Transcription Factor-Directed Re-wiring of Chromatin Architecture for Somatic Cell Nuclear Reprogramming toward trans-Differentiation

Dall’Agnese, Alessandra; Caputo, Luca; Nicoletti, Chiara; Iulio, Julia di; Schmitt, Anthony; Gatto, Sole; Diao, Yarui; Ye, Zhen; Forcato, Mattia; Perera, Ranjan J.; Bicciato, Silvio; Telenti, Amalio; Ren, Bing; Puri, Pier Lorenzo

doi:10.1016/j.molcel.2019.07.036

Cited by 71 publications

(63 citation statements)

References 124 publications

(169 reference statements)

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“…was detected at CTCF-binding sites and H3K27ac regions in both myoblasts and myotubes (Dall' Agnese et al, 2019). Importantly, upon MyoD expression in fibroblasts, inhibition of the original transcriptional program was observed, similar to what is seen in fibroblast reprogramming to induced-pluripotent stem cells (iPSCs) by over-expression of OCT4, SOX2, and NANOG (Ciglar et al, 2014;Chronis et al, 2017).…”

Section: Myod and The Three-dimensional Organization Of Chromatinmentioning

confidence: 55%

“…On the contrary, upon MyoD expression in fibroblasts, increasing levels of the muscle specific genes ITGA7 and RDH5 were detected as well as binding of CTCF and MyoD at ITGA7 and RDH5 promoters. These observations showed that steady expression of MyoD is required for the maintenance of the three-dimensional chromatin landscape in order achieve myogenic commitment and differentiation (Dall' Agnese et al, 2019).…”

Section: Myod and The Three-dimensional Organization Of Chromatinmentioning

confidence: 86%

“…Insulated neighborhoods also constrain gene regulation within their boundaries, by harboring interactions between cis-regulatory elements, such as promoter-enhancer communication (Sun et al, 2019). Since higher genomic structures such as TADs appear to be generally conserved, the fact that chromatin interactions within insulated neighborhoods could rather be cell-type-specific and dynamic (Dixon et al, 2015;Javierre et al, 2016;Bonev et al, 2017;Phanstiel et al, 2017;Siersbaek et al, 2017) is then relevant to note that MyoD is able to reconfigure insulated neighborhoods as nearly as 90% of its interaction sites with CTCF result higher at insulated neighborhoods boundaries (Dall' Agnese et al, 2019).…”

Section: Myod and The Three-dimensional Organization Of Chromatinmentioning

confidence: 99%

“…As MyoD is able to reconfigure chromatin in order to activate myogenic gene expression, it is also capable to repress inhibitors of muscle differentiation (Dall' Agnese et al, 2019). For example, TGF-β is a negative regulator of muscle differentiation (Liu et al, 2001;Hernández-Hernández et al, 2009) and is active in fibroblast.…”

Section: Myod and The Three-dimensional Organization Of Chromatinmentioning

confidence: 99%

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Chromatin Landscape During Skeletal Muscle Differentiation

Hernández-Hernández

Ávila-Avilés

2020

Front. Genet.

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Cellular commitment and differentiation involve highly coordinated mechanisms by which tissue-specific genes are activated while others are repressed. These mechanisms rely on the activity of specific transcription factors, chromatin remodeling enzymes, and higherorder chromatin organization in order to modulate transcriptional regulation on multiple cellular contexts. Tissue-specific transcription factors are key mediators of cell fate specification with the ability to reprogram cell types into different lineages. A classic example of a master transcription factor is the muscle specific factor MyoD, which belongs to the family of myogenic regulatory factors (MRFs). MRFs regulate cell fate determination and terminal differentiation of the myogenic precursors in a multistep process that eventually culminate with formation of muscle fibers. This developmental progression involves the activation and proliferation of muscle stem cells, commitment, and cell cycle exit and fusion of mononucleated myoblast to generate myotubes and myofibers. Although the epigenetics of muscle regeneration has been extensively addressed and discussed over the recent years, the influence of higher-order chromatin organization in skeletal muscle regeneration is still a field of development. In this review, we will focus on the epigenetic mechanisms modulating muscle gene expression and on the incipient work that addresses three-dimensional genome architecture and its influence in cell fate determination and differentiation to achieve skeletal myogenesis. We will visit known alterations of genome organization mediated by chromosomal fusions giving rise to novel regulatory landscapes, enhancing oncogenic activation in muscle, such as alveolar rhabdomyosarcomas (ARMS).

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Section: Myod and The Three-dimensional Organization Of Chromatinmentioning

confidence: 55%

Section: Myod and The Three-dimensional Organization Of Chromatinmentioning

confidence: 86%

Section: Myod and The Three-dimensional Organization Of Chromatinmentioning

confidence: 99%

Section: Myod and The Three-dimensional Organization Of Chromatinmentioning

confidence: 99%

See 2 more Smart Citations

Chromatin Landscape During Skeletal Muscle Differentiation

Hernández-Hernández

Ávila-Avilés

2020

Front. Genet.

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“…However, the molecular mechanisms underlying dynamic changes in 3D genome structure are largely unknown. Although the biological function of MyoD in regulating muscle cell differentiation has been well documented, and very recently, MyoD's transcription activity was found to be regulated by its ability to mediate chromatin interactions during trans-differentiation 41 Table 4). The genes associated with those MyoD-induced loops significantly up-regulated during differentiation and down-regulated when MyoD was absent, indicating the regulatory role of MyoD-induced loops (Fig.…”

Section: The Regulatory Loops Specified By Myod Are Functionally Requmentioning

confidence: 99%

MyoD is a structure organizer of 3D genome architecture in muscle cells

Chen

Wang

et al. 2020

Preprint

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The genome is not a linear molecule of DNA randomly folded in the nucleus, but exists as an organized, three-dimensional (3D) dynamic architecture. Intriguingly, it is now clear that each cell type has a unique and characteristic 3D genome organization that functions in determining cell identity during development. A currently challenging basic question is how cell-type specific 3D genome structures are established during development. Herein, we analyzed 3D genome structures in primary myoblasts and myocytes from MyoD knockout (MKO) and WT mice and discovered that MyoD, a pioneer transcription factor (TF), can function as a “genome organizer” that specifies the proper 3D genome architecture unique to muscle cell development. Importantly, we genetically demonstrate that H3K27ac are insufficient for establishing MyoD-induced chromatin loops in muscle cells. The establishment of MyoD’s “architectural role” should have profound impacts on advancing understanding of other pioneer transcription factors in orchestrating lineage specific 3D genome organization during development in a potentially very large number of cell types in diverse organisms.

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Methods for the Differential Analysis of Hi-C Data

Nicoletti

2021

Methods in Molecular Biology

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Transcription Factor-Directed Re-wiring of Chromatin Architecture for Somatic Cell Nuclear Reprogramming toward trans-Differentiation

Cited by 71 publications

References 124 publications

Chromatin Landscape During Skeletal Muscle Differentiation

Chromatin Landscape During Skeletal Muscle Differentiation

MyoD is a structure organizer of 3D genome architecture in muscle cells

Methods for the Differential Analysis of Hi-C Data

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