Echs1-mediated histone crotonylation facilitates zygotic genome activation and expression of repetitive elements in early mammalian embryos

Introduction

The transition from fertilization to early embryonic development is a highly intricate process, tightly regulated across multiple stages in mammals. A critical event in preimplantation development is zygotic genome activation (ZGA), which initiates at the 2-cell stage in mice and the 4-to-8-cell stage in humans, marking the onset of autonomous gene expression¹. In mice, the previously inactive zygotic genome undergoes two distinct transcriptional waves after fertilization: minor ZGA at the early 2-cell stage and major ZGA at the late 2-cell stage². Histone modifications are pivotal in regulating ZGA by influencing chromatin opening, transcriptional activity, and early developmental programs^{3, 4–5}. Disruptions to these modifications impair transcription, resulting in abnormal embryonic development^6,7.

During the ZGA period in cleavage-stage embryos, histone modifications are tightly coordinated with specific developmental stages and genomic regions, ensuring precise transcription required for normal development. For example, as ZGA occurs, levels of H3K4me3 and H3K27ac increase significantly, promoting the activation of embryonic genes and initiating the transcriptional program^8,9. In contrast, modifications such as H3K9me3 and H3K27me3 are linked to gene repression and heterochromatin formation, maintaining the silencing of specific genomic regions. Among these regulatory mechanisms^10,11, histone methylation and acetylation have been extensively studied and are well-characterized during the cleavage stages of embryonic development, providing insight into the transcriptional regulatory networks involved.

Histone lysine crotonylation (Kcr) is a conserved histone modification that plays a critical role in transcriptional regulation¹². Crotonyl-CoA, the primary substrate for histone Kcr, is produced through multiple metabolic pathways¹³. The conversion of crotonate into crotonyl-CoA is catalyzed by Acyl-CoA synthetase short-chain family member 2 (ACSS2)¹⁴. Additionally, the short-chain enoyl–coenzyme A (CoA) hydratase encoded by ECHS1 regulates histone Kcr levels^15,16. ECHS1 has been implicated in promoting endoderm differentiation of embryonic stem cells, maintaining cardiomyocyte maturation and homeostasis, and constraining tumor progression^{13,15, 16–17}. Furthermore, Chromodomain Y-like protein (CDYL) functions as a crotonyl-CoA hydratase, reducing crotonyl-CoA availability and thereby negatively regulating histone Kcr¹⁸. Recent studies have identified enzymes responsible for both the addition and the removal of histone Kcr^{19, 20–21}. For example, P300-mediated histone Kcr enhances gene transcription more effectively than P300-mediated histone lysine acetylation (Kac)¹⁴....