Employing core regulatory circuits to define cell identity

Almeida, Nathália Alves Araújo de; Chung, Matthew Wai Heng; Drudi, Elena M; Engquist, Elise N.; Hamrud, Eva; Isaacson, Abigail; Tsang, Victoria; Watt, Fiona M.; Spagnoli, Francesca M.

doi:10.15252/embj.2020106785

Cited by 36 publications

(32 citation statements)

References 135 publications

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“…Stemness and differentiation are, ultimately, under the precise control of gene expression programs ( Takahashi and Yamanaka, 2016 ; Almeida et al, 2021 ; Islam et al, 2021 ). The initiation and maintenance of specific gene expression patterns is achieved by specific combinations of transcriptional regulators, subjected to a variety of post translational modifications controlling their activity, molecular interactions, sub cellular localization and half-life.…”

Section: Ups and The Regulation Of Satellite Cell Functionmentioning

confidence: 99%

The Gentle Side of the UPS: Ubiquitin-Proteasome System and the Regulation of the Myogenic Program

Olguín

2022

Front. Cell Dev. Biol.

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In recent years, the ubiquitin-proteasome system (UPS) has emerged as an important regulator of stem cell function. Here we review recent findings indicating that UPS also plays critical roles in the biology of satellite cells, the muscle stem cell responsible for its maintenance and regeneration. While we focus our attention on the control of key transcriptional regulators of satellite cell function, we briefly discuss early studies suggesting the UPS participates more broadly in the regulation of satellite cell stemness and regenerative capacity.

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Section: Ups and The Regulation Of Satellite Cell Functionmentioning

confidence: 99%

The Gentle Side of the UPS: Ubiquitin-Proteasome System and the Regulation of the Myogenic Program

Olguín

2022

Front. Cell Dev. Biol.

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“…On the other hand, cell identity is determined in different ways, with transcription factor (TF) networks playing an essential role. Recent developments in nucleic-acid sequencing, in general, and sc/snRNA-seq, in particular, allow to couple transcriptomic maps with cell identity, defining profiles of gene expression for each cell [110][111][112][113][114][115]. Interestingly, although pseudogenes were considered functionless, TGS has allowed to identify many transcribed pseudogenes, including protein-coding ones in normal and cancer human cells [116].…”

Section: Functional Genomicsmentioning

confidence: 99%

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

et al. 2021

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Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. The third generation is currently pushing technology to its limits, being able to sequence single molecules, without previous amplification, which was previously impossible. Besides, this represents a new revolution, allowing researchers to directly sequence RNA without previous retrotranscription. These technologies are having a significant impact on different areas, such as medicine, agronomy, ecology and biotechnology. Additionally, the study of biomolecules is revealing interesting evolutionary information. That includes deciphering what makes us human, including phenomena like non-coding RNA expansion. All this is redefining the concept of gene and transcript. Basic analyses and applications are now facilitated with new genome editing tools, such as CRISPR. All these developments, in general, and nucleic-acid sequencing, in particular, are opening a new exciting era of biomolecule analyses and applications, including personalized medicine, and diagnosis and prevention of diseases for humans and other animals.

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“…Most, if not all, cell-type decisions involve specific transcription factors (TFs) [ 1 , 2 , 4 , 5 , 13 , 14 ]. These DNA binding proteins control a gene's transcription level by binding to cis -regulatory elements (CREs) in the DNA.…”

Section: Molecular Embodiment Of a Cell Typementioning

confidence: 99%

“…These technologies can reveal cell-type-specific molecular profiles in high throughput. With single-cell RNA sequencing (scRNA-seq), the transcriptomes of individual cells can be obtained [ 1 , 4 , 5 ], which enables the identification of new cell types and cell states in complex tissues [ 36 ]. Multiple large consortia are currently generating transcriptional atlases of entire organisms (reviewed in [ 37 ]).…”

Section: Molecular Profilingmentioning

confidence: 99%

“…Here, we are only concerned with the specification of cell types, which occurs during embryonic development or regeneration of adult tissues. During development, pluripotent embryonic cells differentiate into progenitors with diminishing developmental potential, and eventually fully specified cell types [1,[3][4][5]. In adult tissue, long-lived adult stem cells give rise to multiple types of descendants.…”

Section: Introductionmentioning

confidence: 99%

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How a cell decides its own fate: a single-cell view of molecular mechanisms and dynamics of cell-type specification

Mircea

Semrau

2021

Biochemical Society Transactions

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On its path from a fertilized egg to one of the many cell types in a multicellular organism, a cell turns the blank canvas of its early embryonic state into a molecular profile fine-tuned to achieve a vital organismal function. This remarkable transformation emerges from the interplay between dynamically changing external signals, the cell's internal, variable state, and tremendously complex molecular machinery; we are only beginning to understand. Recently developed single-cell omics techniques have started to provide an unprecedented, comprehensive view of the molecular changes during cell-type specification and promise to reveal the underlying gene regulatory mechanism. The exponentially increasing amount of quantitative molecular data being created at the moment is slated to inform predictive, mathematical models. Such models can suggest novel ways to manipulate cell types experimentally, which has important biomedical applications. This review is meant to give the reader a starting point to participate in this exciting phase of molecular developmental biology. We first introduce some of the principal molecular players involved in cell-type specification and discuss the important organizing ability of biomolecular condensates, which has been discovered recently. We then review some of the most important single-cell omics methods and relevant findings they produced. We devote special attention to the dynamics of the molecular changes and discuss methods to measure them, most importantly lineage tracing. Finally, we introduce a conceptual framework that connects all molecular agents in a mathematical model and helps us make sense of the experimental data.

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Employing core regulatory circuits to define cell identity

Cited by 36 publications

References 135 publications

The Gentle Side of the UPS: Ubiquitin-Proteasome System and the Regulation of the Myogenic Program

The Gentle Side of the UPS: Ubiquitin-Proteasome System and the Regulation of the Myogenic Program

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

How a cell decides its own fate: a single-cell view of molecular mechanisms and dynamics of cell-type specification

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