Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation

PLoS Genetics, Journal Year: 2020, Volume and Issue: 16(1), P. e1008546 - e1008546

Published: Jan. 15, 2020

In many organisms, early embryonic development is driven by maternally provided factors until the controlled onset of transcription during zygotic genome activation. The regulation chromatin accessibility and its relationship to gene activity this transition remain poorly understood. Here, we generated maps with ATAC-seq from activation lineage specification. During period, increases at regulatory elements. This increase independent RNA polymerase II-mediated transcription, exception hypertranscribed miR-430 locus. Instead, often precedes associated genes. Loss maternal Pou5f3, Sox19b, Nanog, which are known be required for zebrafish activation, results in decreased Importantly, regions, especially when established Sox19b predictive future transcription. Our show that Nanog open up prime genes zebrafish.

Language: Английский

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A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program

Cell Systems, Journal Year: 2020, Volume and Issue: 11(1), P. 25 - 41.e9

Published: July 1, 2020

Zygotic genome activation (ZGA) is an essential transcriptional event in embryonic development that coincides with extensive epigenetic reprogramming. Complex manipulation techniques and maternal stores of proteins preclude large-scale functional screens for ZGA regulators within early embryos. Here, we combined pooled CRISPR (CRISPRa) single-cell transcriptomics to identify ZGA-like transcription mouse stem cells, which serve as a tractable, vitro proxy Using multi-omics factor analysis (MOFA+) applied ∼200,000 transcriptomes comprising 230 CRISPRa perturbations, characterized molecular signatures uncovered 24 factors promote response. Follow-up assays validated top screen hits, including the DNA-binding protein Dppa2, chromatin remodeler Smarca5, Patz1, experiments revealed Smarca5's regulation dependent on Dppa2. Together, our transcriptomic profiling CRISPRa-perturbed cells provides both system-level insights into mechanisms orchestrate ZGA.

Language: Английский

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Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation

Developmental Cell, Journal Year: 2023, Volume and Issue: 58(19), P. 1898 - 1916.e9

Published: Aug. 8, 2023

Chromatin accessibility is integral to the process by which transcription factors (TFs) read out cis-regulatory DNA sequences, but it difficult differentiate between TFs that drive and those do not. Deep learning models learn complex sequence rules provide an unprecedented opportunity dissect this problem. Using zygotic genome activation in Drosophila as a model, we analyzed high-resolution TF binding chromatin data with interpretable deep performed genetic validation experiments. We identify hierarchical relationship pioneer Zelda involved axis patterning. consistently pioneers proportional motif affinity, whereas patterning augment contexts where they mediate enhancer activation. conclude occurs two tiers: one through pioneering, makes enhancers accessible not necessarily active, second when correct combination of leads

Language: Английский

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The miR-430 locus with extreme promoter density forms a transcription body during the minor wave of zygotic genome activation

Developmental Cell, Journal Year: 2023, Volume and Issue: 58(2), P. 155 - 170.e8

Published: Jan. 1, 2023

In anamniote embryos, the major wave of zygotic genome activation starts during mid-blastula transition. However, some genes escape global repression, are activated substantially earlier, and contribute to minor activation. The mechanisms underlying little understood. We explored genomic organization cis-regulatory a transcription body, in which is first detected zebrafish. identified miR-430 cluster as having excessive copy number highest density Pol-II-transcribed promoters genome, this required for forming body. body not essential for, nor does it encompasse, globally. Instead, distinct minor-wave-specific promoter architecture suggests that promoter-autonomous regulate features also suggest initiation between waves

Language: Английский

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CBP and Gcn5 drive zygotic genome activation independently of their catalytic activity

Science Advances, Journal Year: 2023, Volume and Issue: 9(16)

Published: April 21, 2023

Zygotic genome activation (ZGA) is a crucial step of embryonic development. So far, little known about the role chromatin factors during this process. Here, we used an in vivo RNA interference reverse genetic screen to identify necessary for development Drosophila melanogaster . Our reveals that histone acetyltransferases (HATs) and deacetylases are ZGA regulators. We demonstrate Nejire (CBP/EP300 ortholog) essential acetylation H3 lysine-18 lysine-27, whereas Gcn5 (GCN5/PCAF lysine-9 at ZGA, with these marks being enriched all actively transcribed genes. Nonetheless, HATs activate distinct sets Unexpectedly, individual catalytic dead mutants either or can zygotic transcription transactivate reporter gene vitro. Together, our data as key regulators ZGA.

Language: Английский

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Epigenetic moonlighting: Catalytic-independent functions of histone modifiers in regulating transcription

Science Advances, Journal Year: 2023, Volume and Issue: 9(16)

Published: April 21, 2023

The past three decades have yielded a wealth of information regarding the chromatin regulatory mechanisms that control transcription. “histone code” hypothesis—which posits distinct combinations posttranslational histone modifications are “read” by downstream effector proteins to regulate gene expression—has guided research uncover fundamental relevant many aspects biology. However, recent molecular and genetic studies revealed function histone-modifying enzymes extends independently beyond their catalytic activities. In this review, we highlight original advances in understanding noncatalytic functions modifiers. Many deposited these enzymes—previously considered be required for transcriptional activation—have been demonstrated dispensable expression living organisms. This perspective aims prompt further examination enigmatic inspiring define “epigenetic moonlighting” chromatin-modifying enzymes.

Language: Английский

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SLAMseq resolves the kinetics of maternal and zygotic gene expression during early zebrafish embryogenesis

Cell Reports, Journal Year: 2023, Volume and Issue: 42(2), P. 112070 - 112070

Published: Feb. 1, 2023

The maternal-to-zygotic transition (MZT) is a key developmental process in metazoan embryos that involves the activation of zygotic transcription (ZGA) and degradation maternal transcripts. We employed metabolic mRNA sequencing (SLAMseq) to deconvolute compound embryonic transcriptome zebrafish. While mitochondrial transcripts prevail prior MZT, we uncover spurious hundreds short intron-poor genes as early 2-cell stage. Upon ZGA, most originate from thousands maternal-zygotic (MZ) are transcribed at rates comparable those purely replenish mRNAs distinct timescales. Rapid replacement MZ transcript decay features unrelated major pathways promotes de novo synthesis core gene expression machinery by increasing poly(A)-tail length translation efficiency. SLAMseq hence provides insights into timescales, molecular features, regulation MZT during zebrafish embryogenesis.

Language: Английский

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Genetic mechanisms of fertilization failure and early embryonic arrest: a comprehensive review

Human Reproduction Update, Journal Year: 2023, Volume and Issue: 30(1), P. 48 - 80

Published: Sept. 27, 2023

Abstract BACKGROUND Infertility and pregnancy loss are longstanding problems. Successful fertilization high-quality embryos prerequisites for an ongoing pregnancy. Studies have proven that every stage in the human reproductive process is regulated by multiple genes any problem, at step, may lead to failure (FF) or early embryonic arrest (EEA). Doctors can diagnose pathogenic factors involved FF EEA using genetic methods. With progress development of new technologies, such as single-cell RNA analysis whole-exome sequencing, a approach has opened up us directly study germ cells development. These findings will help identify unique mechanism(s) leads order find potential treatments. OBJECTIVE AND RATIONALE The goal this review compile current knowledge related EEA, clarifying mechanisms providing clues clinical diagnosis treatment. SEARCH METHODS PubMed was used search relevant research articles reviews, primarily focusing on English-language publications from January 1978 June 2023. terms included failure, arrest, genetic, epigenetic, DNA methylation, chromosome, non-coding RNA, other keywords. Additional studies were identified searching reference lists. This focuses conducted humans. However, it also incorporates data animal models when applicable. results presented descriptively, individual quality not assessed. OUTCOMES A total 233 final review, 3925 records initially. provides overview process. mutations systematically reviewed, example, globozoospermia, oocyte activation maternal effect gene mutations, zygotic genome abnormalities, chromosome epigenetic abnormalities. Additionally, summarizes treatments different defects, offering insights WIDER IMPLICATIONS information provided facilitate more accurate molecular screening tools diagnosing infertility markers networks guide practice identifying appropriate interventions based specific mutations. For obvious FF, ICSI recommended instead IVF. case defects phospholipase C zeta1 (PLCZ1), actin-like7A (ACTL7A), actin-like 9 (ACTL9), IQ motif-containing N (IQCN), fail fertilize. We consider artificial technology with improve rate reduce monetary time costs. In future, fertility expected be improved restored interfering supplementing genes.

Language: Английский

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Pioneer factors — key regulators of chromatin and gene expression

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 24(12), P. 809 - 815

Published: Sept. 22, 2023

Language: Английский

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Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: July 15, 2023

Abstract The first activation of gene expression during development (zygotic genome activation, ZGA) is accompanied by massive changes in chromosome organization. connection between these two processes remains unknown. Using Hi-C for zebrafish embryos, we found that folding starts establishing “fountains”, novel elements organization, emerging selectively at enhancers upon ZGA. polymer simulations, demonstrate fountains can emerge as sites targeted cohesin loading and require two-sided, yet desynchronized, loop extrusion. Specific loss pioneer transcription factors drive ZGA reveals a causal enhancer activity fountain formation. Finally, show early Medaka Xenopus embryos; moreover, cohesin-dependent pattern on mouse embryonic stem cells. Taken together, are the enhancer-specific organization; they constitute starting points development, likely serving loading.

Language: Английский

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