Translatome and transcriptome co-profiling reveals a role of TPRXs in human zygotic genome activation

Science, Journal Year: 2022, Volume and Issue: 378(6615)

Published: Sept. 8, 2022

Translational regulation plays a critical role during the oocyte-to-embryo transition (OET) and zygotic genome activation (ZGA). Here, we integrated ultra-low-input ribosome profiling (Ribo-lite) with messenger RNA sequencing to co-profile translatome transcriptome in human oocytes early embryos. Comparison mouse counterparts identified widespread differentially translated gene functioning epigenetic reprogramming, transposon defense, small biogenesis, part driven by species-specific regulatory elements 3' untranslated regions. Moreover, PRD-like homeobox transcription factors, including TPRXL, TPRX1, TPRX2, are highly around ZGA. TPRX1/2/L knockdown leads defective ZGA preimplantation development. Ectopically expressed TPRXs bind activate key genes embryonic stem cells. These data reveal conservation divergence of translation landscapes OET identify regulators

Language: Английский

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Simultaneous sequencing of genetic and epigenetic bases in DNA

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 41(10), P. 1457 - 1464

Published: Feb. 6, 2023

DNA comprises molecular information stored in genetic and epigenetic bases, both of which are vital to our understanding biology. Most sequencing approaches address either genetics or epigenetics thus capture incomplete information. Methods widely used detect bases fail common C-to-T mutations distinguish 5-methylcytosine from 5-hydroxymethylcytosine. We present a single base-resolution methodology that sequences complete the two most cytosine modifications workflow. is copied enzymatically converted. Coupled decoding across original copy strand provides phased digital readout. demonstrated on human genomic cell-free blood sample patient with cancer. The approach accurate, requires low input has simple workflow analysis pipeline. Simultaneous, reading more picture genomes applications throughout biomedicine.

Language: Английский

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Stage-specific H3K9me3 occupancy ensures retrotransposon silencing in human pre-implantation embryos

Cell stem cell, Journal Year: 2022, Volume and Issue: 29(7), P. 1051 - 1066.e8

Published: July 1, 2022

Language: Английский

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Cynomolgus monkey embryo model captures gastrulation and early pregnancy

Cell stem cell, Journal Year: 2023, Volume and Issue: 30(4), P. 362 - 377.e7

Published: April 1, 2023

Language: Английский

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Seven technologies to watch in 2023

Nature, Journal Year: 2023, Volume and Issue: 613(7945), P. 794 - 797

Published: Jan. 23, 2023

Language: Английский

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Chemical reprogramming for cell fate manipulation: Methods, applications, and perspectives

Cell stem cell, Journal Year: 2023, Volume and Issue: 30(9), P. 1130 - 1147

Published: Aug. 24, 2023

Language: Английский

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Epigenetic regulation of early human embryo development

Cell stem cell, Journal Year: 2023, Volume and Issue: 30(12), P. 1569 - 1584

Published: Oct. 18, 2023

Studies of mammalian development have advanced our understanding the genetic, epigenetic, and cellular processes that orchestrate embryogenesis uncovered new insights into unique aspects human embryogenesis. Recent studies now produced first epigenetic maps early embryogenesis, stimulating ideas about reprogramming, cell fate control, potential mechanisms underpinning developmental plasticity in embryos. In this review, we discuss these regulation importance for safeguarding development. We also highlight unanswered questions key challenges remain to be addressed.

Language: Английский

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Hallmarks of totipotent and pluripotent stem cell states

Cell stem cell, Journal Year: 2024, Volume and Issue: 31(3), P. 312 - 333

Published: Feb. 20, 2024

Though totipotency and pluripotency are transient during early embryogenesis, they establish the foundation for development of all mammals. Studying these in vivo has been challenging due to limited access ethical constraints, particularly humans. Recent progress led diverse culture adaptations epiblast cells vitro form totipotent pluripotent stem cells, which not only deepen our understanding embryonic but also serve as invaluable resources animal reproduction regenerative medicine. This review delves into hallmarks shedding light on their key molecular functional features.

Language: Английский

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Low-input lipidomics reveals lipid metabolism remodelling during early mammalian embryo development

Nature Cell Biology, Journal Year: 2024, Volume and Issue: 26(2), P. 278 - 293

Published: Feb. 1, 2024

Language: Английский

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A comparison of methods for detecting DNA methylation from long-read sequencing of human genomes

Genome biology, Journal Year: 2024, Volume and Issue: 25(1)

Published: March 11, 2024

Abstract Background Long-read sequencing can enable the detection of base modifications, such as CpG methylation, in single molecules DNA. The most commonly used methods for long-read are nanopore developed by Oxford Nanopore Technologies (ONT) and molecule real-time (SMRT) Pacific Bioscience (PacBio). In this study, we systematically compare performance methylation from sequencing. Results We demonstrate that 7179 nanopore-sequenced DNA samples is highly accurate consistent with 132 oxidative bisulfite-sequenced (oxBS) samples, isolated same blood draws. introduce quality filters CpGs further enhance accuracy DNA, while removing at 30% CpGs. evaluate per-site across different genomic features rates how latest R10.4 flowcell chemistry base-calling algorithms improve Additionally, show 50 SMRT-sequenced genomes compares to oxBS. Conclusions This study provides first systematic comparison tools methods. two computational a large number genomes, including sequenced using SMRT samples. provide insights into strengths limitations each method well recommendations standardization evaluation designed genome-scale modified

Language: Английский

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