The video details a procedure for extracting PCR products from chromosome confirmation capture samples using gel extraction. It outlines both commercial and homemade methods, including constructing a purification cartridge. The effectiveness of the extracted DNA is then evaluated through QPCR, revealing positive results in the majority of tested reactions.

identification of the chromosome conformation capture (3c) products

Chromosome Conformation Capture (3C) for Undergraduate Research and Teaching

An organism&#39;s genome not only holds all the genes required for function but also all the instructions on how and when to use them. This makes regulating access to the genome one of the most important functions of the cell. There are many mechanisms to control gene function; however, at its base level, gene regulation comes down to the ability of regulatory transcription factors (trans-factors) to bind to their specific DNA sequences (cis-regulatory sequences). This is not an innate ability; instead, it is governed by the organization/structure of the genome in the nucleus, which controls the availability/exposure of the cis-regulatory sequences to the trans-factors1,2,3. If the trans-factors cannot find their cis-regulatory sequences, then the trans-factors cannot perform their regulatory tasks. This has made understanding how genomes are organized in the nucleus an important source of inquiry.
It is widely accepted that during interphase, eukaryotic chromosomes in the nucleus occupy their own domain anchored to the nuclear lamina and nuclear matrix (Figure 1), thus making the chromosome more like a slice of pizza, rather than a noodle on a plate of spaghetti. Chromosomes are partially condensed by protein-DNA interactions (chromatin) that twist and loop portions of the chromosome. Through electron microscopy, three-dimensional DNA fluorescence in situ hybridization (FISH), and DNA tagging techniques (i.e., fluorescent and artificial DNA methylation), inactive domains of chromatin have been found to be packed tightly along the nuclear periphery4,5,6, while portions of active, less condensed chromatin are found in the interior of the nucleus7,8,9,10. These experiments provide a wide-angle view of chromosome dynamics but do little to capture the changes that occur locally around the gene promotors observed in DNase11,12 and nucleosome13,14,15 studies.
The key to unlocking higher-resolution chromatin dynamics was the formulation of the 3D chromosome mapping technique, 3C. The 3C technique itself comprises four main steps: crosslinking of chromatin, chromatin digestion by restriction enzymes, chromatin ligation, and DNA purification (Figure 2). The new artificial DNA fragments generated by this process can then be characterized to reveal the close physical association between linearly distant pieces of DNA16. The 3C technique became the basis for the creation of multiple spin-off techniques that utilize the initial steps of 3C to ask broader genome-wide questions (e.g., Hi-C, 4C, ChIP-C). This family of 3C techniques has identified that chromosomes are organized into multiple discrete units termed topologically associated domains (TADs). TADs are encoded in the genome and are defined by chromatin loops flanked by unlooped boundaries16,17,18,19. The TAD boundaries are maintained by two evolutionarily conserved and ubiquitous factors, including CCCT binding factor (CTCF) and cohesion, which prevent loops within separate TADs from interacting16,20. The loops are mediated by the interaction of trans-factors with their regulatory sequences, as well as CTCF and cohesion21.
Though many studies using 3C technologies ask broad genome-wide questions and employ complicated sample collection techniques, the formulation of the 3C technique is based on basic molecular biology techniques. This makes 3C intriguing for deployment in both undergraduate research and teaching labs. The 3C technique can be employed for smaller focused questions and is inherently flexible to scaling up or down (single genes22, chromosomes16, and/or genomes18) depending on the focus and direction of the questions asked. This technique has also been applied to a wide range of model systems7,16,19,23 and has been proven to be versatile in its use. This makes 3C an excellent technique for undergraduates in that students can gain experience in common molecular biology techniques while also gaining valuable experience in answering directed questions.
Presented here is an adapted protocol for 3C library preparation based on previously published protocols24,25,26,27. This protocol has been optimized for approximately 1 &#215; 107 cells, though it has generated 3C libraries with as little as 1 &#215; 105 cells. This protocol has proven to be versatile and has been used to generate 3C libraries from zebrafish embryos, zebrafish cell lines, and young-adult (YA) Caenorhabditis elegans (roundworm). The protocol should also be appropriate for mammalian cell lines and, with further adaptation, yeast.
The goal of these adaptations is to make 3C more accessible for undergraduates. Care has been taken to use techniques that are similar to those that can be accomplished in an undergraduate teaching laboratory. The 3C technique provides many learning opportunities for undergraduates to learn basic molecular biology techniques that will benefit their development at the bench, in the classroom, and in their endeavors after graduation.

Author Spotlight: Getting an A with the 3Cs: Chromosome Conformation Capture for Undergraduates  

Getting an A with the 3Cs: Chromosome Conformation Capture for Undergraduates

Our research aims to uncover how chromatin organization controls gene expression. The focus is on determining what factors regulate chromatin at the gene level to control gene activity. Currently, technologies similar to chromosome confirmation capture, or 3C, are used to make progress in this field.Investments in sample collection and sequencing technologies have pushed us what the 3C techniques can show us. The greatest experimental challenge currently is collecting samples having uniform chromatin architecture. Heterogeneity in samples leads to confounding results.In the future, we'll be focusing on how changes in chromatin organization play a role in cancer.

Watch this Scientific Journal Video about Identification of the Chromosome Conformation Capture 3C Products at JoVE.com

Identification of the Chromosome Conformation Capture (3C) Products  

Take the chromosome confirmation capture or 3C sample and controls, and perform QPCR. Excise the product bands corresponding to the expected fragment size. To perform gel extraction of the PCR products, use a commercial kit or follow the homemade protocol.For the latter, construct a homemade purification cartridge by poking a hole in the bottom of a 0.5 milliliter tube with a needle. Pack a small amount of cotton into the bottom of the tube with the hole, filling no more than half of the tube. Place the tube into a 1.5 milliliter tube, ensuring that the smaller tube rests on the lip of the bigger tube, and not in the tube.Carefully cut the gel fragment into smaller pieces, and place it in the small tube of the cartridge. Place the assembly in a minus 20 degrees Celsius freezer for five minutes. Then, spin the assembly for three minutes at 13, 000 G and room temperature.Discard the small tube containing the agoros debris, and keep the 1.5 milliliter tube with the extracted DNA in the buffer. The samples were tested for the presence of long range chromatin contacts between the different genomic loci, using combinations of loci-specific primers and QPCR. The product abundance is relative to a control primer set were calculated and graft for comparison.The data indicated that 8 of the 10 reactions were conditional positives. Gel purification and sequencing of the expected PCR product for the eight conditional positives and one negative reaction were gel purified and sequenced. The results for representative positive and negative reactions are shown.

identification-of-the-chromosome-conformation-capture-3c-products

Research

JoVE Journal

Genetics

490 Views.  Bryant University. Take the chromosome confirmation capture or 3C sample and controls, and perform QPCR. Excise the product bands corresponding to the expected fragment size. To perform gel extraction of the PCR products, use a commercial kit or follow the homemade protocol.For the latter, construct a homemade purification cartridge by poking a hole in the bottom of a 0.5 milliliter tube with a needle. Pack a small amount of cotton into the bottom of the tube with the hole, filling no more than half of t...

Video: Identification of the Chromosome Conformation Capture (3C) Products  

Chromosome conformation capture (3C) is a powerful tool that has spawned a family of similar techniques (e.g., Hi-C, 4C, and 5C, referred to here as 3C techniques) that provide detailed information of the three-dimensional organization of chromatin. The 3C techniques have been used in a wide range of studies, from monitoring the changes in chromatin organization in cancer cells to identifying enhancer contacts made with gene promoters. While many of the studies using these techniques are asking big genome-wide questions with intricate sample types (i.e., single-cell analysis), what is often lost is that the 3C techniques are grounded in basic molecular biology methods that are applicable to a broad range of studies. By addressing tightly focused questions of chromatin organization, this cutting-edge technique can be used to enhance the undergraduate research and teaching lab experience. This paper presents a 3C protocol and provides adaptations and points of emphasis for implementation at primarily undergraduate institutions in undergraduate research and teaching experiences.

Here, we present an adaption of the chromosome conformation capture (3C) technique in detail with an emphasis on undergraduate involvement and learning.

Chromosome conformation capture (3C) is a powerful tool that has spawned a family of similar techniques (e.g., Hi-C, 4C, and 5C, referred to here as 3C ...

Generation and Purification of Chromosome Conformation Capture (3C) Library

On day one after chromatin cross-linking and nuclei collection from 5, 000 young adult Caenorhabditis Elegans worms, transfer the nuclei pellet re-suspended in 450 microliters of clean water to a clean 1.5 milliliter micro centrifuge tube. Then add 60 microliters of 10X DPN2 restriction enzyme buffer to it and mix well. Incubate the samples with 15 microliters of 10%sodium dodecyl sulfate at 37 degrees Celsius for one hour with agitation.Quench the reaction by adding 75 microliters of 20%triton X 100 and incubating as demonstrated previously. Aliquot 10 microliters from the sample, as the undigested control, and store it at four degrees Celsius. After adding 400 units of DPN 2 to the rest of the sample, incubate it overnight at 37 degrees Celsius with agitation for chromatin digestion.On day two, add an additional 200 units of DPN 2 to the sample. To complete the digestion of the cross-linked sample, incubate it at 37 degrees Celsius with agitation for four hours. Heat inactivate the restriction enzyme by incubating the sample for 20 minutes at 65 degrees Celsius.If the enzyme cannot be inactivated by heat, add 80 microliters of 10%sodium dodecyl sulfate and incubate. Then, add 375 microliters of 20%Triton X 100 to the sample and mix by swirling. Keep aside a 10 microliter aliquot from the sample as the digestion control.For chromatin ligation, transfer the sample to a clean 50 milliliter conical tube. Adjust the sample volume to 5.7 milliliters with molecular grade water and mix by swirling. Then, add 700 microliters of 10 X T4 ligase buffer, followed by 60 units of T4 DNA ligase, and incubate the sample overnight at 16 degrees Celsius.On day three, proceed with protein digestion and reverse cross-linking. Add 30 microliters of 10 milligrams per milliliter Proteinase K to the 3C sample and incubate at 65 degrees Celsius overnight with agitation. To begin purification of the 3C library on day four, add 30 microliters of 10 milligrams per milliliter RNase A to the sample and mix by swirling.After incubation, add seven milliliters of phenyl chloroform to the samples and mix by shaking. Centrifuge the sample for 15 minutes at 3, 270 G and room temperature. Collect and transfer the aqueous phase to a clean 50 milliliter conical tube.Add equal volumes of chloroform and mix the sample by shaking. After centrifuging the sample again as demonstrated, transfer the aqueous phase to another clean 50 milliliter conical tube. Add 7.5 milliliters of molecular grade water, 35 milliliters of 100%ethanol and seven microliters of one milligram per milliliter Glycogen.Freeze the properly mixed sample at minus 80 degrees Celsius. While the sample freezes, begin purifying the control samples by adjusting the volume of the controls to 500 microliters using molecular grade water. Add two microliters of 10 milligrams per milliliter RNase A and mix by flicking the tube.Next, add one milliliter of phenyl chloroform to the tubes containing the controls and mix by shaking. Centrifuge the tubes. After transferring the aqueous phase to a clean 1.5 milliliter micro centrifuge tube, add equal volumes of chloroform.Centrifuge as previously demonstrated before collecting the aqueous phase. To the collected aqueous phase, add one milliliter of ethanol and two microliters of one milligram per milliliter glycogen. After mixing the sample by shaking, incubate it at minus 80 degrees Celsius for 30 minutes.Next, centrifuge the sample for 15 minutes at 3, 270 G at four degrees Celsius. After removing the supernatant, add 750 microliters of chilled 70%ethanol and centrifuge. Re-suspend the air dried pellet in 50 microliters of molecular grade water.The suspension can be frozen here if not proceeding further immediately. To continue with the 3C sample purification, remove the sample from the freezer and centrifuge at 3, 270 G for 30 minutes. Add 10 milliliters of chilled 70%ethanol and break up the DNA pellet.After centrifuging and removing the supernatant, partially air dry the sample at room temperature. Re suspend the pellet in 150 microliters of 10 millimolar tris HCL at pH 7.5 by pipetting up and down to obtain the purified 3C library. QPCR performed on the one experimental and two control 3C samples helped generate the digestion efficiency data.The 3C sample had an approximately 88%digestion efficiency across the seven genomic loci tested.