The authors also thank Nicholas Cesari for editing the manuscript. The work was supported by grants from National Institute of Health (S.H., R01DK110108, R01CA204044).

&#8203;1. CTCF sgRNALibrary Design Using an Online Tool
<ol>
	<li>Design the sgRNA targeting CTCF binding sites in the human HOX loci using the genetic perturbation platform (GPP) designer tool (https://portals.broadinstitute.org/gpp/public/analysis-tools/sgrna-design).</li>
	<li>Synthesize a total of 1,070 sgRNAs consisting of sgRNAs targeting 303 random targeting genes, 60 positive controls, 500 non-Human-targeting controls, and 207 CTCF elements or lncRNA targeting genes (Figure 1</stro...

<ol>
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G., 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=Disruptions+of+topological+chromatin+domains+cause+pathogenic+rewiring+of+gene-enhancer+interactions.">Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions.</a> Cell. 161 (5), 1012-1025 (2015).</li><li>Dowen, J. M., 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=Control+of+cell+identity+genes+occurs+in+insulated+neighborhoods+in+mammalian+chromosomes.">Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes.</a> Cell. 159 (2), 374-387 (2014).</li><li>Phillips-Cremins, J. E., 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=Architectural+protein+subclasses+shape+3D+organization+of+genomes+during+lineage+commitment.">Architectural protein subclasses shape 3D organization of genomes during lineage commitment.</a> Cell. 153 (6), 1281-1295 (2013).</li><li>Narendra, V., Bulajic, M., Dekker, J., Mazzoni, E. O., Reinberg, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CTCF-mediated+topological+boundaries+during+development+foster+appropriate+gene+regulation.">CTCF-mediated topological boundaries during development foster appropriate gene regulation.</a> Genes &amp; Development. 30 (24), 2657-2662 (2016).</li><li>Narendra, V., 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=CTCF+establishes+discrete+functional+chromatin+domains+at+the+Hox+clusters+during+differentiation.">CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation.</a> Science. 347 (6225), 1017-1021 (2015).</li><li>Deng, C., 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=HoxBlinc+RNA+Recruits+Set1/MLL+Complexes+to+Activate+Hox+Gene+Expression+Patterns+and+Mesoderm+Lineage+Development.">HoxBlinc RNA Recruits Set1/MLL Complexes to Activate Hox Gene Expression Patterns and Mesoderm Lineage Development.</a> Cell Reports. 14 (1), 103-114 (2016).</li><li>Patel, B., 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=Aberrant+TAL1+activation+is+mediated+by+an+interchromosomal+interaction+in+human+T-cell+acute+lymphoblastic+leukemia.">Aberrant TAL1 activation is mediated by an interchromosomal interaction in human T-cell acute lymphoblastic leukemia.</a> Leukemia. 28 (2), 349-361 (2014).</li><li>Luo, H., 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=CTCF+boundary+remodels+chromatin+domain+and+drives+aberrant+HOX+gene+transcription+in+acute+myeloid+leukemia.">CTCF boundary remodels chromatin domain and drives aberrant HOX gene transcription in acute myeloid leukemia.</a> Blood. 132 (8), 837-848 (2018).</li><li>Dou, D. 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J., 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=Loss+of+expression+of+the+Hoxa-9+homeobox+gene+impairs+the+proliferation+and+repopulating+ability+of+hematopoietic+stem+cells.">Loss of expression of the Hoxa-9 homeobox gene impairs the proliferation and repopulating ability of hematopoietic stem cells.</a> Blood. 106 (12), 3988-3994 (2005).</li><li>Deng, C., 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=USF1+and+hSET1A+mediated+epigenetic+modifications+regulate+lineage+differentiation+and+HoxB4+transcription.">USF1 and hSET1A mediated epigenetic modifications regulate lineage differentiation and HoxB4 transcription.</a> PLOS Genetics. 9 (6), e1003524 (2013).</li><li>Rawat, V. P., Humphries, R. 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We have no conflicts of interest related to this report.

Protein-coding gene related sgRNA libraries have been applied in a functional screening system to identifying genes and networks regulating specific cellular functions through sgRNA enrichment24,25,26,27,28. Several non-coding region related sgRNA libraries were also shown in gene-specific functional screens for distal and proximal regulating elements, includi...

Recent genome interaction studies revealed that the human nuclear genome forms stable topologically associating domains (TADs) that are conserved across cell types and species. The organization of the genome into separate domains facilitates and restricts interactions between regulatory elements (e.g., enhancers and promoters). The CCCTC-binding factor (CTCF) binds to TAD boundaries and plays a critical role in constraining interactions of DNA elements that are located in neighboring TADs1. However, genome wide CTCF binding data revealed that although CTCF mostly interacts with the same DNA-sites in different cell types, it often functions as a chromatin barrier at a specific site in one cell type but not in the other, suggesting that CTCF functions together with other activities in the formation of chromatin boundaries2. What remains unknown is whether the boundary elements (CTCF-binding sites) are directly linked to the biological function of CTCF, and how these links occur. Therefore, we hypothesize that specific CTCF binding sites in the genome directly regulate the formation of TADs and control promoter/enhancer interactions within these domains or between neighboring domains. The completion of the human and mouse genome sequencing projects and subsequent epigenetic analyses have uncovered new molecular and genetic signatures of the genome. However, the role of specific signatures/modifications in gene regulation and cellular function, as well as their molecular mechanism(s), have yet to be fully understood.
Multiple lines of evidence support that the CTCF-mediated TADs represent functional chromatin domains3,4,5. Although CTCF mostly interacts with the same DNA-sites in different cell types, genome wide CTCF ChIP-seq data revealed that CTCF often functions as a chromatin barrier in one cell type but not in the other2. CTCF plays an essential role during development by mediating genome organization4,6,7. Disruption of CTCF boundaries impaired enhancer/promoter interactions and gene expression, leading to developmental blockage. This suggests that CTCF mediated TADs are not only structural components, but also regulatory units required for proper enhancer action and gene transcription5,8,9.
HOX genes play critical roles during embryonic development and they are temporally and spatially restricted in their expression patterns. The HOXA locus forms two stable TADs separating anterior and posterior genes by a CTCF-associated boundary element in both hESCs and IMR90 cells1. Recent reports demonstrated that HoxBlinc, a HoxB locus associated lncRNA, mediates the formation of CTCF directed TADs and enhancer/promoter interactions in the HOXB locus. This leads to anterior HOXB gene activation during ESC commitment and differentiation10. Furthermore, at specific gene loci including the HOXA locus, alteration of CTCF mediated TAD domains changed lineage specific gene expression profiles and was associated with the development of disease states11,12. The evidence supports a primary function for CTCF in coordinating gene transcription and determining cell identity by organizing the genome into functional domains.
Despite its role in the embryonic development, during hematopoiesis, HOX genes regulate hematopoietic stem and progenitor cell (HS/PC) function. This is done by controlling the balance between proliferation and differentiation10,13,14,15. The expression of HOX genes is tightly regulated throughout the specification and differentiation of hematopoietic cells, with highest expression in HS/PCs. HOX gene expression gradually decreases during maturation, with its lowest levels occurring in differentiated hematopoietic cells16. HOX gene dysregulation is a dominant mechanism of leukemic transformation by dysregulating self-renewal and differentiation properties of HS/PCs leading to leukemic transformation17,18. However, the mechanism of establishing and maintaining normal vs. oncogenic expression patterns of HOX genes as well as associated regulatory networks remains unclear.
CRISPR-Cas9 sgRNA library screening has been widely used to interrogate protein-coding genes19 as well as non-coding genes, such as lncRNA20 and miRNA21 in different species. However, the cost to use the CRISPR-Cas9 sgRNA library to identify new genomic targets remains high, because high-throughput genome sequencing is often applied to verify the sgRNA library screening. Our sgRNA screening system is focused on the specific genome loci and evaluates the targeting sgRNAs through one-step RT-PCR according to the marker gene expression, such as HOXA9. Additionally, Sanger sequencing confirmed that the sgRNA was integrated into the genome, and Indel mutations can be detected to identify the sgRNA targeting site. Through the loci-specific CRISPR-Cas9 genetic screening, the CBS7/9 chromatin boundary has been identified as a critical regulator for establishing oncogenic chromatin domain and maintaining ectopic HOX gene expression patterns in AML pathogenesis12. The method can be widely applied to identify not only specific function of CTCF boundary in embryonic development, hematopoiesis, leukemogenesis, but also CTCF boundary as potential therapeutic targets for future epigenetic therapy.

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	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:263px;">Lipofectamine 3000 reagent</td>
			<td style="width:155px;">Thermo Fisher Scientific</td>
			<td style="width:100px;">L3000-008</td>
			<td style="width:172px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Proteinase K</td>
			<td>Thermo Fisher Scientific</td>
			<td>25530049</td>
			<td></td>
		</tr>
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			<td height="21" style="height:21px;">Puromycin</td>
			<td>Thermo Fisher Scientific</td>
			<td>A1113802</td>
			<td></td>
		</tr>
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			<td height="21" style="height:21px;">Stbl3 cells&#160;</td>
			<td>Life Technologies</td>
			<td>&#160;C737303</td>
			<td></td>
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			<td height="21" style="height:21px;">HEK293T</td>
			<td>ATCC</td>
			<td>CRL-3216</td>
			<td></td>
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			<td height="21" style="height:21px;">MOLM-13</td>
			<td>DSMZ</td>
			<td>ACC 554</td>
			<td></td>
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			<td height="21" style="height:21px;">lentiCRISPRv2</td>
			<td>Addgene</td>
			<td>52961</td>
			<td></td>
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			<td height="21" style="height:21px;">pMD2.G</td>
			<td>Addgene</td>
			<td>12259</td>
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			<td height="21" style="height:21px;">psPAX2</td>
			<td>Addgene</td>
			<td>12260</td>
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			<td height="21" style="height:21px;">pGEM&#174;-T Easy Vector Systems&#160;</td>
			<td>Promega</td>
			<td>A137A</td>
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			<td height="21" style="height:21px;">T4 ligase&#160;</td>
			<td>New England Biolabs</td>
			<td>&#160;M0202S</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">QIAquick Gel Extract kit</td>
			<td>QIAGEN</td>
			<td>28706</td>
			<td></td>
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		<tr height="21">
			<td height="21" style="height:21px;">QIAuick PCR purification kit</td>
			<td>QIAGEN</td>
			<td>28106</td>
			<td></td>
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		<tr height="21">
			<td height="21" style="height:21px;">SingleShot&#8482; SYBR&#174;&#160;Green One-Step Kit</td>
			<td>Bio-Rad Laboratories</td>
			<td>1725095</td>
			<td></td>
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		<tr height="21">
			<td height="21" style="height:21px;width:263px;">QIAGEN Plasmid Maxi Kit</td>
			<td>QIAGEN</td>
			<td style="width:100px;">12163</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Dulbecco&#8217;s Modified Eagle Medium&#160;</td>
			<td>Thermo Fisher Scientific</td>
			<td style="width:100px;">&#160;11965084</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">RPMI 1640&#160;</td>
			<td>Thermo Fisher Scientific</td>
			<td style="width:100px;">11875093</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Fetal bovine serum (FBS)&#160;</td>
			<td>Thermo Fisher Scientific</td>
			<td style="width:100px;">10-082-147</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Penicillin/streptomycin/L-glutamine&#160;</td>
			<td>Life Technologies&#160;</td>
			<td style="width:100px;">10378016</td>
			<td></td>
		</tr>
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			<td height="21" style="height:21px;">Lenti-X Concentrator&#160;</td>
			<td style="width:155px;">Clontech</td>
			<td style="width:100px;">631232</td>
			<td></td>
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		<tr height="21">
			<td height="21" style="height:21px;width:263px;">Trypan Blue Solution</td>
			<td>Thermo Fisher Scientific</td>
			<td style="width:100px;">15250061</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:263px;">Polybrene</td>
			<td style="width:155px;">Santa Cruz Biotechnology</td>
			<td>sc-134220</td>
			<td></td>
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		<tr height="21">
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hox loci focused crispr/sgrna library screening identifying critical ctcf boundaries

CCCTC-binding factor (CTCF)-mediated stable topologically associating domains (TADs) play a critical role in constraining interactions of DNA elements that are located in neighboring TADs. CTCF plays an important role in regulating the spatial and temporal expression of HOX genes that control embryonic development, body patterning, hematopoiesis, and leukemogenesis. However, it remains largely unknown whether and how HOX loci associated CTCF boundaries regulate chromatin organization and HOX gene expression. In the current protocol, a specific sgRNA pooled library targeting all CTCF binding sites in the HOXA/B/C/D loci has been generated to examine the effects of disrupting CTCF-associated chromatin boundaries on TAD formation and HOX gene expression. Through CRISPR-Cas9 genetic screening, the CTCF binding site located between HOXA7/HOXA9 genes (CBS7/9) has been identified as a critical regulator of oncogenic chromatin domain, as well as being important for maintaining ectopic HOX gene expression patterns in MLL-rearranged acute myeloid leukemia (AML). Thus, this sgRNA library screening approach provides novel insights into CTCF mediated genome organization in specific gene loci and also provides a basis for the functional characterization of the annotated genetic regulatory elements, both coding and noncoding, during normal biological processes in the post-human genome project era.

CRISPR-Cas9 technology is a powerful research tool for functional genomic studies. It is rapidly replacing conventional gene editing techniques and has high utility for both genome-wide and individual gene-focused applications. Here, the first individually cloned loci-specific CRISPR-Cas9-arrayed sgRNA library contains 1,070 sgRNAs consisting of sgRNAs targeting 303 random targeting genes, 60 positive controls, 500 non-Human-targeting controls, and 207 CTCF elements or lncRNA targeting ge...

Watch this Scientific Journal Video about HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries at JoVE.com

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries

A CRISPR/sgRNA library has been applied to interrogating protein-coding genes.However, the feasibility of a sgRNA library to uncover the function of a CTCF boundary in gene regulation remains unexplored. Here, we describe a HOX loci specific sgRNA library to elucidate the function of CTCF boundaries in HOX loci.

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries

CCCTC-binding factor (CTCF)-mediated stable topologically associating domains (TADs) play a critical role in constraining interactions of DNA elements ...

Our pooled sgRNA called the library screening, is a powerful genetic approach to identify and evaluate the biological function of the noncoding elements throughout the genome. This technique allows us to examine the effect of disrupting the binding sites associated, chromatic boundaries or other regulatory elements on targeted genes expression. Our approach can be used to identify the role of CTCF, long non-coding RNAs and enhancers, in HOX gene regulation in early embryonic development, as well as certain leukemias with an aberrant HOX gene signature.Begin this procedure with the design of an sgRNA targeting CTCF binding sites. Cloning of the sgRNA library in cell preparation as described in the text protocol. To package the lentivirus, cotransfect HEK293 T cells with 20 micrograms of purified library vectors, 15 micrograms of the packaged plasmid, and 10 micrograms of the envelope plasmid, for 48 hours before harvesting the viruses.After 48 hours, collect the virus supernatant and filter it through a 0.45 micron low-protein binding PVDF membrane. Next, concentrate the lentiviral supernatant by 50 fold, using the concentrator. Aliquot the concentrated viruses and store them in a minus 80 degrees celsius freezer.Work in separate wells of a 12 well plate to mix MOLM13 cells with various doses of the concentrated lentivirus for six total groups. Immediately centrifuge these mixtures at 1000 times g for two hours at 33 degrees celsius. Transfer the 12 well plates back to the incubator at 37 degrees celsius and 5%carbon dioxide for four hours.Gently aspirate the supernatant without disturbing the cell palette, and re-suspend the transduced cells with fresh supplemented RPMI 1640 Medium. Then transfer the re-suspended cells to T25 flasks and incubate at 37 degrees celsius for 48 hours without puromycin. After 48 hours split these cells into two flasks, an experimental group treated with one microliter per milliliter puromycin for five days, and a control group without puromycin treatment for five days.Measure the optimized MOI value for transduction by dividing the number of live cells treated with puromycin by the number of cells without puromycin treatment. To transduce the cells with the pooled library, infect 1.5 million MOLM13 cells in a 6 well plate with 0.3 MOI of sgRNA pooled lentivirus in medium. Use the cells without the lentivirus infection as a control.Immediately centrifuge the six well plate at 1000 times g for two hours at 33 degrees celsius to spinfect the cells. Then, transfer the plates back to the incubator at 37 degrees celsius in 5%carbon dioxide for four hours. Gently aspirate supernatant without disturbing the cell palette, and re-suspend the transduced cells with fresh medium.Then, transfer the cells to T25 flasks and incubate at 37 degrees celsius for 48 hours without puromycin. After 48 hours, treat the cells with one microgram per milliliter puromycin for five days. Exchange for fresh medium after two days and maintain an optimal cell density.Seed the single clone in 96 well plates with limiting dilution methods. Incubate these single clone at 37 degrees celsius and 5%carbon dioxide. Culture them for 3-4 weeks.Count the sgRNA integrated MOLM13 cells with 0.4%Trypan Blue solution staining and then transfer 10, 000 live cells per well to a 96 well PCR plate. Centrifuge the plate at 1000 times g for five minutes and then thoroughly remove and discard the supernatant with a pipette. Avoid disturbing the cell palette.After washing the cells as described in the text add 50 microliters of the cell lysis master mix to each well. Pipette up and down five times to re-suspend the cell palette. Incubate the mix for 10 minutes at room temperature.Then, transfer the mixture to 37 degrees celsius for five minutes, and then 75 degrees celsius for an additional five minutes. Now add one microliter of cell lysate to the PCR wells containing the RT qPCR reaction mix. This mix includes the marker genes forward and reverse primer, reverse transcriptase and One-Step reaction mix.Run the reverse transcription reaction for 10 minutes at 50 degrees celsius followed by polymerization activation, and DNA-denaturation for one minute at 95 degrees celsius. Perform RT PCR with 40 cycles of PCR reaction as detailed in the text protocol. Verify the HOXA9 decreased expression clones through Sanger sequencing and perform PCR with MOLM13 genome DNA as described in the text protocol.Extract and purify the PCR products with the PCR purification kit. Ligate the purified PCR products into the T vector with T4 ligation buffer, T vector DNA, PCR DNA and T4 ligase. Place the ligation mix into an incubator at 16 degrees celsius overnight.Transfer the ligation mix into DH5 alpha competent cells and plate on an LB ampicillin antibiotic agar plate. Incubate the plates overnight at 37 degrees celsius. Pick the single clones from the LB plate and verify them by genotyping and Sanger sequencing.Set up the heteroduplex mixture group with 200 nanograms of the reference, and 200 nanograms of test PCR amplicons in a 0.2 milliliter PCR tube. Include the homoduplex mixture group with only 400 nanograms of reference PCR amplicons as a control. Separately incubate the heteroduplex and homoduplex mixture at 95 degrees celsius for five minutes in a one liter beaker filled with 800 milliliters of water.Then, cool down the mixtures gradually to room temperature to anneal and form the heteroduplex or homoduplex. Now, separately digest 400 nanograms of the annealed heteroduplex and homoduplex mixture with one microliter of indel mutation detection nuclease, and two microliters of nuclease reaction buffer at 42 degrees celsius for 60 minutes. Analyze the digested samples with agarose gel electrophoresis.The heteroduplex mixture DNA should be cut into small fragments and the homoduplex DNA should not be cut. sgRNA targeting MOLM13 positive clones were confirmed with the RT qPCR method, based on the expression levels of HOXA9 genes with the comparison with the control cells. Out of the 528 surviving clones screened, 10 clones exhibited more than 50%reduction in HOXA9 levels.sgRNAs integrated into the HOXA9 reduced, HOXA9 unchanged and HOXA9 increased clones, were further confirmed by PCR amplification of the sgRNA and identification by Sanger sequence. Six of ten clones showing a reduction in HOXA9 levels contained sgRNAs targeting the CBS79 site, as determined by Sanger sequencing. Indel mutations of integrated sgRNA positive clones were determined by PCR-based genotyping and nuclease digestion.The heterozygous deletion of the CTCF site located between HOXA7 and HOXA9 genes was identified by PCR-based genotyping. HOXA9-decreased clones five, six, 28 and 121 exhibited deletion in the CBS79 boundary location. Similar results were observed for the indel mutations in the CBS79 site that were analyzed by the nuclease digestion assay.When performing this procedure, it's important to make equal amounts of heteroduplexes and homoduplexes in order to detect sgRNA-induced indel mutations through the nuclease digestion assay. Our approach enables utilization of the selected marker, to carry out next-generation sequencing on the target gene to discover the gene's effects on leukemogenesis. Overall our approach prevents RPC's for the functional correct and reduction of a noted genetic irregular elements during normal biological process and leukemogenesis in the posthumous genome project error.

hox-loci-focused-crisprsgrna-library-screening-identifying-critical

Research

JoVE Journal

Genetics

8.1K Görüntüleme.  Pennsylvania State University College of Medicine. Kütüphane taraması adı verilen birleştirilmiş sgRNA'mız, genom boyunca kodlamayan elementlerin biyolojik işlevini belirlemek ve değerlendirmek için güçlü bir genetik yaklaşımdır. Bu teknik, ilişkili bağlayıcı bölgeleri, kromatik sınırları veya diğer düzenleyici unsurların hedeflenen genlerin ekspresyonu üzerindeki etkisini incelememize olanak sağlar. Yaklaşımımız, erken embriyonik gelişimde HOX gen regülasyonunda CTCF, uzun kodlamayan RNA'lar ve arttırıcı...