1a and Methods) whereas for ATAC-seq libraries of the nuclei, we made some modifications to the conventional ATAC-seq protocol 14 to reduce the loss of low-abundant genomic DNA. The cytoplasm containing mRNA was subjected to a modified Smart-seq2 13 protocol (Fig. LiCAT-seq physically separates cytoplasm and nuclei, enabling parallel library construction for CA and GE profiles from both cellular components. Profiling of CA and GE with low-input samples Our work thus suggests the important roles of early TFs in the remodeling of the closed chromatin during human pre-implantation embryo development. In one such example, we observe widespread DUX4 binding on MLT2A1, which flanks HERVL, a subfamily of ERV that become accessible during major EGA. In particular, we find that a large proportion of the early activated genes and endogenous retrovirus (ERV) elements possess DUX4-binding sites and become accessible as early as the 2- to 4-cell stages. We apply this technique to profiling chromatin structure and GE dynamics during human pre-implantation embryos and demonstrate the key regulatory dynamics for genes activated during embryonic genome activation (EGA). In this study, we develop LiCAT-seq (low-input chromatin accessibility (CA) and transcriptome sequencing), a technique that enables the simultaneous assay of CA and gene expression (GE) with low-input samples (Fig. However, because of the limitations on low-input technologies and the difficulties in obtaining human embryonic materials, the dynamics of higher-order chromatin structure (e.g., chromatin accessibility (CA) and histone modifications) in early human embryogenesis remain poorly understood. By using mouse models, previous studies have demonstrated multiple landscapes including the transcriptome 2, 3, methylome 4, 5, chromatin accessibility 6, 7, histone modifications 8, 9, 10, and 3-D genome contacts 11, 12 which can precisely characterize the key molecular events during mammalian embryo development. It is therefore of crucial importance to map the chromatin state of regulatory elements and the transcriptional outcomes using omics tools during this process to understand the role of major cis-regulatory elements (e.g., promoters and enhancers) or trans-factors (e.g., transcription factors (TFs) and epigenetic modifiers) that drive embryonic development. Our results thus offer mechanistic insights into the molecular events inherent to human pre-implantation development.Įarly mammalian embryos undergo widespread epigenetic reprogramming to allow the conversion of terminally committed gametes to a totipotent state 1. In particular, a large proportion of the early activated genes and ERVs are bound by DUX4 and become accessible as early as the 2- to 4-cell stages. Integrative analyses between the two datasets reveals strong association between the establishment of accessible chromatin and embryonic genome activation (EGA), and uncovers transcription factors and endogenous retrovirus (ERVs) specific to EGA. We observed global difference in chromatin accessibility between sperm and all stages of embryos, finding that the accessible regions in sperm tend to occur in gene-poor genomic regions. Here, we report on LiCAT-seq, a technique that enables simultaneous profiling of chromatin accessibility and gene expression with ultra-low input of cells, and map the chromatin accessibility and transcriptome landscapes for human pre-implantation embryos. Human pre-implantation embryonic development involves extensive changes in chromatin structure and transcriptional activity.
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