺伝学

Chromatin Immunoprecipitation from Human Embryonic Stem Cells

The functional and structural complexity of the myriad of cells in metazoan organisms arises from a small number of stem cells. Stem cells are characterized by two fundamental properties: self-renewal and multipotency that allows a stem cell to differentiate into virtually any cell type 1. The progression stem cell to differentiated cell is characterized by loss of multipotency, structural and morphological changes and the hierarchic activity of transcription factors and signaling molecules, whose activities establish and maintain cell-type specific gene expression patterns. At the molecular level, cell differentiation involves dynamic changes of the structure and composition of chromatin and the detection of those dynamic changes can provide valuable insights into the functional features of stem cells and the cell differentiation process 2,3. Chromatin is a highly compacted DNA-protein complex that forms when cells package chromosomal DNA with proteins, mainly histones 4. Stemcellness and cell differentiation has been correlated with the presence of specific arrays of regulatory proteins such as epigenetic factors, histone variants, and transcription factors 2,3,5.
 Chromatin immunoprecipitation (ChIP) provides a valuable method to monitor the presence of RNA, proteins, and protein modifications in chromatin 6,7. The comparison of chromatin from different cell types can elucidate dynamic changes in protein-chromatin associations that occur during cell differentiation.
Chromatin immunoprecipitation involves the purification of in vivo cross-linked chromatin. The isolated chromatin is reduced to smaller fragments by enzymatic digestion or mechanical force. Chromatin fragments are precipitated using specific antibodies to target proteins or protein and DNA modifications. The precipitated DNA or RNA is purified and used as a template for PCR or DNA microarray based assays. Prerequisites for a successful ChIP are high quality antibodies to the desired antigen and the availability of chromatin from control cells that do not express the target molecule. ChIP can correlate the presence of proteins, protein and RNA modifications, and RNA with specific target DNA, and depending on the choice of outread tool, detects the association of target molecules at specific target genes or in the context of an entire genome. The comparison of the distribution of proteins in the chromatin of differentiating cells can elucidate the dynamic changes of chromatin composition that coincide with the progression of cells along a cell lineage.

The differentiation of ESC coincides with cell-type specific changes in the structure and composition of chromatin. The detection of those changes provides valuable insights into the mechanisms that define stemcellness and cell differentiation. Chromatin immunoprecipitation (ChIP) represents a valuable method to dissect the molecular mechanisms underlying stem cell differentiation.

ヒト胚性幹細胞からクロマチン免疫沈降

The functional and structural complexity of the myriad of cells in metazoan organisms arises from a small number of stem cells. Stem cells are ...

生物学

Chromatin Immunoprecipitation Assay Using Micrococcal Nucleases in Mammalian Cells

To express cellular phenotypes in organisms, living cells execute gene expression accordingly, and transcriptional programs play a central role in gene expression. The cellular transcriptional machinery and its chromatin modification proteins coordinate to regulate transcription. To analyze transcriptional regulation at the molecular level, several experimental methods such as electrophoretic mobility shift, transient reporter and chromatin immunoprecipitation (ChIP) assays are available. We describe a modified ChIP assay in detail in this article because of its advantages in directly showing histone modifications and the interactions between proteins and DNA in cells. One of the key steps in a successful ChIP assay is chromatin shearing. Although sonication is commonly used for shearing chromatin, it is difficult to identify reproducible conditions. Instead of shearing chromatin by sonication, we utilized enzymatic digestion with micrococcal nuclease (MNase) to obtain more reproducible results. In this article, we provide a straightforward ChIP assay protocol using MNase.

Chromatin immunoprecipitation (ChIP) is a powerful tool for understanding the molecular mechanisms of gene regulation. However, the method involves difficulties in obtaining reproducible chromatin fragmentation by mechanical shearing. Here, we provide an improved protocol for a ChIP assay using enzymatic digestion.

哺乳類細胞における微小コッカルヌクレアーゼを用いてクロマチン免疫沈殿アッセイ

To express cellular phenotypes in organisms, living cells execute gene expression accordingly, and transcriptional programs play a central role in gene ...

CARIP-Seq and ChIP-Seq: Methods to Identify Chromatin-Associated RNAs and Protein-DNA Interactions in Embryonic Stem Cells

Embryonic stem (ES) cell self-renewal&#160;and differentiation is governed by extrinsic signals and intrinsic networks of transcription factors, epigenetic regulators, and post-translation modifications of histones that combinatorially influence the gene expression state of nearby genes. RNA has also been shown to interact with various proteins to regulate chromatin dynamics&#160;and gene expression. Chromatin-associated RNA immunoprecipitation (CARIP) followed by next-generation sequencing (CARIP-Seq) is a novel method to survey RNAs associated with chromatin proteins, while chromatin immunoprecipitation followed by next-generation sequencing (ChIP-Seq) is a powerful genomics technique to map the location of post-translational modification of histones, transcription factors, and epigenetic modifiers on a global-scale in ES cells. Here, we describe methods to perform CARIP-Seq and ChIP-Seq, including library construction for next-generation sequencing, to generate global chromatin-associated RNA and epigenomic maps in ES cells.

Here, we describe methods to perform ChIP-Seq and CARIP-Seq, including library preparation for next-generation sequencing, to generate global epigenomic and chromatin-associated RNA maps in ES cells.

CARIP Seq とチップ Seq: クロマチン結合 Rna および胚性幹細胞における蛋白質 DNA 相互作用を識別する方法

Embryonic stem (ES) cell self-renewal&#160;and differentiation is governed by extrinsic signals and intrinsic networks of transcription factors, ...

Chromatin Immunoprecipitation Assay for Tissue-specific Genes using Early-stage Mouse Embryos

Chromatin immunoprecipitation (ChIP) is a powerful tool to identify protein:chromatin interactions that occur in the context of living cells 1-3. This technique has been widely exploited in tissue culture cells, and to a lesser extent, in primary tissue. The application of ChIP to rodent embryonic tissue, especially at early times of development, is complicated by the limited amount of tissue and the heterogeneity of cell and tissue types in the embryo. Here we present a method to perform ChIP using a dissociated embryonic day 8.5 (E8.5) embryo. Sheared chromatin from a single E8.5 embryo can be divided into up to five aliquots, which allows the investigator sufficient material for controls and for investigation of specific protein:chromatin interactions.
We have utilized this technique to begin to document protein:chromatin interactions during the specification of tissue-specific gene expression programs. The heterogeneity of cell types in an embryo necessarily restricts the application of this technique because the result is the detection of protein:chromatin interactions without distinguishing whether the interactions occur in all, a subset of, or a single cell type(s). However, examination of tissue-specific genes during or following the onset of tissue-specific gene expression is feasible for two reasons. First, immunoprecipitation of tissue specific factors necessarily isolates chromatin from the cell type where the factor is expressed. Second, immunoprecipitation of coactivators and histones containing post-translational modifications that are associated with gene activation should only be found at genes and gene regulatory sequences in the cell type where the gene is being or has been activated. The technique should be applicable to the study of most tissue-specific gene activation events.
In the example described below, we utilized E8.5 and E9.5 mouse embryos to examine factor binding at a skeletal muscle specific gene promoter. Somites, which are the precursor tissues from which the skeletal muscles of the trunk and limbs will form, are present at E8.5-9.54,5. Myogenin is a regulatory factor required for skeletal muscle differentiation 6-9. The data demonstrate that myogenin is associated with its own promoter in E8.5 and E9.5 embryos. Because myogenin is only expressed in somites at this stage of development 6,10, the data indicate that myogenin interactions with its own promoter have already occurred in skeletal muscle precursor cells in E8.5 embryos.

We demonstrate a chromatin immunoprecipitation (ChIP) method to identify factor interactions at tissue-specific genes during or after the onset of tissue-specific gene expression in mouse embryonic tissue. This protocol should be widely applicable for the study of tissue-specific gene activation as it occurs during normal embryonic development.

初期段階のマウス胚を用いて組織特異的遺伝子のためのクロマチン免疫沈降アッセイ

Chromatin immunoprecipitation (ChIP) is a powerful tool to identify protein:chromatin interactions that occur in the context of living cells 1-3. This ...

Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark

Brain development is a complex process, which is controlled in a temporo-spatial manner by gradients of morphogens and different transcriptional programs. Additionally, epigenetic chromatin modifications, like histone methylation, have an important role for establishing and maintaining specific cell fates within this process. The vast majority of histone methylation occurs on the flexible histone tail, which is accessible to histone modifiers, erasers, and histone reader proteins. In contrast, H3K79 methylation is located in the globular domain of histone 3 and is implicated in different developmental functions. H3K79 methylation is evolutionarily conserved and can be found in a wide range of species from Homo sapiens to Saccharomyces cerevisiae. The modification occurs in different cell populations within organisms, including neural progenitors. The location of H3K79 methylation in the globular domain of histone 3 makes it difficult to assess. Here, we present methods to isolate and culture cortical progenitor cells (CPCs) from embryonic cortical brain tissue (E11.5-E14.5) or cerebellar granular neuron progenitors (CGNPs) from postnatal tissue (P5-P7), and to efficiently immunoprecipitate H3K79me2 for quantitative PCR (qPCR) and genome-wide sequencing.

We present an effective and reproducible method to isolate and culture neural progenitor cells from embryonic and postnatal brain tissue for chromatin immunoprecipitation (ChIP) of histone 3 lysine 79 dimethylation (H3K79me2) - a histone mark located within the globular domain of histone 3.

3 ヒストンのリジン 79 ジメチル化マークのクロマチン免疫沈降に続いて神経前駆細胞の分離と培養

Brain development is a complex process, which is controlled in a temporo-spatial manner by gradients of morphogens and different transcriptional programs. ...

神経科学

Efficient Chromatin Immunoprecipitation using Limiting Amounts of Biomass

Chromatin immunoprecipitation (ChIP) is a widely-used method for determining the interactions of different proteins with DNA in chromatin of living cells. Examples include sequence-specific DNA binding transcription factors, histones and their different modification states, enzymes such as RNA polymerases and ancillary factors, and DNA repair components. Despite its ubiquity, there is a lack of up-to-date, detailed methodologies for both bench preparation of material and for accurate analysis allowing quantitative metrics of interaction. Due to this lack of information, and also because, like any immunoprecipitation, conditions must be re-optimized for new sets of experimental conditions, the ChIP assay is susceptible to inaccurate or poorly quantitative results.
Our protocol is ultimately derived from seminal work on transcription factor:DNA interactions1,2 , but incorporates a number of improvements to sensitivity and reproducibility for difficult-to-obtain cell types. The protocol has been used successfully3,4 , both using qPCR to quantify DNA enrichment, or using a semi-quantitative variant of the below protocol.
This quantitative analysis of PCR-amplified material is performed computationally, and represents a limiting factor in the assay. Important controls and other considerations include the use of an isotype-matched antibody, as well as evaluation of a control region of genomic DNA, such as an intergenic region predicted not to be bound by the protein under study (or anticipated not to show changes under the experimental conditions). In addition, a standard curve of input material for every ChIP sample is used to derive absolute levels of enrichment in the experimental material. Use of standard curves helps to take into account differences between primer sets, regardless of how carefully they are designed, and also efficiency differences throughout the range of template concentrations for a single primer set. Our protocol is different from others that are available5-8 in that we extensively cover the later, analysis phase.

We describe a robust method for chromatin immunoprecipitation using primary T cells. The method is founded on standard approaches, but uses a specific set of conditions and reagents that improve efficiency for limited a quantities of cells. Importantly, a detailed description of the data analysis phase is presented.

バイオマスの制限額を使用して効率的なクロマチン免疫沈降

Chromatin immunoprecipitation (ChIP) is a  widely-used method for determining the interactions of different proteins with  DNA in chromatin of living ...

Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo

Intricate gene regulatory networks orchestrate biological processes and developmental transitions in plants. Selective transcriptional activation and silencing of genes mediate the response of plants to environmental signals and developmental cues. Therefore, insights into the mechanisms that control plant gene expression are essential to gain a deep understanding of how biological processes are regulated in plants. The chromatin immunoprecipitation (ChIP) technique described here is a procedure to identify the DNA-binding sites of proteins in genes or genomic regions of the model species Arabidopsis thaliana. The interactions with DNA of proteins of interest such as transcription factors, chromatin proteins or posttranslationally modified versions of histones can be efficiently analyzed with the ChIP protocol. This method is based on the fixation of protein-DNA interactions in vivo, random fragmentation of chromatin, immunoprecipitation of protein-DNA complexes with specific antibodies, and quantification of the DNA associated with the protein of interest by PCR techniques. The use of this methodology in Arabidopsis has contributed significantly to unveil transcriptional regulatory mechanisms that control a variety of plant biological processes. This approach allowed the identification of the binding sites of the Arabidopsis chromatin protein EBS to regulatory regions of the master gene of flowering FT. The impact of this protein in the accumulation of particular histone marks in the genomic region of FT was also revealed through ChIP analysis.

Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo

Chromatin immunoprecipitation is a powerful technique for the identification of DNA binding sites of Arabidopsis proteins in vivo. This procedure includes chromatin cross-linking and fragmentation, immunoprecipitation with selective antibodies against the protein of interest, and qPCR analysis of bound DNA. We describe a simple ChIP assay optimized for Arabidopsis plants.

シロイヌナズナタンパク質-DNA相互作用の同定のための免疫沈降アッセイクロマチン<em&gt;インビボ</em

Intricate gene regulatory networks orchestrate biological processes and developmental transitions in plants. Selective transcriptional activation and ...

クロマチン免疫沈降 (チップ) プロトコル低豊富な胚サンプル

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クロマチンレギュレータと米国でのゲノムワイドスナップショット