Breakthrough Tools for Epigenetics Studies

Structural Genomics Consortium and Life Technologies Collaborate on First Antibody Master Set

(See a list of products discussed in this article.)

Gene regulation during both normal development and disease states is impacted by epigenetic features such as DNA methylation, chromatin structure, and noncoding RNAs (ncRNAs). The fields of epigenetics and ncRNA research have seen explosive growth and are poised for major advances in the coming years. To fully realize the potential of this research, however, scientists must first overcome a number of biological and technical challenges.

Life Technologies has developed advanced technologies that provide researchers with tools for sample preparation, sequencing, quantitative PCR (qPCR), and functional analysis assays. Through this diverse portfolio, we are focused on delivering improved solutions for epigenetics and ncRNA research.

Solutions Through Collaboration

Here we describe our collaborative partnership with the Structural Genomics Consortium (SGC), a network of more than 200 scientists from the Universities of Chicago, Toronto, and Oxford, as well as partners from the pharmaceutical companies Abbott, Eli Lilly, GlaxoSmithKline, Novartis, Pfizer, and Takeda. These leading scientists in antibody technology have joined forces to design and generate the first-ever master set of recombinant epigenetics antibodies for use in disease-related research. The first 58 of 200 highly specific monoclonal antibodies are now available (Table 1).

Table 1. Targets for the Life Technologies/SGC antibody master set and for the ChIP-validated antibodies.

Targets for Life Technologies/SGC epigenetics antibodies released to date*
  • ATAD2B
  • BAZ2B (Recombinant)
  • BAZ2B (Biotin conjugate)
  • BRD3
  • BRD4 (Recombinant)
  • BRD4 (Biotin conjugate)
  • CBX2
  • CBX3 (Recombinant)
  • CBX3 (Biotin conjugate)
  • CBX5 (Recombinant)
  • CBX5 (Biotin conjugate)
  • CECR2
  • EHMT1
  • EP300 (Recombinant)
  • EP300 (Biotin conjugate)
  • KDM5C
  • L3MBTL1
  • L3MBTL2 (Recombinant)
  • L3MBTL2 (Biotin conjugate)
  • L3MBTL3 (Recombinant)
  • L3MBTL3 (Biotin conjugate)
  • L3MBTL4
  • MEN1 (Recombinant)
  • MEN1 (Biotin conjugate)
  • PB1A
  • PRDM4 (Recombinant)
  • PRDM4 (Monoclonal)
  • PRDM4 (Biotin conjugate)
  • PRDM9
  • PRDM10
  • PRMT3
  • PRMT5
  • SCML2
  • SETD3
  • SETD7
  • SFMBT1
  • SFMBT2 (Recombinant)
  • SFMBT2 (Biotin conjugate)
  • SMARCA4 (Recombinant)
  • SMARCA4 (Biotin conjugate)
  • SMYD3
  • SUV420H2
  • TAF1
  • TAF1A
  • TDRD3 (Recombinant)
  • TDRD3 (Monoclonal)
  • TDRD3 (Biotin conjugate)
  • TOPK (Recombinant)
  • TOPK (Biotin conjugate)
  • TRIM28
  • TSC2 (Recombinant)
  • TSC2 (Biotin conjugate)
  • WDR5
  • WHSC1L1
Targets for ChIP-validated antibodies
  • ENX-1/EZH2
  • Estrogen receptor-α
  • H3K27me1
  • H3K27me2
  • H3K27me3
  • H3K27me3S28p
  • H3K36me3
  • H3K4me1
  • H3K4me2
  • H3K4me3
  • H3K79me1
  • H3K79me2
  • H3K79me3
  • H3K9/14ac
  • H3K9ac
  • H3K9acS10p
  • H3K9me1
  • H3K9me2
  • H3K9me3
  • H3R17me2
  • H4K20me3
  • H4K8ac
  • HDAC1
  • HDAC2
  • HDAC3
  • Hepatocyte nuclear factor-4α
  • hGR
  • HIST3H3
  • HIST3H3 (Methylated)
  • HIST3H3 (Phospho)
  • MBD1
  • MECP2
  • NF-YB
  • p53
  • Pol II
  • PPAR-γ (clone A3409A)
  • PPAR-γ (clone K8713)
  • Retinoid X receptor-α
  • Sox2
  • STAT3
  • STAT4
  • STAT5-ϐ
  • Suz12
  • TBP
  • TIP5

*Antibodies not listed in the ChIP-validated set have been validated for target-protein immunoprecipitation (IP) but not yet for ChIP. Updated application information on individual antibodies can be found on our website.


Recombinant Antibodies for Epigenetics Research

Because they play a critical role in a variety of chronic diseases including cancer, epigenetic regulatory proteins are key targets of drug discovery. These proteins function in a complex regulatory circuit that determines which genes are turned on and off on both a temporal and spatial scale. A lack of industry-wide standards for quality antibodies, however, has plagued the study of these proteins, leading to an influx of products on the market that do not perform consistently or with the promised specificity. The recombinant monoclonal antibodies produced from the Life Technologies/SGC partnership (Table 1) address this important issue.

“The [Life Technologies/SGC] partnership is prepared to produce a set of 200 highly specific, highly sensitive antibodies that are validated for specific applications,” says Dr. Aled Edwards, Director and CEO of SGC. “These 58 now being launched are the first step toward developing the de facto standard set of quality epigenetics antibodies that researchers can use for generations to come.”

Each of the recombinant monoclonal antibodies in this master set are derived by isolating the clones of antibody heavy and light chains that have been carefully tested for their sensitivity and selectivity, and then expressing these clones in mammalian cells. Because recombinant antibodies are produced from renewable and stable clones, they provide peak specificity and performance with every lot. Furthermore, these recombinant antibodies are selected and validated for specific applications, including immunoprecipitation and western blotting, representing a significant improvement over existing antibodies on the market today.

Antibodies Qualified for Chromatin Immunoprecipitation

Chromatin immunoprecipitation (ChIP) experiments examine histone and nonhistone proteins such as transcription factors, as well as the DNA sequences bound to specific regulatory proteins. In ChIP, protein–DNA complexes are crosslinked in vivo, immunoprecipitated with specific antibodies, and purified. The precipitated DNA is then ready for locus-specific analyses using quantitative PCR (qPCR) or for genome-wide analyses using promoter-tiling arrays or massively parallel sequencing.

In addition to optimized reagents and workflows, a successful ChIP experiment must employ the right ChIP antibody. We have therefore qualified several important epigenetics antibodies for use in this application (Table 1). It is crucial to choose an antibody carefully, as different antibody preparations have distinct properties that can critically affect ChIP results. Our ChIP-validated antibodies overcome this limitation, delivering target specificity and performance with every lot. Furthermore, antibodies that are validated for western blot applications, where proteins are also typically in a fixed state, are not necessarily suitable for ChIP, and even fully characterized antibodies may not be useful in some cases, as the crosslinking step can alter protein epitopes.

Complete Workflow Kits for Chromatin Analysis

Life Technologies’ chromatin analysis solutions range from modular ChIP-qualified antibodies and kits to more integrated workflows for biochemical and cell-based assays as well as next-generation sequencing. The MAGnify™ Chromatin Immunoprecipitation System, which includes all reagents needed to perform ChIP except the antibody of interest, can reduce your overall ChIP protocol time by one full day. In addition, the MAGnify™ ChIP system is designed to improve reproducibility and decrease background levels caused by nonspecific binding through the use of Dynabeads® reagents, the DynaMag™-PCR magnetic separator, and an optimized magnetic DNA purification method.

The MAGnify™ ChIP system is also compatible with ChIP-sequencing library preparations. Direct sequencing of enriched fragments has proven more effective than microarrays for determining protein-binding sites in an unbiased manner. The throughput, accuracy, and flexibility of the Ion Personal Genome Machine® (PGM™) Sequencer and the 5500 Series Genetic Analysis Systems make them well suited for massively parallel sequencing in ChIP applications.


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