Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes

Zhang, Weiyu; Chen, Fuquan; Chen, Ruiqing; Xie, Dan; Yang, Jiao; Zhao, Xin; Guo, Renpeng; Zhang, Yongwang; Shen, Yang; Göke, Jonathan; Liu, Lin; Lu, Xinyi

doi:10.1093/nar/gkz594

Cited by 69 publications

(97 citation statements)

References 85 publications

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“…S4B), highlighting the specificity of these screen hits in upregulating a ZGA-like signature. Similarly, the ZGA-associated MERVL elements (Macfarlan et al 2012), major satellite repeats (Casanova et al 2013), ERV1 (Zhang et al 2019) and SINE B2 elements (Vasseur et al 1985), but not other repeat families, were upregulated by these sgRNA hits ( Fig. 3C, S4C), consistent with these repeat families ranking top in the MOFA ZGA-like factor ( Fig.…”

Section: Identification Of Activators Of a Zga-like Transcriptional Ssupporting

confidence: 65%

“…The upregulation of ZGA genes upon MERVL LTR activation is consistent with MERVL LTRs acting as functional promoters driving the expression of hundreds of chimeric ZGA transcripts (Macfarlan et al 2012;Huang et al 2017;Franke et al 2017). Similarly, Zscan4c cDNA overexpression has recently been shown to induce the expression of ZGA genes (Eckersley-Maslin et al 2019;Zhang et al 2019). Collectively, the results from this pilot experiment not only validated 10X Genomics scRNA-seq as a suitable readout of ZGA-like expression following CRISPRa of relevant regulators, but also enabled us to estimate that approximately 400 cells per sgRNA (power 0.8, corrected p-value <0.0005, see Materials and Methods) are required to detect a ZGA-like transcriptional response upon CRISPRa of a positive hit exerting a similar effect to MERVL and Zscan4 activation.…”

Section: A Crispr-activation Screen For Zga Regulators At Single-cellsupporting

confidence: 58%

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A single-cell transcriptomics CRISPR-activation screen identifies new epigenetic regulators of zygotic genome activation

Alda-Catalinas

Bredikhin

Hernando-Herraez

et al. 2019

Preprint

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Zygotic genome activation (ZGA) is a crucial developmental milestone that remains poorly understood. This first essential transcriptional event in embryonic development coincides with extensive epigenetic reprogramming processes and is orchestrated, in part, by the interplay of transcriptional and epigenetic regulators. Here, we developed a novel high-throughput screening method that combines pooled CRISPR-activation (CRISPRa) with single-cell transcriptomics to systematically probe candidate regulators of ZGA. We screened 230 epigenetic and transcriptional regulators by upregulating their expression with CRISPRa in mouse embryonic stem cells (ESCs). Through single-cell RNAsequencing (scRNA-seq) of CRISPRa-perturbed cells, we generated approximately 200,000 single-cell transcriptomes, each transduced with a unique short-guide RNA (sgRNA) targeting a specific candidate gene promoter. Using integrative dimensionality reduction of the perturbation scRNA-seq profiles, we characterized molecular signatures of ZGA and uncovered 44 factors that promote a ZGA-like response in ESCs, both in the coding and non-coding transcriptome. Upon upregulation of these factors, including the DNA binding protein Dppa2, the chromatin remodeller Smarca5 and the transcription factor Patz1, ESCs adopt an early embryonic-like state. Supporting their roles as ZGA regulators, Dppa2 and Smarca5 knock-out ESCs lose expression of ZGA genes, however, overexpression of Dppa2 in Smarca5 knock-out ESCs, but not vice versa, rescues ZGA-like expression, suggesting that Smarca5 regulates ZGA upstream and via Dppa2. Together, our single-cell transcriptomic profiling of CRISPRaperturbed cells provides comprehensive system-level insights into the molecular mechanisms that orchestrate ZGA. Highlights• First large-scale screen combining pooled CRISPRa with scRNA-seq. • Multi-omics factor analysis identifies a ZGA-like signature for 44 of the candidate regulators. • Dppa2, Smarca5 and Patz1 were validated as strong inducers of ZGA gene expression. • Smarca5 regulates zygotic genome activation in a Dppa2-dependent manner.

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Section: Identification Of Activators Of a Zga-like Transcriptional Ssupporting

confidence: 65%

Section: A Crispr-activation Screen For Zga Regulators At Single-cellsupporting

confidence: 58%

A single-cell transcriptomics CRISPR-activation screen identifies new epigenetic regulators of zygotic genome activation

Alda-Catalinas

Bredikhin

Hernando-Herraez

et al. 2019

Preprint

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“…Strikingly, Obox6 highly expressed at the 2-cell stage, which indicates another identity of Obox6 as ZGA key factor in addition to the reprogramming efficiency enhancer (Schiebinger et al , 2019) (Fig 4I and J, Appendix Fig S3C) (data from (Liu et al , 2018; Wang et al , 2018; Xue et al , 2013)). Furthermore, we also observed Zscan4 family members were mainly activated in the 2-cell phase, which is different from that the high expression of Gm4981 before ZGA (Fig 4G) (data from (Liu et al , 2016)), indicating that the importance of Zscan4 family genes in early embryos development (Zhang et al , 2019).…”

Section: Resultscontrasting

confidence: 82%

“…The endogenous retrovirus MERVL was also defined as a 2-cell marker (Macfarlan et al , 2012; Yan et al , 2019). And Zscan4c was newly reported as important inducers of endogenous retrovirus MERVL and cleavage embryo genes (Zhang et al , 2019). However, we still know little about how TFs drives complex transcriptional regulation events of ZGA and the coordination among them.…”

Section: Introductionmentioning

confidence: 99%

Dppa2/4 promotes zygotic genome activation by binding to GC-rich region in signaling pathways

Long

Xiang

et al. 2020

Preprint

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9Developmental pluripotency associated 2 (Dppa2) and Dppa4 as positive drivers 10 were helpful for transcriptional regulation of ZGA, but it remains poorly understood 11 how these two factors regulate the zygotic transcriptional program. Here, we 12 systematically assessed the cooperative interplay between Dppa2 and Dppa4 in 13 regulating cell pluripotency of three cell types and found that simultaneous 14 overexpression of Dppa2/4 can make induced pluripotent stem cells (IPSCs) closer to 15 embryonic stem cells (ESCs). Motif occupancy analysis revealed that the repertoire of 16 Dppa2/4 targets depends upon the CG content, in which GC-rich region is the prior 17 binding signatures. Compared with other pluripotency transcription factors (TFs), 18 Dppa2 and 4 tend to bind on proximal promoter (0-500bp), especially GC-rich region 19of proximal promoter. We also found that the target regulation ability of Dppa4 is 20 superior to that of Dppa2 in ESCs, whereas the coordinately binding ability of both 21 was the most substantial. Moreover, there was more potent effect of Dppa2/4 22 regulation on signaling pathways compared with other TFs, in which 75% and 85% 23 signaling pathways were significantly activated by Dppa2 and Dppa4, respectively. 24Notably, Dppa2/4 also can dramatically trigger the decisive signaling pathways 25 associated with developmental reprogramming for facilitating ZGA, including Hippo, 26 MAPK and TGF-beta signaling pathways and so on. At last, we predicted that 27 Alkaline phosphatase, placental-like 2 (Alppl2) was directly regulated by Dppa2 and 28 Dppa4 as a new ZGA regulator. Collectively, our studies show how Dppa2/4 triggers 29 the decisive signaling pathways waves for facilitating ZGA, and Alppl2 was predicted 30 serve as a candidate driver of ZGA to regulate pre-embryonic development.31 32

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“…Zscan4 plays pivotal roles during development 39 , cell fate fidelity 16, , regulation of transcription 40,41 , telomere and genomic stability 42 and is a specific marker of 2cell like embryonic stem cells 42,43 . Also, misregulation of Zscan4 accompanies failure of progression through embryo development 15,44,45 , and imbalance of protein synthesis 40 .…”

Section: Intriguingly Comparison Between Rna-seq Data From the Cabz mentioning

confidence: 99%

The H3.3 chaperone Hira complex orchestrates oocyte developmental competence

Smith

Jiang

Šušor

et al. 2020

Preprint

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Reproductive success relies on a healthy oocyte competent for fertilisation and capable of sustaining early embryo development. By the end of oogenesis, the oocyte is characterised by a transcriptionally silenced state, but the significance of this state and how it is achieved remains poorly understood. Histone H3.3, one of the H3 variants, has unique functions in chromatin structure and gene expression that are cell cycle-independent. We report here a comprehensive characterisation of the roles of the subunits of the Hira complex (i.e. Hira, Cabin1 and Ubn1), which is primarily responsible for H3.3 deposition during mouse oocyte development. Loss-offunction of any component of the Hira complex led to early embryogenesis failure.Transcriptome and nascent RNA analyses revealed that mutant oocytes fail to silence global transcription. Hira complex mutants are unable to establish the H3K4me3 and H3K9me3 repressive marks, resulting in aberrant chromatin accessibility. Among the misregulated genes in mutant oocytes is Zscan4, a 2-cell specific gene that is involved in zygote genome activation. Overexpression of Zscan4 recapitulates the phenotypes of Hira mutants, illustrating that temporal and spatial expression of Zscan4 is fine-tuned at the oocyte-to-embryo transition. Thus, the H3.3 chaperone Hira complex has a maternal effect function in oocyte developmental competence and early embryogenesis by modulating chromatin condensation and transcriptional quiescence.

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Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes

Cited by 69 publications

References 85 publications

A single-cell transcriptomics CRISPR-activation screen identifies new epigenetic regulators of zygotic genome activation

A single-cell transcriptomics CRISPR-activation screen identifies new epigenetic regulators of zygotic genome activation

Dppa2/4 promotes zygotic genome activation by binding to GC-rich region in signaling pathways

The H3.3 chaperone Hira complex orchestrates oocyte developmental competence

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