Related Experiment Video
Updated: Jan 21, 2026
Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation
Published on: June 21, 2016
Mapping Retinoic Acid-Dependant 5mC Derivatives in Mouse Embryonic Fibroblasts
Haider M Hassan1,2, T Michael Underhill3, Joseph Torchia4,5
1Department of Biochemistry, Western University, London, ON, Canada.
Abstract:
Methylase-assisted bisulfite sequencing (MAB-seq) is a derivatization technique to evaluate the presence of 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC) at base-pair resolution. Although MAB-seq was originally designed to study these metabolites under steady-state conditions, we have developed an alternative protocol to evaluate the dynamics of 5-fC/5-caC accumulation in response to agonists, such as all-trans retinoic acid (ATRA). In addition, this protocol utilizes a lower quantity of the M.SssI enzyme without compromising methylation efficiency and requires less bench time. Herein, we describe the use of MAB-seq assay to evaluate the generation of 5-fC/5-caC in response to ATRA in mouse embryonic fibroblasts, using the hypermethylated in cancer 1 (Hic1) locus as a model system.
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01:25Acidity and Basicity of Carboxylic Acid Derivatives
The relative acidic strength of the derivatives can be explained based on the extent of resonance stabilization of the conjugate base. The...
01:28Structures of Carboxylic Acid Derivatives
Carboxylic acid derivatives contain an acyl group attached to a heteroatom such as chlorine, oxygen, or nitrogen. The carbonyl carbon and oxygen are both sp2-hybridized with an unhybridized p orbital.
The three sp2 orbitals of the carbonyl carbon form three σ bonds, one each with the carbonyl oxygen, the α carbon, and the heteroatom, whereas the other two sp2 orbitals of the carbonyl oxygen are occupied by the lone pairs. Further, the unhybridized p...
01:26Spectroscopy of Carboxylic Acid Derivatives
01:16Nomenclature of Carboxylic Acid Derivatives: Acid Halides, Esters, and Acid Anhydrides
The IUPAC and common names of acid halides are derived from the corresponding carboxylic acids, by changing “ic acid” to “yl halide.” For example, as shown below, the IUPAC name ethanoyl chloride is derived from ethanoic acid, and the common name, acetyl chloride, is obtained from acetic acid.
01:15Carboxylic Acid Derivatives: Overview
01:13Relative Reactivity of Carboxylic Acid Derivatives
A key factor in assessing the reactivity of the acid derivatives is the basicity of the substituent or the leaving group. The lower the basicity of the leaving group, the higher the reactivity of the derivative. The basicity of the leaving group follows this order:
Halide ions < Acyloxy ions < Alkoxy ions < Amine ions