Recent Achievements in Characterizing the Histone Code and Approaches to Integrating Epigenomics and Systems Biology

Abstract

Functional epigenetic regulation occurs by dynamic modification of chromatin, including genetic material (i.e. DNA methylation), histone proteins, and other nuclear proteins. Due to the highly complex nature of the histone code, mass spectrometry (MS) has become the leading technique in identification of single and combinatorial histone modifications. MS has now overcome antibody based strategies due to its automation, high resolution and accurate quantitation. Moreover, multiple approaches to analysis have been developed for global quantitation of post-translational modifications (PTMs), including large-scale characterization of modification co-existence (middle-down and top-down proteomics), which is not currently possible with any other biochemical strategy. Recently, our group and others have simplified and increased the effectiveness of analyzing histone PTMs by improving multiple MS methods and data analysis tools. This review provides an overview of the major achievements in the analysis of histone PTMs using MS with a focus on the most recent improvements. We speculate that the workflow for histone analysis at its state-of-the-art is highly reliable in terms of identification and quantitation accuracy, and it has the potential to become a routine method for systems biology thanks to the possibility of integrating histone MS results with genomics and proteomics datasets.

An optimised Chromatin Immunoprecipitation (ChIP) method for starchy leaves of Nicotiana benthamiana to study histone modifications of an allotetraploid plant

“…The next crucial step in ChIP protocol is chromatin shearing and generally a Bioruptor® sonicator is used. We tested different number of sonication cycles (14,16,18,20,22) to determine the optimum number of cycles to achieve the required sheared DNA fragment range (200-500 bp). This was achieved with 22 cycles and the lower number of sonication cycles resulted in incomplete shearing and larger fragment sizes ( Fig.…”

“…This 'nucleosome code' allows the assembly of different epigenetic states to allow diverse readouts of underlying genetic information such as gene activation or gene silencing (20). Histone code hypothesis was proven to be correct with the identi cation of enzymes that recognise combinatorial patterns of histone marks (22). The key proteins associated with these histone modi cations are categorised as histone writers, readers and erasers.…”

Conclusiones. Nutrición y gastronomía en las distintas comunidades autónomas. La gastronomía segoviana en el contexto nacional

“…Existen otros elementos reguladores de la expresión, y, por tanto, susceptibles de estar relacionados con los estados de salud-enfermedad, que no implican un cambio de base en la secuencia del ADN. Así, la epigenómica estudia los elementos funcionales claves que regulan la expresión génica en una célula que no implican cambio de base en la secuencia (31). Una limitación de la epigenómica en comparación con la genómica es que el genoma es el mismo en todas las células somáticas; sin embargo, el epigenoma es específico de cada tipo celular, lo que añade más complejidad al estudio y hace muy relevante el origen de la muestra que se ha tomado para su análisis (32).…”

Unravelling the biology of chromatin in health and cancer using proteomic approaches

“…To be able to analyze histone variants and isoforms with different modifications globally, quantitative mass spectrometry (MS) is one of the most powerful tools. The analysis of histones and their modifications by proteomics is a highly active area of research, and we recommend excellent recent reviews for much greater detail on this topic [8, 9]. …”