Human embryonic genome activation initiates at the one-cell stage

Cell stem cell, Journal Year: 2021, Volume and Issue: 29(2), P. 209 - 216.e4

Published: Dec. 21, 2021

In human embryos, the initiation of transcription (embryonic genome activation [EGA]) occurs by eight-cell stage, but its exact timing and profile are unclear. To address this, we profiled gene expression at depth in metaphase II oocytes bipronuclear (2PN) one-cell embryos. High-resolution single-cell RNA sequencing revealed previously inaccessible oocyte-to-embryo changes. This confirmed transcript depletion following fertilization (maternal degradation) also uncovered low-magnitude upregulation hundreds spliced transcripts. Gene analysis predicted embryonic processes including cell-cycle progression chromosome maintenance as well transcriptional activators that included cancer-associated regulators. Transcription was disrupted abnormal monopronuclear (1PN) tripronuclear (3PN) These findings indicate initiates sooner than thought. The pattern promises to illuminate involved onset development, with implications for epigenetic inheritance, stem-cell-derived cancer.

Language: Английский

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What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome?

Molecular & Cellular Proteomics, Journal Year: 2023, Volume and Issue: 22(9), P. 100631 - 100631

Published: Aug. 11, 2023

Ribosome profiling (Ribo-Seq) has proven transformative for our understanding of the human genome and proteome by illuminating thousands noncanonical sites ribosome translation outside currently annotated coding sequences (CDSs). A conservative estimate suggests that at least 7000 ORFs are translated, which, first glance, potential to expand number protein CDSs 30%, from ∼19,500 over 26,000 CDSs. Yet, additional scrutiny these raised numerous questions about what fraction them truly produce a product those can be understood as proteins according conventional term. Adding further complication is fact published estimates vary widely around 30-fold, several thousand hundred thousand. The summation this research left genomics proteomics communities both excited prospect new regions in but searching guidance on how proceed. Here, we discuss current state ORF research, databases, interpretation, focusing assess whether given said "protein coding."

Language: Английский

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The role of noncoding RNAs in Parkinson’s disease: biomarkers and associations with pathogenic pathways

Journal of Biomedical Science, Journal Year: 2021, Volume and Issue: 28(1)

Published: Nov. 18, 2021

Abstract The discovery of various noncoding RNAs (ncRNAs) and their biological implications is a growing area in cell biology. Increasing evidence has revealed canonical noncanonical functions long small ncRNAs, including microRNAs, ncRNAs (lncRNAs), circular RNAs, PIWI-interacting tRNA-derived fragments. These have the ability to regulate gene expression modify metabolic pathways. Thus, they may important roles as diagnostic biomarkers or therapeutic targets diseases, neurodegenerative disorders, especially Parkinson’s disease. Recently, through diverse sequencing technologies wide variety bioinformatic analytical tools, such reverse transcriptase quantitative PCR, microarrays, next-generation long-read sequencing, numerous been shown be associated with In this review article, we will first introduce biogenesis different pros cons detection platforms reproducibility tools discussed second part. Finally, recent PD-associated association diagnosis pathophysiology PD are reviewed, microRNAs that transported by exosomes biofluids particularly emphasized.

Language: Английский

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Uncovering the impacts of alternative splicing on the proteome with current omics techniques

Wiley Interdisciplinary Reviews - RNA, Journal Year: 2022, Volume and Issue: 13(4)

Published: Jan. 3, 2022

The high-throughput sequencing of cellular RNAs has underscored a broad effect isoform diversification through alternative splicing on the transcriptome. Moreover, differential production transcript isoforms from gene loci been recognized as critical mechanism in cell differentiation, organismal development, and disease. Yet, extent impact protein function remains matter debate. Multiple experimental computational approaches have developed recent years to address this question. These studies unveiled how molecular changes at different steps RNA processing pathway can lead differences functional effects. New emerging technologies open exciting new opportunities develop methods fully establish connection between messenger expression further investigate variation impacts proteome function. This article is categorized under: Processing > Splicing Regulation/Alternative Translation Regulation Evolution Genomics Computational Analyses RNA.

Language: Английский

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Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells

Genome biology, Journal Year: 2021, Volume and Issue: 22(1)

Published: Aug. 13, 2021

Nonsense-mediated mRNA decay (NMD) is a eukaryotic, translation-dependent degradation pathway that targets mRNAs with premature termination codons and also regulates the expression of some encode full-length proteins. Although many genes express NMD-sensitive transcripts, identifying them based on short-read sequencing data remains challenge.

Language: Английский

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mRNA Vaccines: Why Is the Biology of Retroposition Ignored?

Genes, Journal Year: 2022, Volume and Issue: 13(5), P. 719 - 719

Published: April 20, 2022

The major advantage of mRNA vaccines over more conventional approaches is their potential for rapid development and large-scale deployment in pandemic situations. In the current COVID-19 crisis, two have been conditionally approved broadly applied, while others are still clinical trials. However, there no previous experience with use on a large scale general population. This warrants careful evaluation vaccine safety properties by considering all available knowledge about molecular biology evolution. Here, I discuss pervasive claim that mRNA-based cannot alter genomes. Surprisingly, this notion widely stated literature but never supported referencing any primary scientific papers would specifically address question. discrepancy becomes even puzzling if one considers work evolutionary aspects retroposition murine human populations clearly documents frequent integration molecules into genomes, including contexts. By performing basic comparisons, show sequence features meet known requirements using L1 elements-the most abundant autonomously active retrotransposons genome. fact, many factors associated increase possibility L1-mediated retroposition. conclude unfounded to priori assume therapeutics do not impact genomes route genome mRNAs via endogenous retroelements easily conceivable. implies we urgently need experimental studies rigorously test mRNAs. At present, insertional mutagenesis should be considered unresolved.

Language: Английский

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Sperm RNA Payload: Implications for Intergenerational Epigenetic Inheritance

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(6), P. 5889 - 5889

Published: March 20, 2023

There is mounting evidence that ancestral life experiences and environment can influence phenotypes in descendants. The parental regulates offspring potentially via modulating epigenetic marks the gametes. Here, we review examples of across-generational inheritance paternal environmental effects current understanding role small RNAs such inheritance. We discuss recent advances revealing RNA payload sperm how conditions modulate RNAs. Further, potential mechanism by focusing on RNA-mediated regulation early embryonic gene expression its influencing phenotypes.

Language: Английский

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Differential protein repertoires related to sperm function identified in extracellular vesicles (EVs) in seminal plasma of distinct fertility buffalo (Bubalus bubalis) bulls

Frontiers in Cell and Developmental Biology, Journal Year: 2024, Volume and Issue: 12

Published: July 29, 2024

Buffalo bulls are backbone of Indian dairy industry, and the quality semen donating determine overall production efficiency farms. Seminal plasma harbor millions lipid bilayer nanovesicles known as extracellular vesicles (EVs). These EVs carry a heterogenous cargo essential biomolecules including fertility-associated proteins which contribute to fertilizing potential spermatozoa. In this study, we explored size, concentration, complete proteome profiles SP from two distinct fertility groups uncover influencing bull fertility. Through Dynamic Light Scattering (DLS) it was found that purified were present in 7-14 size exclusion chromatographic (SEC) fractions with sizes ranging 146.5 258.7 nm high fertile (HF) low (LF) bulls. Nanoparticle Tracking Analysis (NTA) confirmed seminal up 200 nm, concentrations varying 2.84 6.82 × 10

Language: Английский

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Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns

Genome Research, Journal Year: 2022, Volume and Issue: 32(4), P. 726 - 737

Published: March 17, 2022

Long-read transcriptomics require understanding error sources inherent to technologies. Current approaches cannot compare methods for an individual RNA molecule. Here, we present a novel platform-comparison method that combines barcoding strategies and long-read sequencing sequence cDNA copies representing molecule on both Pacific Biosciences (PacBio) Oxford Nanopore Technologies (ONT). We these pairs in terms of content isoform patterns. Although read show high similarity, find differences (1) aligned length, (2) transcription start site (TSS), (3) polyadenylation (poly(A)-site) assignment, (4) exon–intron structures. Overall, 25% disagree either TSS, poly(A)-site, or splice site. Intron-chain disagreement typically arises from alignment errors microexons complicated sites. Our single-molecule technology comparison reveals inconsistencies are often caused by error–induced inaccurate ONT alignments, especially downstream GUNNGU donor motifs. However, annotation-disagreeing upstream shifts NAGNAG acceptors confirmed PacBio thus likely real. In barcoded nonbarcoded reads, intron number proximity GU/AGs better predict with the annotation than quality alone. summarize findings annotation-based algorithm spliced correction improves subsequent transcript construction reads.

Language: Английский

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A program of successive gene expression in mouse one-cell embryos

Cell Reports, Journal Year: 2023, Volume and Issue: 42(2), P. 112023 - 112023

Published: Feb. 1, 2023

At the moment of union in fertilization, sperm and oocyte are transcriptionally silent. The ensuing onset embryonic transcription (embryonic genome activation [EGA]) is critical for development, yet its timing profile remain elusive any vertebrate species. We here dissect during EGA by high-resolution single-cell RNA sequencing precisely synchronized mouse one-cell embryos. This reveals a program gene expression (immediate [iEGA]) initiating within 4 h fertilization. Expression iEGA produces canonically spliced transcripts, occurs substantially from maternal genome, mostly downregulated at two-cell stage. Transcribed genes predict regulation factors (TFs) associated with cancer, including c-Myc. Blocking c-Myc or other predicted regulatory TF activities disrupts induces acute developmental arrest. These findings illuminate intracellular mechanisms that regulate mammalian development hold promise study cancer.

Language: Английский

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