The dynamic landscape of enhancer-derived RNA during mouse early embryo development

RNA multi-omics in single cells reveal rhythmical RNA reshaping during human and mouse oocyte maturation

BACKGROUND

Omics technologies are widely applied in assisted reproductive technology (ART), such as embryo selection, investigation of infertility causes, and mechanisms underlying reproductive cell development. While RNAomics has shown great potential in investigating the physiology and pathology in female reproductive system, its applications are still not fully developed. More studies on epitranscriptomic regulation mechanisms and novel sequencing methods are needed to advance the field.

RESULTS

Here, we developed a method named Cap to Tail sequencing application (C2T-APP) and simultaneously characterized the m7G cap, poly(A) tail structure, and gene expression level for the intact RNA molecules in single cells. C2T-APP distinguished the N6, 2'-O-dimethyladenosine modification (m6Am) from N6-methyladenosine (m6A) modification with our published single-cell m6A sequencing (scm6A-seq) data. During oocyte maturation, we found a positive correlation of m7G and m6Am with translation efficiency and finely dissected the step-wised maternal RNA de-capping and de-tailing of different types of genes. Strikingly, we uncovered a subtle structural mechanism regulating poly(A) tails in oocytes: maternal RNA translation is temporarily suppressed by removing the poly(A) tails without complete degradation, while the poly(A)-tail regulators themselves depend strictly on translation initiated after meiotic resumption. Furthermore, we profiled single-cell RNA-multi-omic features of human oocytes with different qualities during in vitro culture maturation (IVM). Defects of epi-transcriptome features, including m6A, m6Am, m7G, and poly(A) structure of maternal RNA in the oocytes with poor quality, were detected.

CONCLUSIONS

Our results provided a valuable tool for RNAomics research and data resources provided novel insights into human oocyte maturation, which is helpful for IVM and oocyte selection for ART.

Epigenome dynamics in early mammalian embryogenesis

During early embryonic development in mammals, the totipotency of the zygote - which is reprogrammed from the differentiated gametes - transitions to pluripotency by the blastocyst stage, coincident with the first cell fate decision. These changes in cellular potency are accompanied by large-scale alterations in the nucleus, including major transcriptional, epigenetic and architectural remodelling, and the establishment of the DNA replication programme. Advances in low-input genomics and loss-of-function methodologies tailored to the pre-implantation embryo now enable these processes to be studied at an unprecedented level of molecular detail in vivo. Such studies have provided new insights into the genome-wide landscape of epigenetic reprogramming and chromatin dynamics during this fundamental period of pre-implantation development.

Enhancer RNA in cancer: identification, expression, resources, relationship with immunity, drugs, and prognosis

Enhancer RNA (eRNA), a type of non-coding RNA transcribed from enhancer regions, serves as a class of critical regulatory elements in gene expression. In cancer biology, eRNAs exhibit profound roles in tumorigenesis, metastasis, and therapeutic response modulation. In this review, we outline eRNA identification methods utilizing enhancer region prediction, histone H3 lysine 4 monomethyl chromatin signatures, and nucleosome positioning analysis. We quantitate eRNA expression through RNA-seq, single-cell transcriptomics, and epigenomic integration approaches. Functionally, eRNAs regulate gene expression, protein function modulation, and chromatin modification. Key databases detailing eRNA annotations and interactions are highlighted. Furthermore, we analyze the connection of eRNA with immune cells and its potential in immunotherapy. Emerging evidence demonstrates eRNA's critical involvement in immune cell crosstalk and tumor microenvironment reprogramming. Notably, eRNA signatures show promise as predictive biomarkers for immunotherapy response and chemoresistance monitoring in multiple malignancies. This review underscores eRNA's transformative potential in precision oncology, advocating for integrated multiomics approaches to fully realize their clinical applicability.