Myod1 and GR coordinate myofiber-specific transcriptional enhancers

Rovito, Daniela; Rerra, Anna-Isavella; Ueberschlag-Pitiot, Vanessa; Joshi, Shilpy; Karasu, Nezih; Dacleu-Siewe, Vanessa; Rayana, Khalil Ben; Ghaibour, Kamar; Parisotto, Maxime; Ferry, Arnaud; Jelinsky, Scott A.; Laverny, Gilles; Klaholz, Bruno P.; Sexton, Tom; Billas, I. M. L.; Duteil, Delphine; Metzger, Daniel

doi:10.1093/nar/gkab226

Cited by 23 publications

(23 citation statements)

References 78 publications

(62 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Encouraged by these findings, we next compared our hPTM profiles with public ChIP-seq datasets [ 5 , 34 , 35 , 39 – 41 ]. We included public datasets (matching our tissues) from hPTMs commonly used to identify enhancers, i.e., H3K4me1 and H3K27ac (active enhancers only [ 42 ]).…”

Section: Resultsmentioning

confidence: 99%

“…Mouse gastrocnemius peaks were obtained from Rovito et al . [ 35 ]. mESC peaks were obtained from Perino et al [ 40 ] and ENCODE [ 34 ].…”

Section: Methodsmentioning

confidence: 99%

“…mESC enhancers were obtained from the SCREEN project from ENCODE, using pELS and dELS regions from the E14-specific cCRE-set [ 34 ]. Mouse muscle (gastrocnemius) enhancers were obtained from Rovito et al [ 35 ]. Mouse macrophage enhancers were obtained from Denisenko et al [ 37 ].…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

H3K18 lactylation marks tissue-specific active enhancers

et al. 2022

View full text Add to dashboard Cite

Background Histone lactylation has been recently described as a novel histone post-translational modification linking cellular metabolism to epigenetic regulation. Results Given the expected relevance of this modification and current limited knowledge of its function, we generate genome-wide datasets of H3K18la distribution in various in vitro and in vivo samples, including mouse embryonic stem cells, macrophages, adipocytes, and mouse and human skeletal muscle. We compare them to profiles of well-established histone modifications and gene expression patterns. Supervised and unsupervised bioinformatics analysis shows that global H3K18la distribution resembles H3K27ac, although we also find notable differences. H3K18la marks active CpG island-containing promoters of highly expressed genes across most tissues assessed, including many housekeeping genes, and positively correlates with H3K27ac and H3K4me3 as well as with gene expression. In addition, H3K18la is enriched at active enhancers that lie in proximity to genes that are functionally important for the respective tissue. Conclusions Overall, our data suggests that H3K18la is not only a marker for active promoters, but also a mark of tissue specific active enhancers.

show abstract

Section: Resultsmentioning

confidence: 99%

“…Mouse gastrocnemius peaks were obtained from Rovito et al . [ 35 ]. mESC peaks were obtained from Perino et al [ 40 ] and ENCODE [ 34 ].…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

H3K18 lactylation marks tissue-specific active enhancers

et al. 2022

View full text Add to dashboard Cite

show abstract

“…3j). Myod1, which plays a role in myogenesis, was enriched in muscle cell clusters of the brain 16 (Supplementary Fig. 3k).…”

mentioning

confidence: 99%

Simultaneous profiling of spatial gene expression and chromatin accessibility for mouse brain development

Peng

Jiang

Zhou

et al. 2022

Preprint

View full text Add to dashboard Cite

Brain are complex biological tissues which function relies on coordinated anatomical and molecular structure comprised by a large number of specialized cells. The spatial architecture of brain which is key to the understanding of its physiological and pathological significance is formed during embryo development. However, the molecular basis for discrete neuroanatomical domains particularly in the context of spatial organization of the brain is inadequate. Here, we introduced Spatial-ATAC-RNA-seq by crisscross indexing (SPARC-seq), a method for parallel profiling of gene expression and chromatin accessibility with spatial information retained in developing mouse brain. Our study has established a direct means to spatially determine the coordination between chromatin accessibility and transcriptome, identified the chromatin potential to define cell fate determination of brain structure, and uncovered spatiotemporal regulatory principles during mammalian brain development.

show abstract

“…Myod1 is important for muscle cell differentiation (Huang et al, 2016). It is a key player in muscle-specific enhancer-promoter communication, coordinating the regulation of muscle fiber size (Rovito et al, 2021). Muscle enhancers are regulated via coordinated binding of TFs, including c-Jun, Jdp2, Meis, and Runx1.…”

Section: Transcription Factors Involved In Differentiationmentioning

confidence: 99%

Changes of Gene Expression Patterns of Muscle Pathophysiology-Related Transcription Factors During Denervated Muscle Atrophy

Yang

et al. 2022

Front. Physiol.

View full text Add to dashboard Cite

Peripheral nerve injury is common, and can lead to skeletal muscle atrophy and dysfunction. However, the underlying molecular mechanisms are not fully understood. The transcription factors have been proved to play a key role in denervated muscle atrophy. In order to systematically analyze transcription factors and obtain more comprehensive information of the molecular regulatory mechanisms in denervated muscle atrophy, a new transcriptome survey focused on transcription factors are warranted. In the current study, we used microarray to identify and analyze differentially expressed genes encoding transcription factors in denervated muscle atrophy in a rat model of sciatic nerve dissection. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were used to explore the biological functions of differentially expressed transcription factors and their target genes related to skeletal muscle pathophysiology. We found that the differentially expressed transcription factors were mainly involved in the immune response. Based on correlation analysis and the expression trends of transcription factors, 18 differentially expressed transcription factors were identified. Stat3, Myod1, Runx1, Atf3, Junb, Runx2, Myf6, Stat5a, Tead4, Klf5, Myog, Mef2a, and Hes6 were upregulated. Ppargc1a, Nr4a1, Lhx2, Ppara, and Rxrg were downregulated. Functional network mapping revealed that these transcription factors are mainly involved in inflammation, development, aging, proteolysis, differentiation, regeneration, autophagy, oxidative stress, atrophy, and ubiquitination. These findings may help understand the regulatory mechanisms of denervated muscle atrophy and provide potential targets for future therapeutic interventions for muscle atrophy following peripheral nerve injury.

show abstract

Myod1 and GR coordinate myofiber-specific transcriptional enhancers

Cited by 23 publications

References 78 publications

H3K18 lactylation marks tissue-specific active enhancers

H3K18 lactylation marks tissue-specific active enhancers

Simultaneous profiling of spatial gene expression and chromatin accessibility for mouse brain development

Changes of Gene Expression Patterns of Muscle Pathophysiology-Related Transcription Factors During Denervated Muscle Atrophy

Contact Info

Product

Resources

About