On the Hunt for the Histone Code

Abstract

Our genome is not made of naked DNA but a fiber (chromatin) composed of DNA and proteins packaged into our chromosomes. The basic building block of chromatin is the nucleosome, which has two copies of each of the proteins called histones (H2A, H2B, H3, and H4) wrapped by 146 base pairs of DNA. Regions of our genetic material are found between the more open (euchromatin) and more compact (heterochromatin) regions of the genome that can be variably accessible to the underlying genes. Furthermore, post-translational modifications (PTMs) on histones, such as on H3, are critical for regulating chromatin accessibility and gene expression. While site-specific antibodies were the tool of choice for histone PTM analysis in the early days (pre-2000s), enter Don Hunt changing the histone PTM field forever. Don's clever thinking brought new innovative mass spectrometry-based approaches to the epigenetics field. His lab's effort led to the discovery of many new histone modifications and methods to facilitate the detection and quantification of histone PTMs, which are still considered state of the art in the proteomics field today. Due to Don's pioneering work in this area, many labs have been able to jump into the epigenetics field and "Hunt" down their own histone targets. A walkthrough of those early histone years in the Hunt Lab is described by three of us who were fortunate enough to be at the right place, at the right time.

Keywords: epigenetics; histone; mass spectrometry; post-translational modifications; proteomics.

Graphical abstract

Fig. 1

Professor Donald F. Hunt and Dr. Jeffrey Shabanowitz and all the Hunt-lings (circa ∼2004).Front row: Erin Jeffery, Sahana Mollah, Dina Bai and Melanie Schroeder. Second row: Jeff Shabanowitz, Joy Polefrone, Annie Evans, An Chi, Celeste Ptak, Leann Mikesh and Don Hunt. Third row: Mark Platt, Trixi Ueberheide, Ben Garcia and Scott Busby. (In bold are the founding Histone Posse members).

Fig. 2

MS/MS spectrum of the 6 to 20 residue fragment of histone H3. Propionylation of this histone H3 peptide facilitates the analyses by converting the N-terminus and both K14 and K18 residues to propylamides (pr, +56 Da), while the K9 residue is not chemically modified as it is endogenously blocked by trimethylation. The peak at [M+2H]²⁺ −29.5 m/z corresponds to the loss of the trimethyl group (CH3)3N from the K9 residue (mechanism depicted). Adapted from Mollah et al. (28).