Enzymes of epigenetics. Part B

Başlık:

ISBN:

9780128119020

Yayın Bilgileri:

Cambridge, MA : Academic Press is an imprint of Elsevier, 2016.

Fiziksel Tanımlama:

1 online resource : illustrations (chiefly color)

Series:

Methods in enzymology ; volume 574

Methods in enzymology ; v. 574.

Contents:

Front Cover; Enzymes of Epigenetics, Part B; Copyright; Contents; Contributors; Preface; Part I: Epigenetic Technologies; Chapter One: Identification and Quantification of Histone PTMs Using High-Resolution Mass Spectrometry; 1. Introduction; 2. Histone Extraction from Cells; 2.1. Materials and Buffer Recipes; 2.2. Cell Harvest; 2.2.1. Cell Harvest: Tissue Samples; 2.2.2. Cell Harvest: Cell Cultures; 2.3. Nuclei Isolation; 2.4. Acid Extraction; 3. Bottom-Up Mass Spectrometry; 3.1. Materials and Buffer Recipes; 3.2. Derivatization and Digestion; 3.3. Desalting

3.4. Online RP-HPLC and MS Acquisition3.5. Data Analysis; 3.5.1. Software-Based Peak Area Extraction and Abundance Calculation; 4. Offline Fractionation of Histone Species; 4.1. Materials and Buffer Recipes; 4.2. Histone Variant Purification; 5. Middle-Down Mass Spectrometry; 5.1. Materials and Buffer Recipes; 5.2. Digestion; 5.2.1. GluC; 5.2.2. AspN (Alternative to GluC); 5.3. WCX-HILIC and MS; 5.4. Data Analysis; 6. Top-Down Mass Spectrometry; 6.1. Materials and Buffer Recipes; 6.2. Top-Down MS Using Direct Infusion; 6.3. Data Analysis; References

Chapter Two: Substrate Specificity Profiling of Histone-Modifying Enzymes by Peptide Microarray1. Introduction; 2. Assay Optimization; 2.1. Design of Custom Print Formats; 2.2. Detection Reagent Considerations; 2.2.1. Radioisotopes; 2.2.2. Antibodies; 3. Assay Methodology; 3.1. Microarray-Based Lysine Methyltransferase (KMT) Assays with G9a; 3.2. Solution-Based KMT Assays with G9a; 3.3. Microarray-Based Lysine Demethylase (KDM) Assays with JMJD2A; 4. Enzyme Specificity Profiling by Microarray; 4.1. High-Throughput Profiling of G9a KMT Activity

4.2. High-Throughput Profiling of JMJD2A KDM Activity5. Summary and Perspectives; Acknowledgments; References; Chapter Three: ArrayNinja: An Open Source Platform for Unified Planning and Analysis of Microarray Experiments; 1. Introduction; 2. ArrayNinja; 2.1. Obtaining and Running ArrayNinja; 2.2. Overview of the ArrayNinja Database; 3. Planning Custom Microarrays with ArrayNinja; 4. Data Analysis Features of ArrayNinja; 4.1. Microarray Image Preparation; 4.2. Quantification of Microarray Data; 5. Benchmarking ArrayNinja Against ImageQuant TL; 5.1. Homogeneous Noise; 5.2. Inhomogeneous Noise

5.3. Implicit Assumption of Local Noise Correction6. Methodological Details; 6.1. Default (Whole Spot) Quantification; 6.2. Nonlocal Noise Thresholding; 6.3. Local Noise Thresholding; 6.4. Variegated Spot Morphology; 7. Limitations, Assumptions, Other Features, and Future Development; 7.1. Limitations and Assumptions; 7.2. Other Features; 7.3. Future Development; 8. Summary; Acknowledgments; References; Chapter Four: Chemical Biology Approaches for Characterization of Epigenetic Regulators; 1. Introduction; 1.1. Chemical Probes and Their Use in Biology

Abstract:

Enzymes of Epigenetics, a two volume set in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. The two volumes cover research methods that are employed to study epigenetic regulation and includes structural, biochemical, molecular, biological, cellular, computational, and systems approaches. Topics include chromatin structure and histones, posttranslational histone modification enzymes and complexes, histone modification binders, DNA modifications and nucleic acid regulators, epigenetic technologies and small molecule epigenetic regulators, and biological connections.

Local Note:

Elsevier

Subject Term:

SCIENCE -- Life Sciences -- Biochemistry.

Enzymology

Epigenetics

Added Author: