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Motif Vations APRIL 2016 | VOLUME 17 NUMBER 1 THE NEWSLETTER OF ACTIVE MOTIF motif vations APRIL 2016 | VOLUME 17 NUMBER 1 CANCER EPIGENETICS EDITION Enabling Epigenetics Research Antibodies, Kits and Services for Epigenetics & Gene Regulation Research Epigenetics & Cancer Epigenetics, or the heritable changes in gene function that occur independent of DNA sequence, has become a major focus of development and disease research. Countless studies link epigenetic alterations to developmental processes, including X-chromosome inactivation, genomic imprinting, axis patterning and differentiation, as well as to diseases such as cancer, chromosomal instabilities and mental retardation. Because genetics alone does not provide an adequate explanation for the complexity of these processes, a deeper understanding of the role of epigenetics is crucial to unraveling the underlying mechanisms responsible for regulating IN THIS ISSUE development and disease. 2 Epigenetics & Cancer. DNA methylation & gene regulation Methylation & the cancer epigenome 4 RNA Analysis Techniques to Advance DNA methylation is an important Changes in DNA methylation have our Understanding of the Transcriptome regulator of gene expression and been well characterized in cancer. 5 NEW: Tools to Study Nrf2 Transcription chromosome conformation. It occurs In general, the cancer epigenome is Factor Activation at the cytosine bases of eukaryotic marked by global DNA hypomethylation DNA, which are converted to 5-methyl- and promoter-specific DNA hyper- 6 Practical Guide to Chromatin cytosine (5-mC) by DNA methyltrans- methylation, which often leads to Immunoprecipitation Techniques ferase enzymes. DNA methylation silencing of tumor suppressor genes. 10 NEW: Determine CRISPR/Cas9 occurs almost exclusively in the context This link to cancer is supported by the Specificity Using enChIP of CpG dinucleotides that are relatively finding that mutations in DNMT3A are rare in the mammalian genome and found in acute myeloid leukemia, and 11 Quantify Global Changes in 5-mC tend to be clustered in CpG islands. there are currently two FDA approved & 5-hmC in Normal and Diseased Approximately 60% of gene promoters cancer drugs that target DNMTs. The Samples are associated with CpG islands and are recently characterized DNA modifica- 12 A Genome-wide 3’UTR Collection for normally unmethylated. CpG methylation tion 5-hydroxymethylcytosine (5-hmC) High-throughput Functional Screening of gene promoters is usually associated has also been linked to cancer. Both a of miRNA Targets with transcriptional silencing, which reduction in 5-hmC and in expression of can occur through a number of the TET enzymes that convert 5-mC to 13 Validated Antibodies Reveal Histone- mechanisms, including the recruit- 5-hmC have been reported in breast, mediated Effects on miRNA in ment of methyl binding domain (MBD) liver, lung, prostate and pancreatic Non-small Cell Lung Cancer proteins. DNA methylation is involved cancer. 14 High Quality Bromodomain Proteins in a number of cellular functions, such for Developing Robust Assays for as embryonic development, genetic Tools for DNA methylation analysis Epigenetic Drug Discovery imprinting, X chromosome inactivation Active Motif offers a number of products and control of gene expression. 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(MeDIP) and immunofluorescence. 2 www.activemotif.com EPIGENETICS & CANCER For complete details on all of our DNA and the first miRNA mimic entered the the functional relevance of a specific methylation products, or to download a clinic for cancer therapy in 2013. miRNA, including the LightSwitch™ free copy of our new DNA Methylation Luciferase Reporter Assay System. & Cancer eBook, please visit us at Tools for miRNA analysis 3’UTR reporter assays have become www.activemotif.com/dnamt. Inherent to the rapid advancements an important component of thorough and general excitement surrounding miRNA target studies because they The role of non-coding RNAs in cancer miRNA discoveries is the need for provide functional evidence for, and The discovery of non-coding RNAs applicable and validated experimental quantitate the effects of, specific (ncRNAs) and their role in gene regu- tools to enable researchers to accurately miRNA-3’UTR interactions in a cell- lation represents a significant advance study the expression and biological based system. For complete details on in cancer research. These ncRNAs function of miRNAs. There are a number all our miRNA products, or to download interact with DNA, RNA or protein of diverse methodologies available for a free copy of our new microRNAs in molecules and/or some combination miRNA detection and target identification, Cancer eBook, please visit us at www. thereof, acting as essential regulators as well as to determine the functional activemotif.com/ncRNAs-and-cancer. in chromatin organization, and tran- effects of a specific miRNA of interest. scriptional and post-transcriptional These include computational tools, Let us do the work for you - regulation. The functional relevance expression and proteomics assays, Active Motif Epigenetic Services of ncRNAs is particularly evident for 3’UTR reporter assays and chromatin Our Epigenetic Services team provides microRNAs (miRNAs) and long non- immunoprecipitation (ChIP) based a wide variety of DNA Methylation and coding RNAs (lncRNAs), which have techniques. Active Motif offers a wide Gene Regulation services. For more been associated with all stages of selection of tools to enable researchers complete information, or to get a quote, cancer including diagnosis, staging, to identify mRNA targets and elucidate visit www.activemotif.com/services. progression, prognosis and response to treatment. Their misexpression 2. Loss of normal repressive Transcription Factors epigenetic marks onco-miRNAs confers upon a cancer cell the capacity miRNA gene 1. CpG promotor for tumor initiation, growth and Genomic loss methylation onco-suppressor Loss of histone acetylation metastasis, making ncRNAs attractive DNA miRNAs therapeutic targets and potentially Aberrant DNA hypermethylation useful diagnostic tools. MicroRNAs in cancer MicroRNAs are important epigenetic regulators of gene expression and 5 Cap AAA have been shown to play a role in Pri-mRNA numerous biological processes, such Cropping 3. Drosha downregulation as cellular signaling, cell differentiation, growth, development and apoptosis. Mutations and improper regulation of Nucleus Pre-miRNA miRNAs have been linked to a variety of physiological disorders, such as 4. XPO5 mutation XPO5 cancer and heart disease (Figure 1). Cytoplasm The recent emergence of miRNAs has Oncogene been one of the defining developments accumulation 5. DICER1 downregulation in cancer biology. Many studies have 5. TARBP2 mutation demonstrated how miRNAs impact cancer progression through controlling 7. tumor 6. oncogenic suppressor expression of their target mRNAs to miRNA miRNA loss accumulation facilitate tumor growth, invasion, Unwinding of miRNA duplex angiogenesis and immune response. The explosion of knowledge since their Loss of tumor discovery in 1993 has brought forward suppressor genes new diagnostic and therapeutic oppor- tunities. Clinical trials utilizing miRNA Figure 1: DNA methylation and miRNA mysregulation in cancer. profiling for patient prognosis and A schematic representation of alterations in DNA methylation and in the miRNA biogenesis pathway that commonly lead to cancer development clinical response are now underway, (adapted from Bertoli G. et al. (2015). Theranostics 5, 1122–43). [email protected] 3 TOOLS FOR RNA ANALYSIS RNA Analysis Techniques to Advance our Understanding of the Transcriptome Technological advances in the field of RNA analysis have expanded our understanding of the transcriptome beyond messenger RNA (mRNA) to introduce new classes of RNAs that include short and long non-coding RNA (ncRNA). These non-coding RNAs vary in cellular localization and appear to have unique regulatory functions. Combining RNA analysis with high quality RNA isolation from subcellular fractions, such as with Active Motif’s RNA Subcellular Isolation Kit, or with next-generation sequencing (NGS) by utilizing Active Motif’s RNA Sequencing (RNA-Seq) Service, enables you to achieve a greater understanding of RNA function in your biological system. High quality RNA fractions improve data interpretation by reducing the RNA Subcellular Isolation Kit downstream RNA analysis sensitivity of detection for low abundance Active Motif’s RNA Subcellular Isolation transcripts and the ability to study • Separates nuclear & Kit is designed to efficiently isolate sepa- RNA processing dynamics. The RNA cytoplasmic RNA without rate nuclear and cytoplasmic fractions Subcellular Isolation Kit reduces this cross-contamination of RNA for downstream analysis. This complexity to improve downstream method can be used to isolate both long analysis and also provides information • Works with cell or tissue samples and short RNA sequences from cells regarding RNA localization. • Spin columns included for or tissue without cross-contamination
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