Genome-wide in Silico Identification of New Conserved and Functional Retinoic Acid Receptor Response Elements (Direct Repeats Separated by 5 bp)

Lalevée, Sébastien; Anno, Yannick N.; Chatagnon, Amandine; Samarut, Éric; Poch, Olivier; Laudet, Vincent; Galand, Benoît; Lecompte, Odile; Rochette‐Egly, Cécile

doi:10.1074/jbc.m111.263681

Cited by 87 publications

(89 citation statements)

References 60 publications

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“…A detailed list of differentially expressed genes as a sequel to ATRA treatment has been previously reported in HeLa cells (41). Upon ZMYND8 silencing, we found an overlap of at least 90 up-and 83 downregulated candidates that are ATRA-inducible (Fig.…”

Section: Zmynd8 Regulates Global Gene Transcription In Chd4-independentmentioning

confidence: 62%

Selective Recognition of H3.1K36 Dimethylation/H4K16 Acetylation Facilitates the Regulation of All-trans-retinoic Acid (ATRA)-responsive Genes by Putative Chromatin Reader ZMYND8

Adhikary

Sanyal

Basu

et al. 2016

Journal of Biological Chemistry

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ZMYND8 (zinc finger MYND (Myeloid, Nervy and DEAF-1)-type containing 8), a newly identified component of the transcriptional coregulator network, was found to interact with the Nucleosome Remodeling and Deacetylase (NuRD) complex. Previous reports have shown that ZMYND8 is instrumental in recruiting the NuRD complex to damaged chromatin for repressing transcription and promoting double strand break repair by homologous recombination. However, the mode of transcription regulation by ZMYND8 has remained elusive. Here, we report that through its specific key residues present in its conserved chromatin-binding modules, ZMYND8 interacts with the selective epigenetic marks H3.1K36Me2/H4K16Ac. Furthermore, ZMYND8 shows a clear preference for canonical histone H3.1 over variant H3.3. Interestingly, ZMYND8 was found to be recruited to several developmental genes, including the all-trans-retinoic acid (ATRA)-responsive ones, through its modified histone-binding ability. Being itself inducible by ATRA, this zinc finger transcription factor is involved in modulating other ATRA-inducible genes. We found that ZMYND8 interacts with transcription initiation-competent RNA polymerase II phosphorylated at Ser-5 in a DNA templatedependent manner and can alter the global gene transcription. Overall, our study identifies that ZMYND8 has CHD4-independent functions in regulating gene expression through its modified histone-binding ability.ZMYND8 (zinc finger MYND (Myeloid, Nervy and DEAF-1)-type containing 8) is a putative chromatin reader/effector harboring a PWWP domain, a bromodomain, and a PHD type zinc finger. It associates with the CHD4 protein of NuRD chromatin remodeling complex implicated in gene transcription, cell cycle progression, and genome integrity (1, 2). Reader proteins specifically recognize histone post-translational modifications (PTMs) 5 and translate such recognition(s) into meaningful biological outcomes by virtue of either their intrinsic activities or those of their interacting partners (3). These readers may interpret histone PTMs via "monovalent" or "multivalent" recognition (4). In monovalent recognition, a chromatin reader recognizes one histone PTM. In contrast, in multivalent recognition, readers recognize multiple histone modifications intra/inter-nucleosomally. An accessible surface is provided by these readers (such as a cavity or surface groove), which accommodates the modified histone residues, and determines the modification (e.g. acetylation versus methylation) or state specificity (such as mono-versus trimethylation of lysine) (3).ZMYND8 is a well known component of the transcription coregulator complex and is associated with several demethylase machinery components, including KDM5A, KDM5C, or LSD1 (5, 6). Through its ability to interact with Xenopus RCoR2, ZMYND8 plays a significant role in embryonic neural differentiation (7). Apart from this, ZMYND8 is also involved in T-cell lymphoma and breast and cervical cancer (8 -10). Another interesting feature is that ZMYND8 is significantly involved...

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Section: Zmynd8 Regulates Global Gene Transcription In Chd4-independentmentioning

confidence: 62%

Selective Recognition of H3.1K36 Dimethylation/H4K16 Acetylation Facilitates the Regulation of All-trans-retinoic Acid (ATRA)-responsive Genes by Putative Chromatin Reader ZMYND8

Adhikary

Sanyal

Basu

et al. 2016

Journal of Biological Chemistry

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“…Each isoform from retinoic acid receptors and retinoid X receptors binds to the retinoic acid response elements in the promoter regions of target genes as a heterodimer and works as a transcriptional factor. All-trans retinoic acid regulates Igf-1 mRNA expression in rat osteoblasts (30), and a genomewide in silico study presented potential candidates for the retinoic acid response elements in the promoter region of murine Igf-1 (31). We are attempting to assess how b-carotene has beneficial effects on Igf-1 expression in skeletal muscle.…”

Section: Discussionmentioning

confidence: 99%

β-Carotene Increases Muscle Mass and Hypertrophy in the Soleus Muscle in Mice

Kitakaze

Harada

Imagita

et al. 2015

Journal of Nutritional Science and Vitaminology, J Nutr Sci Vit

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Summary Supplements and naturally occurring nutraceuticals effective for maintenance or enhancement of skeletal muscle mass are expected to contribute to prevention of decreased mobility and increased risk of developing metabolic diseases. However, information about available food components remains widely unavailable. In the present study, we investigated the effects of dietary b-carotene on the quantity and quality of skeletal muscle under physiological conditions. Male ddY mice (8 wk old) were orally administered b-carotene (0.5 mg once daily) for 14 d. Dietary b-carotene had no influence on body weight, but increased the soleus muscle/body weight ratio. The cross-sectional area (CSA) in muscle fibers of the soleus muscle was increased, indicating that administration of b-carotene induces muscle hypertrophy. In the soleus muscle of the b-carotene-administered mice, twitch force tended to be increased (p50.06) and tetanic force was significantly increased, whereas specific force (force per CSA) remained unchanged. Dietary b-carotene increased the mRNA level of insulin-like growth factor 1 (Igf-1) as its splicing variant Igf-1ea, but had no influence on the liver Igf-1 mRNA level or serum IGF-1 level. b-Carotene promoted protein synthesis in the soleus muscle and reduced levels of ubiquitin conjugates, but had no influence on the mRNA levels of two atrogenes, Atrogin-1 and Murf1. On the other hand, b-carotene had no influence on the processing of the autophagy marker protein light chain 3. These results indicate that in mice, administration of b-carotene increases mass and induces functional hypertrophy in the soleus muscle, perhaps by promoting IGF-1-mediated protein synthesis and by reducing ubiquitin-mediated protein degradation.

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“…22,42 These results are consistent with an in silico study showing that the Hic1 gene contains multiple RA receptor response elements. 43 However, HIC1 is dispensable for RA-mediated expression of intestinal homing molecules and RA-dependent suppression of IL-17A production in vitro, suggesting that the RA-HIC1 axis has a specific role in regulating intestinal T-cell homeostasis that remains to be defined.…”

Section: Hic1 Is Required To Limit Stat3 Signaling In T H 17 Cellsmentioning

confidence: 99%

The transcriptional repressor HIC1 regulates intestinal immune homeostasis

et al. 2017

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Genome-wide in Silico Identification of New Conserved and Functional Retinoic Acid Receptor Response Elements (Direct Repeats Separated by 5 bp)

Cited by 87 publications

References 60 publications

Selective Recognition of H3.1K36 Dimethylation/H4K16 Acetylation Facilitates the Regulation of All-trans-retinoic Acid (ATRA)-responsive Genes by Putative Chromatin Reader ZMYND8

Selective Recognition of H3.1K36 Dimethylation/H4K16 Acetylation Facilitates the Regulation of All-trans-retinoic Acid (ATRA)-responsive Genes by Putative Chromatin Reader ZMYND8

β-Carotene Increases Muscle Mass and Hypertrophy in the Soleus Muscle in Mice

The transcriptional repressor HIC1 regulates intestinal immune homeostasis

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Genome-wide in Silico Identification of New Conserved and Functional Retinoic Acid Receptor Response Elements (Direct Repeats Separated by 5 bp)

Cited by 87 publications

References 60 publications

Selective Recognition of H3.1K36 Dimethylation/H4K16 Acetylation Facilitates the Regulation of All-trans-retinoic Acid (ATRA)-responsive Genes by Putative Chromatin Reader ZMYND8

Selective Recognition of H3.1K36 Dimethylation/H4K16 Acetylation Facilitates the Regulation of All-trans-retinoic Acid (ATRA)-responsive Genes by Putative Chromatin Reader ZMYND8

&beta;-Carotene Increases Muscle Mass and Hypertrophy in the Soleus Muscle in Mice

The transcriptional repressor HIC1 regulates intestinal immune homeostasis

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β-Carotene Increases Muscle Mass and Hypertrophy in the Soleus Muscle in Mice