Histones are an important part of the nucleosome, the basic structure of chromosomes. It consists of two molecules each of four histones H2A, H2B, H3 and H4, forming a histone octamer. A DNA molecule of about 146 bp in length coils around a core structure of histone octamers, forming a nucleosome. Each core histone N-terminal amino acid residue can undergo various covalent modifications such as acetylation, methylation, phosphorylation, ubiquitination, and poly ADP glycosylation. Histone modification plays a very important role in the life process, and the occurrence of many human diseases is closely related to histone modification.
Histone modifications refer to the process of histone modifications such as methylation, acetylation, phosphorylation, adenylation, ubiquitination, and ADP ribosylation under the action of related enzymes. In mammalian genomes, histones can have many modifications. A nucleosome consists of an octamer consisting of two H2A, two H2B, two H3, two H4 and 147bp of DNA wrapped around the outside. The state of the core part of the histones that make up the nucleosome is roughly uniform, and the free N-terminus can be subjected to various modifications, which all affect the transcriptional activity of genes.
Under physiological conditions, formaldehyde is used to cross-link the specifically modified histones and DNA in cells, and then ultrasonic waves are used to break them into small chromatin fragments of a certain length. Then, by using an antibody corresponding to a specific histone modification, the target fragment (the fragment with specific modification of histone) is precipitated, and the target fragment is purified and sequenced to obtain the relevant gene fragment information.
In the article "GenomeWide Analysis of Histone Modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica", chromatin immunoprecipitation combined with high-throughput sequencing (CHIP-seq) was used to study the four Genome-wide distribution of individual histone modifications in rice. By analyzing published DNase-seq data, this study explored DNase hypersensitive (DH) sites along the rice genome. Histone modifications were mainly found in gene regions and were enriched around gene transcription start sites (TSSs). This analysis demonstrated that all four histone modifications and DNase hypersensitivity sites were associated with active transcription. In addition, the four histone modifications were highly co-occurring in the transcribed region, presumably a possible feature for predicting missing genes in rice gene annotations. Further studies validated this prediction, confirming the transcription of the two predicted missing genes. At the same time, the study also constructed a sequence motif analysis method to identify DH sites and many putative transcription factor binding sites.