New to the field and want to get up to speed quick? Take a dive into our epigenetics background section. With a field that's changing so rapidly, we can't promise every bit will still hold true, but it should point you in the right direction.
Epigenetics has been changing so fast that it makes maintaining a “Background” section almost impossible. Fortunately for us, our friends at Zymo Research and Active Motif produced some really nice review content with the help of some of the field’s top researchers and their own scientists. What's even nicer is that they let us use it. If you’d like to print out a hard copy, you can find links to the downloads in each of these expanded sections.
The field of epigenetics, transcending genetics, genomics, and molecular biology, is now poised to be the vanguard of biological science. The rise of epigenetics marks a maturation of the field, which only 50 years ago was given its name and a vague definition, but is now a dynamic discipline, challenging and revising traditional paradigms of inheritance. Through epigenetics the classic works of Charles Darwin, Gregor Mendel, and Jean-Baptiste Lamarck are now seen in different ways. As more factors influencing heredity are discovered, today’s scientists are using epigenetics to decipher the roles of DNA, RNA, proteins, and environment in inheritance. The future of epigenetics will reveal the complexities of genetic regulation, cellular differentiation, embryology, aging, cancer, and other diseases. In this review fundamental concepts of epigenetics will be described, including chromatin structure, epigenetic markers, model systems, research methods, and future directions. Read more on Epigenetics Background
DNA methylation, histone modifications and higher order chromatin structure play a central role in the regulation of mammalian genome organization. The epigenetic signature of any cell provides valuable information about its cellular state, its developmental potential, and its health. A detailed description and understanding of the epigenome will notably expand our understanding of human health and disease. The aim of this review is to provide a broad overview of epigenetic modifications and mechanisms in large mammalian genomes. Read more on Epigenetic Regulation in Mammalian Genomes.
Cancer is caused by failure of checks and balances that control cell numbers in response to the needs of the whole organism. Inappropriate function of genes that promote or inhibit cell growth or survival can be caused by errors introduced into the genetic code itself or by faulty epigenetic mechanisms deciding which genes can and cannot be expressed. Epigenetic lesions and genetic mutations are acquired during the life of an individual and accumulate with aging. Both types of events, either individually or in cooperation, can result in the loss of control over cell growth and development of cancer. Read more on Epigenetics in Cancer.
Epigenetic gene regulatory mechanisms are important in a variety of phenomena throughout the eukaryotes including the silencing of transposons, sex chromosome dosage compensation, imprinting,and the inappropriate gene expression that occurs in cancer cells. In addition, recent findings suggest that epigenetic mechanisms play an unforeseen and expanding role in the normal regulation of genes during development. This review will focus on advances made in our understanding of epigenetic gene regulation in insect and plants. Read more on Epigenetic Regulation of Gene Expression in Insects and Plants.
The role of histone acetylation and its involvement in the regulation of transcription has long been a topic of research in cell and molecular biology labs. Recent studies have revealed the role of histone acetylation in other important processes regulating the structure and function of chromatin, and hence, the eukaryotic genome. The process of organizing the millions (billions in the case of humans) of base pairs of genetic material in the eukaryotic nucleus has profound effects on DNA-dependent events, such as transcription, recombination, replication and repair. DNA is organized by its incorporation into chromatin, the basic subunit of chromatin being the nucleosome. A nucleosome is composed of 147 base pairs of DNA coiled around an octamer of histone proteins, two molecules each of histone H2A, H2B, H3 and H4. Histone H1 associates with chromatin outside the core octamer unit and regulates higher order chromatin structure.
Chromatin and chromosomes undergo dramatic and dynamic changes in organization in response to a myriad of cellular signals. Chromosomes condense and relax during the cell division process. Damaged DNA adopts a unique structure that facilitates repair. Critical to cell function, most of the genome must remain in a transcriptionally silent state, save for specific combinations of genes, which vary significantly between cell types. These processes must be tightly regulated to maintain the integrity of the genome and the proper function of the cell. Read more on Histone Acetylation and Genome Function.
The sequence of the human genome does not differ considerably from that of other species. The source of variability are DNA repeat elements, termed “junk DNA” in former times, but gaining more and more importance in gene regulation and disease. About half of the genome is comprised of DNA repetitive elements, satellite DNA being one type of repetitive DNA. Satellite DNA is categorized in four groups: The alpha satellite (building up the centromer), microsatellites (units of about 6 nucleotides spanning about 100 base pairs), minisatellites (e.g. telomeres; units of 6-100 nucleotides spanning several kilobases) and macrosatellites (units of about 3000 nucleotides spanning several hundred kilobases). Read more on Macrosatellite Epigenetics.
Epigenetic mechanisms can contribute to each step of cancer development and progression; DNA methylation is the dominant factor that is deregulated in cancer. DNA methylation is a reversible process which typically occurs at CpG dinucleotides. In normal cells, CpG islands (mostly in gene promoter regions) are unmethylated, and repetitive elements and transposons are mostly methylated. DNA methylation is achieved by DNA methyltransferases (DNMTs) and interferes with gene transcription in several ways. A direct impact on gene transcription is by inhibition of binding of transcription factors to target sequences by methylation CpGs. Read more on DNA Methylation Changes in Cancer.
If you're looking for some slick tools and databases out there, we've compiled a list of some of the ones we've bumped into over the years. If you've got one to add to our list, don't hesitate to send it our way.
Bisulfite Primer Seeker: Provides designs even in CG-rich sequences, but it will also give multiple options for amplicons that span different regions within the sequence.
CpG Island Detection: IDs promoter regions associated with CpG Islands in mammals.
CpGPlot: Finds regions of genomic sequence that are CpG rich.
CpG Viewer: Tool for analyzing bisulfite sequencing data.
CpG Island Searcher: Screens for CpG islands within given criteria.
CpG and GC Plotter: Plots variation in CpG and GC content in a given sequence.
CpGfinder: Maps your sequence to known CpG islands.
CpG Promoter: Maps promoters with CpG islands
MethyCancer Database: Database of human DNA methylation and cancer.
PubMeth Database: Methylation database in cancer.
MethDB: Database for methylation and epigenetic effects with emphasis on environment effects on DNA methylation.
methPrimerDB: Database of primers used in DNA methylation analysis
MethPrimer: Design bisulfite conversion primers for MSP or BSP Methyl Primer Express: Designs primers for methylation analysis.
ChIPOTle: A Microsoft Excel Macro that facilitates ChIP Tiling array data in yeast.
PeakSeq: Systematic scoring of ChIP-Seq experiments relative to controls
Mpeak: A model-based method for identifying peaks in ChIP array data.
ChIP-Seq Analysis Server: Home to a number of tools for analyzing ChIP-Seq and other types mass genome annotation data.
CisGenome: ChIP-seq and ChIP-Chip analysis suite facilitating peak detection, de novo motif discovery and mapping.
MicroCosm Targets: Predicted Targets for miRNAs for many species. Isomir Database: Lists miRNA seqence variants found by NextGen sequencing.
miRanda miRNA Target Database: Predicted miRNA targets and expression.
TargetScan miRNA Target Database: Predicted miRNA targets in mammals.
DIANA microT 3.0: miRNA target prediction.
RNAHybrid: miRNA hybridization and target prediction.
STarMir: miRNA folding and structure software.
RNA22: miRNA target and precursor prediction
miRDeep: An algorithm that was developed to discover active known or novel miRNAs from deep sequencing data.
miReduce: A tool that correlates the logarithm of expression fold changes of a set of genes with the motif content of the regulatory sequences of these genes.
GOmir: Application for human miRNA target analysis and gene ontology clustering