Multi-omic analysis of gametogenesis reveals a novel signature at the promoters and distal enhancers of active genes

Abstract

Epigenetic regulation of gene expression is tightly controlled by the dynamic modification of histones by chemical groups, the diversity of which has largely expanded over the past decade with the discovery of lysine acylations, catalyzed from acyl-coenzymes A. We investigated the dynamics of lysine acetylation and crotonylation on histones H3 and H4 during mouse spermatogenesis. Lysine crotonylation appeared to be of significant abundance compared to acetylation, particularly on Lys27 of histone H3 (H3K27cr) that accumulates in sperm in a cleaved form of H3. We identified the genomic localization of H3K27cr and studied its effects on transcription compared to the classical active mark H3K27ac at promoters and distal enhancers. The presence of both marks was strongly associated with highest gene expression. Assessment of their co-localization with transcription regulators (SLY, SOX30) and chromatin-binding proteins (BRD4, BRDT, BORIS and CTCF) indicated systematic highest binding when both active marks were present and different selective binding when present alone at chromatin. H3K27cr and H3K27ac finally mark the building of some sperm super-enhancers. This integrated analysis of omics data provides an unprecedented level of understanding of gene expression regulation by H3K27cr in comparison to H3K27ac, and reveals both synergistic and specific actions of each histone modification.

Dynamic profiling and functional interpretation of histone lysine crotonylation and lactylation during neural development

“…Genome-wide associations between histone Kcr and gene expression have been studied in various organisms [4,9,12,14,[26][27][28], which indicate that it may act as a transcription activating histone PTMs. By contrast, histone Kla is only been reported to implicate in inflammation and oncogenesis-related transcription programs [5,7].…”

Small Mass but Strong Information: Diagnostic Ions Provide Crucial Clues to Correctly Identify Histone Lysine Modifications

“…In a previous study exploring histone lysine crotonylation in the context of mouse spermatogenesis, we have shown that H3K27 is modified by this acylation at a similar level to acetylation in the latest stages of the differentiation process. More precisely, H3K27cr was detected in combination with either H3K36unmod or H3K36me2 [ 10 ]. In that work, we did not optimize MS analysis conditions to produce the diagnostic/immonium ions of Kcr; of note, its structure containing an unsaturation dramatically reduces possibilities of isobaric PTM combinations.…”

“…Further acylations were successively discovered including crotonylation [ 5 ], hydroxybutyrylations [ 6 , 7 ], benzoylation [ 8 ] and lactylation [ 9 ]. Of note, even though these histone PTMs remained “ignored” for decades, it appears that their relative stoichiometry to acetylation is far from negligible on certain lysine residues and in given cellular contexts [ 6 , 10 ].…”

“…The nature of the in vivo modified peptide was then determined by comparing its LC retention time and MS/MS fragmentation pattern with those of synthetic peptides bearing the tentative chemical structures of PTMs. This strategy was successfully implemented to validate all newly described acylations on a few histone tryptic peptides [ 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 ]. Next, the presence of the same mass increment on lysine residues from other histone tryptic peptides was assumed to correspond to the same PTM and led to the establishment of mappings on the sequences of histones H2A, H2B, H3 and H4, indicating that each newly discovered PTM likely modified a large number of histone lysine sites.…”

Role of SOX Protein Groups F and H in Lung Cancer Progression

“…The SOX30 protein (SRY-box containing gene 30), the only member of group H, has been characterized briefly only in a few species so far. SOX30 has been isolated from mice, humans and Nile tilapis, and it has been connected with mammalian spermatogonial differentiation and spermatogenesis [69][70][71][72]. Recently, it has been demonstrated that the SOX30 protein could be a novel epigenetic silenced tumor suppressor that acts through the direct regulation of p53 in human lung cancer [73,74].…”