THE NEWSLETTER OF ACTIVE MOTIF motif vations OCTOBER 2014 | VOLUME 15 NUMBER 2 Special Neuroepigenetics Edition Enabling Epigenetics Research Antibodies, Kits and Services for Epigenetics & Gene Regulation Research New to Neuroepigenetics? We Can Help. There is increasing evidence that several neurodevelopmental, neurodegenerative and psychiatric disorders are, in part, caused by aberrant epigenetic modifications. As a result, researchers in neurogenetics are now beginning to investigate the mechanisms underlying epigenetic regulation in neuronal gene expression and how this impacts normal brain function. IN THIS ISSUE The transition into epigenetics research does not have to be intimidating because there are an increasing number of tools 2 New to Neuroepigenetics? available to help researchers obtain their desired results. We Can Help. 4 5-hmC and the Brain 5 Tools for Neuroepigenetic Research Various epigenetic modifications are The epigenetic tool kit 6 NEW: Quantify Global Changes in found in neurons The development of methods such as DNA Methylation These modifications include classi- chromatin immunoprecipitation (ChIP) 7 NEW: ChIP-Bisulfite-Sequencing for cal epigenetic marks such as DNA and DNA methylation enrichment tech- Mapping Allele-Specific Methylation methylation and histone modifica- niques, along with Next-Generation Se- of Protein/DNA Binding Sequences tions. Other epigenetic mechanisms in quencing tools, is allowing researchers play include histone subunit exchange, to get a better picture of the genome- 8 NEW: High-Resolution ChIP Analysis cytosine methylation variants and wide changes associated with neuro- of Transcription Factors non-coding RNAs. In recent years, logical and other diseases. There are 10 NEW: Nucleosome Substrates for there has been a rapid increase in the a number of techniques that are key to More Biologically Relevant number of publications suggesting a epigenetic analysis. These include: role for epigenetics in regulating the Screening Assays • Antibodies to discriminate between Central Nervous System (CNS) and the multiple post-translational 11 NEW: Epigenetic Services: A Novel a growing body of evidence linking modifications on the histone tails, ChIP-Seq Spike-in Strategy epigenetic mechanisms to neural and to detect methylated DNA 12 NEW: Validate the Specific mRNA plasticity and CNS disorders, such as Targets of miRNAs schizophrenia and drug addiction (Ta- • ChIP and ChIP-Seq techniques to en- ble 1). More than a dozen neurological able scientists to link specific states 13 miRNAs in Neural Development & syndromes so far have been linked to of chromatin to individual gene loci Neurological Diseases mutations in single genes that encode in a cell to understand how genes 14 Tools to Streamline Epigenetic Drug DNA methyltransferase and histone are regulated modifying enzymes. This list includes Research • Enrichment methods for isolation of neurological disorders that appear in methylated DNA variants (5-meth- 15 NEW: Small Molecules to Modulate early childhood (Rett syndrome) or ylcytosine, or 5-mC, and 5-hydroxy- Epigenetic Processes later in life, such as Hereditary Sen- methylcytosine, or 5-hmC) sory and Autonomic Neuropathy Type 1 (HSAN1). • Bisulfite conversion of methylated DNA prior to sequencing to allow detection of methylated cytosines “What Roles do Epigenetic Mechanisms Play in Complex Human Diseases of the Nervous System?” 2 www.activemotif.com Epigenetics of the Nervous System Using the right tools for ChIP enrich for DNA fragments that contain Histonemodification DNA methylationNoncodingRNA ChIP is a technically challenging 5-mC and 5-hmC. Many of our DNA Learning and memory √ √ √ method. Numerous factors can cause methylation antibodies have been vali- Addiction √ √ √ it to fail, so researchers who are not dated for use in ChIP, methylated DNA Autism spectrum ??? experts in the techniques are best immunoprecipitation (MeDIP) and/or Epilepsy √ √ √ served using well-validated and reli- immunofluorescence. For complete PTSD √ √ able kits to perform these assays. details on all of our DNA methylation Alzheimer's disease √ √ products, please visit us at Stress √ √ √ Active Motif has developed a number www.activemotif.com/dnamt. Schizophrenia √ √ of kits and accessory reagents tailored to help the researcher with their ChIP Bipolar disorder √ √ √ experiments. We provide all the criti- Epigenetic techniques require Adult neurogenesis √ √ cal components needed in a single kit, validated antibodies Table 1: Examples of neural processes and disorders along with easy to follow instructions. One of the greatest challenges for epi- associated with epigenetic modifications. These kits and associated antibodies genetic-based research has been the have been used in hundreds of labs lack of antibodies that show proper and cited in over 1,000 papers in peer- specificity and that have been validat- reviewed journals. For the full list of ed for use in techniques such as ChIP kits and reagents for ChIP, please visit and ChIP-Seq. Histones have multiple Let us do the work for you - us at www.activemotif.com/chip. post-translational modifications along Active Motif Epigenetic Services the so-called tail portion of the protein Reproducibly generating high quality, that appear to be involved in gene interpretable data from ChIP ex- regulation and disease. Antibodies periments can be challenging, as it “How is DNA Methylation need to be able to clearly differenti- requires prior knowledge of working Actively Regulated ate between these multiple small antibodies, optimized protocols for in Neurons?” modifications. It is a major challenge various cell types and knowledge of to develop antibodies with sufficient cell type-specific binding sites. Add specificity that will also perform in in the technical and bioinformatics demanding techniques such as ChIP. challenges associated with generat- What is the role of DNA methylation ing whole-genome data sets, and in brain function? Active Motif has established a vali- ChIP-Seq may literally be beyond your DNA methylation of genes is found dation program for its antibodies to reach. That’s why our Epigenetic Ser- in all human tissues, including the qualify them for their intended use. This vices team provides a wide variety of brain. There are several methylation includes ChIP-Seq testing, ChIP valida- ChIP services. This makes it possible variants, and one of these, 5-hmC, is tion, as well as a test on the specificity for you to utilize our expertise and highly expressed in the brain relative of our histone antibodies with a unique research tools without having to be an to other parts of the body. This has led Modified™ Histone Peptide Array expert in the techniques yourself. to speculation that 5-hmC may have (Catalog No. 13001). For the full list of a unique biological role in the CNS. our epigenetics antibodies please visit To find out more, or to get a quote, go Also, recent studies have shown a www.activemotif.com/abs. to www.activemotif.com/services. correlation between DNA methylation levels and mental health problems, such as anxiety and depression. In addition, mutations in genes involved in DNA methylation (e.g. MeCP2) are linked to neurological diseases. How- ever, the mechanism by which DNA methylation exerts these effects is not fully understood. Tools for DNA methylation analysis Active Motif offers a number of prod- ucts specific for this area of research, including kits and antibodies that [email protected] 3 5-Hydroxymethylcytosine (5-hmC) 5-hmC and the Brain Epigenetic regulation is an important part of human brain development. It links our environment and our genome and influences learning and memory processes by what many now refer to as behavioral epigenetics, or neuroepigenetics. Neurogenesis is said to continue in certain parts of the brain throughout adult life. However, it may be neuroepigenetic changes that hold the key to under- standing disease-related risk factors associated with our neural development and the aging process. One of the most studied epigenetic modifications, DNA methylation, is at the center of research involving brain diseases, major psychosis and addictions. DNA methylation 5-hmC and methyl CpG binding diseases. In the case of Rett syn- DNA methylation functions to regulate protein 2 (MeCP2), a member of the drome, there is a strong correlation gene transcription in normal cells. MBD family that is important for between 5-hmC and MeCP2 binding Aberrant DNA methylation is respon- neuronal maturation. While 5-hmC when these mutations are present. sible for repression of genes through has limited binding affinity to most promoter hypermethylation, which is MBD proteins, in the case of MeCP2, As researchers continue to study implicated in tumorigenesis, and the both 5-mC and 5-hmC can bind it 5-hmC’s contribution to disease and ubiquitous hypomethylation common with high affinity (Figure 1) raising the to normal brain function, Active Motif in early carcinogenesis. Abnormal question of how each affects neuronal offers highly characterized and vali- DNA methylation is also linked to processes. While MeCP2’s repres- dated 5-hmC antibodies for a number various neurological diseases. sive properties are important for of important applications, including normal brain function, it has recently hMeDIP-Seq, IF and IHC. For more been shown that mutations in MeCP2 information please visit us at 5-hmC and the brain proteins are associated with certain www.activemotif.com/dnamethabs. Ten-eleven translocation