Name: carip-seq and chip-seq: methods to identify chromatin-associated rnas and protein-dna interactions in embryonic stem cells
Uploaded: 2018-05-25T14:00:00
Description: Watch this Scientific Journal Video about CARIP-Seq and ChIP-Seq: Methods to Identify Chromatin-Associated RNAs and Protein-DNA Interactions in Embryonic Stem Cells at JoVE.com

Dette arbejde blev støttet af Wayne State University, Karmanos Cancer Institute, et tilskud fra National Heart, Lung og Blood Institute (1K22HL126842-01A1) tildeles B.L.K. Dette arbejde udnyttes Wayne State University høj Performance Computing gitteret for it-ressourcer (< https://www.grid.wayne.edu/>). Vi takker Jiji Kurup for bistand med CARIP-Seq dataanalyse.
FORFATTERNES BIDRAG:
B.L.K. udtænkt af metoden CARIP-FF., designet og udført ChIP-FF. og CARIP FF. eksperimenter, analyseret sequencing data og udarbejdet manuskriptet. Alle forfattere har læst og godkendt den endelige version af dette manuskript.

1. kultur af musen ES-celler i Feeder-fri betingelser.
Bemærk: Mus ES celler er konventionelt kulturperler i medierne på en celle kultur fad belagt med gelatine og et mono-lag af musen embryonale fibroblaster (MEF), der har været mitotically inaktiverede (iMEFs). MEFs skal dog fjernes inden downstream epigenetiske eller udtryk analyser at forhindre forurening af MEF-associerede kromatin og RNA.
<ol><li>Forberedelse af en feeder lag: gelatine coat en 6-godt celle kultur plade ved tilsætni...

<ol>
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L., Hu, G., Zhao, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ChIP-Seq:+technical+considerations+for+obtaining+high-quality+data.">ChIP-Seq: technical considerations for obtaining high-quality data.</a> Nat Immunol. 12 (10), 918-922 (2011).</li><li>Quail, M. 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=A+large+genome+center's+improvements+to+the+Illumina+sequencing+system.">A large genome center's improvements to the Illumina sequencing system.</a> Nat Methods. 5 (12), 1005-1010 (2008).</li><li>Schmidl, C., Rendeiro, A. F., Sheffield, N. 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ChIP-Seq er en nyttig metode til at vurdere placeringen af globale protein-DNA interaktioner (fx., transskription faktorer/Histon ændre enzymer/Histon ændringer og DNA) i ES-celler, mens den nyudviklede CARIP-Seq protokol er nyttige i afhører genome-wide association af RNA'er med kromatin bestanddele. ChIP-Seq er et grundlæggende redskab, der bruges til at evaluere epigenetiske landskaber af ES-celler og andre celletyper. Kvaliteten af ChIP-FF. og CARIP FF. biblioteker er i vid udstrækning afhængig af ChIP...

Embryonale stamceller (ES) celle skæbne beslutninger er reguleret af kommunikation mellem ekstracellulære signaler og et væld af transcriptional-regulatorer, herunder Histon modifikatorer, og efter oversættelse ændring af Histon haler. Disse interaktioner lette kromatin tilgængelighed og emballering af kromatin i en af to tilstande: euchromatin, som er åben og transcriptionally aktive, og heterochromatin, som er kompakt og generelt transcriptionally inaktive. Transkriptionsfaktorer med DNA sekvens-specifikke bindende tilhørsforhold og epigenetiske modifikatorer associeret med euchromatic regioner til at deltage i kontrol af genekspression. Næste generations sekventering metoder, herunder ChIP-Seq1, har været medvirkende til kortlægning genome-wide transcriptional netværk, der er grundlæggende for ES celle selvfornyelse og pluripotency2,3,4 ,5,6. Desuden, mens RNA immunopreciation efterfulgt af næste generation sequencing (RIP-Seq)7 evalueringer af RNA-protein interaktioner tyder på, at DNA-bindende proteiner interagere med RNA'er at regulere transcriptional begivenheder7, 8 , 9 , 10 , 11 , 12, få studier har undersøgt genome-wide lokalisering af RNA'er tilknyttet kromatin12eller globale interaktioner mellem RNA og Histon ændringer. Længe ikke-kodende RNA'er (lncRNAs) er en klasse af RNA'er, som er blevet fundet for at regulerer aktiviteten af kromatin-associerede proteiner13,14,15. For eksempel, er Xist en lncRNA, der regulerer, i kvindelige pattedyrceller, inaktivering af et X-kromosom, gennem ansættelse af epigenetiske repressors16,17. Men det fulde spektrum af RNA'er tilknyttet kromatin er stort set ukendt. Her, beskriver vi en roman protokol, kromatin-associerede RNA immunoprecipitation (CARIP) efterfulgt af næste generation sequencing (CARIP-FF.), at identificere kromatin-associerede RNA'er på basis genome-wide i ES-celler, herunder bibliotek forberedelse til næste generation sequencing, og ChIP-Seq at kortlægge globale belægning af Histon ændringer, transkriptionsfaktorer og epigenetiske modifikatorer. I modsætning til andre RIP-Seq metoder7omfatter CARIP-Seq crosslinking og ultralydbehandling trin, som giver mulighed for direkte identifikation af RNA'er tilknyttet kromatin. Sammen, ChIP-Seq er et kraftfuldt værktøj til at identificere genome-wide protein-DNA interaktion, mens CARIP-Seq er en kraftfuld metode til at kortlægge RNA'er tilknyttet kromatin komponenter.

<table>
	<tbody>
		<tr>
			<td>Mouse leukemia inhibitory factor (ESGRO LIF)</td>
			<td>EMD Millipore</td>
			<td></td>
			<td>106 or 107 units</td>
		</tr>
		<tr>
			<td>GSK3&#946; inhibitor CHIR99021 (GSK3i)</td>
			<td>Stemgent</td>
			<td></td>
			<td>Solvent: DMSO 10mM</td>
		</tr>
		<tr>
			<td>MEK inhibitor PD0325901 (MEKi)</td>
			<td>Stemgent</td>
			<td></td>
			<td>Solvent: DMSO 10mM</td>
		</tr>
		<tr>
			<td>Dulbecco&#39;s Modified Eagle Medium (DMEM), high glucose</td>
			<td>Invitrogen</td>
			<td>11965092</td>
			<td></td>
		</tr>
		<tr>
			<td>PBS (phosphate buffered saline)</td>
			<td>Invitrogen</td>
			<td>10010031</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypsin-EDTA (0.25%), phenol red</td>
			<td>Gibco</td>
			<td>25200056</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin (10,000 U/mL)</td>
			<td>Gibco</td>
			<td>15140122</td>
			<td></td>
		</tr>
		<tr>
			<td>2-Mercaptoethanol (50 mM)</td>
			<td>Gibco</td>
			<td>31350010</td>
			<td></td>
		</tr>
		<tr>
			<td>MEM Non-Essential Amino Acids Solution (100X)</td>
			<td>Gibco</td>
			<td>11140076</td>
			<td></td>
		</tr>
		<tr>
			<td>EmbryoMax ES Cell Qualified Fetal Bovine Serum, 500 ml</td>
			<td>EMD Millipore</td>
			<td>ES-009-B</td>
			<td></td>
		</tr>
		<tr>
			<td>EmbryoMax 0.1% Gelatin Solution</td>
			<td>EMD Millipore</td>
			<td>ES-006-B</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycine</td>
			<td>Sigma</td>
			<td>G7126-500G</td>
			<td>1.25 M stock conentration in water</td>
		</tr>
		<tr>
			<td>Formaldehyde solution</td>
			<td>Sigma</td>
			<td>F8775-500ML</td>
			<td></td>
		</tr>
		<tr>
			<td>TE (Tris EDTA) pH 8.0 1X</td>
			<td>Quality Biological</td>
			<td>351-011-131</td>
			<td></td>
		</tr>
		<tr>
			<td>Phenylmethanesulfonyl fluoride (PMSF) solution</td>
			<td>Sigma</td>
			<td>93482-250ML-F</td>
			<td></td>
		</tr>
		<tr>
			<td>cOmplete Protease Inhibitor Cocktail</td>
			<td>Roche</td>
			<td>11697498001</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium dodecyl sulfate solution (20%)</td>
			<td>Quality Biological</td>
			<td>A611-0837-10</td>
			<td></td>
		</tr>
		<tr>
			<td>Q125 sonifier</td>
			<td>Qsonica</td>
			<td>4422</td>
			<td></td>
		</tr>
		<tr>
			<td>Triton X-100 solution</td>
			<td>Sigma</td>
			<td>93443-100ML</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium deoxycholate</td>
			<td>Sigma</td>
			<td>30970</td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Sigma</td>
			<td>S7653</td>
			<td></td>
		</tr>
		<tr>
			<td>Dynabeads Protein G for Immunoprecipitation</td>
			<td>Invitrogen</td>
			<td>10004D</td>
			<td></td>
		</tr>
		<tr>
			<td>Dynabeads Protein A for Immunoprecipitation</td>
			<td>Invitrogen</td>
			<td>10002D</td>
			<td></td>
		</tr>
		<tr>
			<td>Dynabeads Protein A/Protein G and Magnet Starter Pack</td>
			<td>Invitrogen</td>
			<td>10015D</td>
			<td></td>
		</tr>
		<tr>
			<td>Lithium chloride</td>
			<td>Sigma</td>
			<td>L4408</td>
			<td></td>
		</tr>
		<tr>
			<td>IGEPAL CA-630</td>
			<td>Sigma</td>
			<td>I8896</td>
			<td></td>
		</tr>
		<tr>
			<td>RNeasy Mini Kit</td>
			<td>Qiagen</td>
			<td>74104</td>
			<td></td>
		</tr>
		<tr>
			<td>Dynabeads mRNA Purification Kit (for mRNA purification from total RNA preps)</td>
			<td>Invitrogen</td>
			<td>61006</td>
			<td></td>
		</tr>
		<tr>
			<td>SuperScript Double-Stranded cDNA Synthesis Kit</td>
			<td>Invitrogen</td>
			<td>11917010</td>
			<td></td>
		</tr>
		<tr>
			<td>QIAquick PCR Purification Kit</td>
			<td>Qiagen</td>
			<td>28104</td>
			<td></td>
		</tr>
		<tr>
			<td>End-It DNA End-Repair Kit</td>
			<td>Lucigen</td>
			<td>ER81050</td>
			<td></td>
		</tr>
		<tr>
			<td>Klenow Fragment (3&#39;&#8594;5&#39; exo-)</td>
			<td>NEB</td>
			<td>M0212L</td>
			<td></td>
		</tr>
		<tr>
			<td>dATP (10 mM)</td>
			<td>Invitrogen</td>
			<td>18252015</td>
			<td></td>
		</tr>
		<tr>
			<td>T4 DNA ligase</td>
			<td>NEB</td>
			<td>M0202L</td>
			<td></td>
		</tr>
		<tr>
			<td>TrackIt 1 Kb Plus DNA Ladder</td>
			<td>Invitrogen</td>
			<td>10488085</td>
			<td></td>
		</tr>
		<tr>
			<td>E-gel EX agarose gels, 2%</td>
			<td>Invitrogen</td>
			<td>G402002</td>
			<td></td>
		</tr>
		<tr>
			<td>Phusion high-fidelity 2X master mix with HF buffer</td>
			<td>Thermo Fisher</td>
			<td>F531LPM</td>
			<td></td>
		</tr>
		<tr>
			<td>ChIPAb+ Trimethyl-Histone H3 (Lys4) - ChIP Validated Antibody</td>
			<td>EMD Millipore</td>
			<td>17-614</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-Histone H3 (di methyl K4) antibody [Y47] - ChIP Grade (ab32356)</td>
			<td>Abcam</td>
			<td>ab32356</td>
			<td></td>
		</tr>
		<tr>
			<td>Corning Costar Flat Bottom Cell Culture Plates (6-well)</td>
			<td>Fisher</td>
			<td>720083</td>
			<td></td>
		</tr>
		<tr>
			<td>Falcon Standard Tissue Culture Dishes (10cm)</td>
			<td>Fisher</td>
			<td>08772E</td>
			<td></td>
		</tr>
		<tr>
			<td>Bioruptor pico</td>
			<td>Diagenode</td>
			<td>B01010001</td>
			<td></td>
		</tr>
		<tr>
			<td>Qubit Flurometer 2.0</td>
			<td>Thermo Fisher</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Qubit dsDNA HS Assay Kit</td>
			<td>Thermo Fisher</td>
			<td>Q32851</td>
			<td></td>
		</tr>
		<tr>
			<td>MinElute Reaction Cleanup Kit</td>
			<td>Qiagen</td>
			<td>28204</td>
			<td></td>
		</tr>
		<tr>
			<td>MinElute Gel Extraction Kit</td>
			<td>Qiagen</td>
			<td>28604</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-Histone H4 (tri methyl K20) antibody - ChIP Grade (ab9053)</td>
			<td>Abcam</td>
			<td>ab9053</td>
			<td></td>
		</tr>
		<tr>
			<td>Labquake rotator</td>
			<td>Thermo Fisher</td>
			<td>400110Q</td>
			<td></td>
		</tr>
		<tr>
			<td>Illumina HiSeq platform</td>
			<td>Illumina</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>TURBO DNase</td>
			<td>Invitrogen</td>
			<td>AM2238</td>
			<td></td>
		</tr>
	</tbody>
</table>

carip-seq and chip-seq: methods to identify chromatin-associated rnas and protein-dna interactions in embryonic stem cells

Embryonale stamceller (ES) celle selvfornyelse og differentiering er underlagt udefrakommende signaler og iboende netværk af transkriptionsfaktorer, epigenetiske regulatorer og efter oversættelse ændringer af histoner, combinatorially indflydelse på genet udtrykket tilstand af nærliggende gener. RNA har også vist sig at interagere med forskellige proteiner til at regulere kromatin dynamics og genekspression. Kromatin-associerede RNA immunoprecipitation (CARIP) efterfulgt af næste generation sequencing (CARIP-FF.) er en roman metode til undersøgelse RNA'er tilknyttet kromatin proteiner, mens kromatin immunoprecipitation efterfulgt af næste generation sequencing ( ChIP-Seq) er en kraftfuld genomforskning teknik til at kortlægge placeringen af posttranslationel modifikation af histoner, transkriptionsfaktorer og epigenetiske modifikatorer på et globalt i ES-celler. Her, beskriver vi metoder til at udføre CARIP-FF. og ChIP-FF., herunder bibliotek opbygning til næste generation sequencing, for at skabe globale kromatin-associerede RNA og epigenomiske kort i ES-celler.

Vi forhørt med held genome-wide bindingen af H3K4me3, H3K4me2 og KDM5B i ES-celler ved hjælp af denne ChIP-Seq protokol6. ES-celler blev kulturperler i feeder-fri betingelser (figur 1), og tværbunden som beskrevet ovenfor. Sonikering blev efterfølgende udført som beskrevet i trin 3.2 i ChIP-Seq-protokollen, og evalueres af kører DNA på en 2%-agarosegel (figur 2). Næste, ChIP blev udført som beskre...

Watch this Scientific Journal Video about CARIP-Seq and ChIP-Seq: Methods to Identify Chromatin-Associated RNAs and Protein-DNA Interactions in Embryonic Stem Cells at JoVE.com

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

Her, vi beskriver metoder til at udføre ChIP-FF. og CARIP-FF., herunder bibliotek forberedelse til næste generation sequencing, til at skabe global epigenomiske og kromatin-associerede RNA kort i ES-celler.

CARIP-FF. og ChIP-Seq: metoder til at identificere kromatin-associerede RNA'er og Protein-DNA interaktioner i embryonale stamceller

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

Research

JoVE Journal

Developmental Biology

Derivation of Cardiac Progenitor Cells from Embryonic Stem Cells

Afledning af Cardiac progenitorceller af embryonale stamceller

Cardiac progenitor cells (CPCs) have the capacity to differentiate into cardiomyocytes, smooth muscle cells (SMC), and endothelial cells and hold great ...

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

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

Genom-dækkende Snapshot af Chromatin Regulators og stater i<em&gt; Xenopus</em&gt; Embryoner af 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 ...

Neural Differentiation of Mouse Embryonic Stem Cells in Serum-free Monolayer Culture

Neural Differentiering af Mouse Embryonale stamceller i Serumfrit monolagskultur

The ability to differentiate mouse embryonic stem cells (ESC) to neural progenitors allows the study of the mechanisms controlling neural specification as ...

Generating CRISPR/Cas9 Mediated Monoallelic Deletions to Study Enhancer Function in Mouse Embryonic Stem Cells

Generering CRISPR / Cas9 Mediated monoallelisk Sletninger til Studieinformationen Enhancer funktion i mus embryonale stamceller

Enhancers control cell identity by regulating tissue-specific gene expression in a position and orientation independent manner. These enhancers are often ...

Epigenetic Regulation of Cardiac Differentiation of Embryonic Stem Cells and Tissues

Epigenetisk forordning af Cardiac Differentiering af embryonale stamceller og væv

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

Isolation of Murine Embryonic Hemogenic Endothelial Cells

Isolering af murint embryonale Hemogenic endotelceller

The specification of hemogenic endothelial cells from embryonic vascular endothelium occurs during brief developmental periods within distinct tissues, ...

A Simple Method to Identify Kinases That Regulate Embryonic Stem Cell Pluripotency by High-throughput Inhibitor Screening

En simpel metode til at identificere kinaser, der regulerer embryonisk stamcellepluripotens ved høj gennemstrømningshæmmende screening

Embryonic stem cells (ESCs) can self-renew or differentiate into all cell types, a phenomenon known as pluripotency. Distinct pluripotent states have been ...

Horizontal Whole Mount: A Novel Processing and Imaging Protocol for Thick, Three-dimensional Tissue Cross-sections of Skin

Horisontal Hel Mount: En Novel Processing and Imaging Protocol for Tykke, Tredimensionale Tissue Tværsnit af Skin

Processing a tissue of interest to generate a microscopic image that supports a scientific argument can be challenging. The acquisition of high-quality ...

Rapid, Directed Differentiation of Retinal Pigment Epithelial Cells from Human Embryonic or Induced Pluripotent Stem Cells

Hurtig, instrueret differentiering af retinale Pigment epitel celler fra menneskelige embryonale eller induceret pluripotente stamceller

We describe a robust method to direct the differentiation of pluripotent stem cells into retinal pigment epithelial cells (RPE). The purpose of providing ...

Single-cell Photoconversion in Living Intact Zebrafish

Encellede Photoconversion i levende intakt zebrafisk

Animal and plant tissue is composed of distinct populations of cells. These cells interact over time to build and maintain the tissue and can cause ...