Combinatorial action of NF–Y and TALE at embryonic enhancers defines distinct gene expression programs during zygotic genome activation in zebrafish

Stanney, William; Ladam, Franck; Donaldson, Ian J.; Parsons, Teagan J.; Maehr, René; Bobola, Nicoletta; Sagerström, Charles G.

doi:10.1016/j.ydbio.2019.12.003

Cited by 10 publications

(6 citation statements)

References 80 publications

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“…Third, NF-Y/PREP1/PBX complexes have been dissected biochemically in vitro : an important role is played by Sp2, which binds to composite NF-Y/PBX sites, favoring stabilization of the binary complexes [ 39 ]. Fourth, the interplay is evolutionarily conserved in Zebrafish , where it promotes Zygotic Transcriptional Activation, the earliest event of gene expression in development [ 52 , 53 ]. The NF-Y/TALE interplay is a typical example of genomic studies inviting further structural characterization of complexes at the biochemical level, to gain a better comprehension of the synergistic vs opposing functional effects.…”

Section: Resultsmentioning

confidence: 99%

On the NF-Y regulome as in ENCODE (2019)

et al. 2020

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NF-Y is a trimeric Transcription Factor -TF- which binds with high selectivity to the conserved CCAAT element. Individual ChIP-seq analysis as well as ENCODE have progressively identified locations shared by other TFs. Here, we have analyzed data introduced by ENCODE over the last five years in K562, HeLa-S3 and GM12878, including several chromatin features, as well RNA-seq profiling of HeLa cells after NF-Y inactivation. We double the number of sequence-specific TFs and co-factors reported. We catalogue them in 4 classes based on co-association criteria, infer target genes categorizations, identify positional bias of binding sites and gene expression changes. Larger and novel co-associations emerge, specifically concerning subunits of repressive complexes as well as RNA-binding proteins. On the one hand, these data better define NF-Y association with single members of major classes of TFs, on the other, they suggest that it might have a wider role in the control of mRNA production.

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Section: Resultsmentioning

confidence: 99%

On the NF-Y regulome as in ENCODE (2019)

et al. 2020

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“…bHLH factors initiate neural development in bilateria and cnidaria ( Arendt et al 2016 ), perhaps by binding to these conserved E-boxes. CCAAT boxes bind to the transcription factor NF-Y, which controls many developmental genes ( Stanney et al 2020 ). One CArG box was found, conserved from human to sea anemone (though imperfect in coral), in the Nr2f promoter ( Fig.…”

Section: Resultsmentioning

confidence: 99%

DNA Conserved in Diverse Animals Since the Precambrian Controls Genes for Embryonic Development

Frith,

2023

Molecular Biology and Evolution

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DNA that controls gene expression (e.g. enhancers, promoters) has seemed almost never to be conserved between distantly related animals, like vertebrates and arthropods. This is mysterious, because development of such animals is partly organized by homologous genes with similar complex expression patterns, termed “deep homology.” Here, we report 25 regulatory DNA segments conserved across bilaterian animals, of which 7 are also conserved in cnidaria (coral and sea anemone). They control developmental genes (e.g. Nr2f, Ptch, Rfx1/3, Sall, Smad6, Sp5, Tbx2/3), including six homeobox genes: Gsx, Hmx, Meis, Msx, Six1/2, and Zfhx3/4. The segments contain perfectly or near-perfectly conserved CCAAT boxes, E-boxes, and other sequences recognized by regulatory proteins. More such DNA conservation will surely be found soon, as more genomes are published and sequence comparison is optimized. This reveals a control system for animal development conserved since the Precambrian.

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“…Furthermore, NFYA contributes to activating a subset of genes in the major wave of EGA and is important for progression to the blastocyst stage [24]. Moreover, a previous study stated that NFYA regulates the expression of transcriptional regulatory genes during the embryonic genome activation in zebrafish embryos [30]. Previous studies have shown that SP1, GSC, DUXA, ARGFX, and DPRX were involved in mammalian EGA [31][32][33][34].…”

Section: Discussionmentioning

confidence: 97%

PDGFRβ Activation Induced the Bovine Embryonic Genome Activation via Enhanced NFYA Nuclear Localization

Perera,

Idrees,

Khan

et al. 2023

IJMS

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Embryonic genome activation (EGA) is a critical step during embryonic development. Several transcription factors have been identified that play major roles in initiating EGA; however, this gradual and complex mechanism still needs to be explored. In this study, we investigated the role of nuclear transcription factor Y subunit A (NFYA) in bovine EGA and bovine embryonic development and its relationship with the platelet-derived growth factor receptor-β (PDGFRβ) by using a potent selective activator (PDGF-BB) and inhibitor (CP-673451) of PDGF receptors. Activation and inhibition of PDGFRβ using PDGF-BB and CP-673451 revealed that NFYA expression is significantly (p < 0.05) affected by the PDGFRβ. In addition, PDGFRβ mRNA expression was significantly increased (p < 0.05) in the activator group and significantly decreased (p < 0.05) in the inhibitor group when compared with PDGFRα. Downregulation of NFYA following PDGFRβ inhibition was associated with the expression of critical EGA-related genes, bovine embryo development rate, and implantation potential. Moreover, ROS and mitochondrial apoptosis levels and expression of pluripotency-related markers necessary for inner cell mass development were also significantly (p < 0.05) affected by the downregulation of NFYA while interrupting trophoblast cell (CDX2) differentiation. In conclusion, the PDGFRβ-NFYA axis is critical for bovine embryonic genome activation and embryonic development.

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Combinatorial action of NF–Y and TALE at embryonic enhancers defines distinct gene expression programs during zygotic genome activation in zebrafish

Cited by 10 publications

References 80 publications

On the NF-Y regulome as in ENCODE (2019)

On the NF-Y regulome as in ENCODE (2019)

DNA Conserved in Diverse Animals Since the Precambrian Controls Genes for Embryonic Development

PDGFRβ Activation Induced the Bovine Embryonic Genome Activation via Enhanced NFYA Nuclear Localization

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