Emerging Chemistry Strategies for Engineering Native Chromatin

Abstract

Chromosomes present one of most challenging of all substrates for biochemical study. This is because genomic DNA is physically associated with an astonishing collection of nuclear factors, which serve to not only store the nucleic acid in a stable form, but also grant access to the information it encodes when needed. Understanding this complex molecular choreography is central to the field of epigenetics. One of the great challenges in this area is to move beyond correlative type information, which is now in abundant supply, to the point where we can truly connect the dots at the molecular level. Establishing such causal relationships requires precise manipulation of the covalent structure of chromatin. Tools for this purpose are currently in short supply, creating an opportunity that, as we will argue in this Perspective, is well suited to the sensibilities of the chemist.

A simple and versatile system for the ATP-dependent assembly of chromatin

“…We are entering an exciting new era of chromatin research with the advent of new technologies such as techniques for the synthesis of customized histones (40). The dNLP-ISWI assembly system could be used in conjunction with conventional or customized histones for the assembly of many different types of chromatin that could be used for a diverse range of potential applications.…”

“…In addition, a second important advantage of recombinant histones is their ability to use mutant histones, histone variants, or specifically modified histones (for recent review, see Ref. 40). Such customized chromatin would allow the investigation of specific biological phenomena.…”

Proteomics of Long‐Lived Mammals

“…Since PTMs are not directly genetically encoded, engineering these features in vivo was beyond reach until recently. Novel engineering strategies such as protein ligation/splicing, non‐natural amino acid mutagenesis, or inactive CRISPR/Cas9‐fusion protein‐based localization of epigenetic modifiers may permit the engineering of designer PTMs/proteoforms in vivo . We expect that future proteomics studies of longevity will incorporate these approaches to correlate PTMs/proteoforms with lifespan.…”

Analytical epigenetics: single-molecule optical detection of DNA and histone modifications

“…In the following, labeling strategies for the most-important cytosine modifications will be discussed. Covalent labeling schemes for histone tails are still in early development and were not yet utilized for analytical work [20,21]. …”