Transcriptional Control of Lung Morphogenesis

2007 ◽  
Vol 87 (1) ◽  
pp. 219-244 ◽  
Author(s):  
Yutaka Maeda ◽  
Vrushank Davé ◽  
Jeffrey A. Whitsett
Keyword(s):  
Transcription Factors ◽  
Transcriptional Control ◽  
Family Members ◽  
Cell Types ◽  
Branching Morphogenesis ◽  
Early Embryo ◽  
Normal Lung ◽  
Thyroid Transcription Factor 1 ◽  
Lung Morphogenesis ◽  
And Function

The vertebrate lung consists of multiple cell types that are derived primarily from endodermal and mesodermal compartments of the early embryo. The process of pulmonary organogenesis requires the generation of precise signaling centers that are linked to transcriptional programs that, in turn, regulate cell numbers, differentiation, and behavior, as branching morphogenesis and alveolarization proceed. This review summarizes knowledge regarding the expression and proposed roles of transcription factors influencing lung formation and function with particular focus on knowledge derived from the study of the mouse. A group of transcription factors active in the endodermally derived cells of the developing lung tubules, including thyroid transcription factor-1 (TTF-1), β-catenin, Forkhead orthologs (FOX), GATA, SOX, and ETS family members are required for normal lung morphogenesis and function. In contrast, a group of distinct proteins, including FOXF1, POD1, GLI, and HOX family members, play important roles in the developing lung mesenchyme, from which pulmonary vessels and bronchial smooth muscle develop. Lung formation is dependent on reciprocal signaling among cells of both endodermal and mesenchymal compartments that instruct transcriptional processes mediating lung formation and adaptation to breathing after birth.

scholarly journals Building and Regenerating the Lung Cell by Cell

2019 ◽  
Vol 99 (1) ◽  
pp. 513-554 ◽  
Author(s):  
Jeffrey A. Whitsett ◽  
Tanya V. Kalin ◽  
Yan Xu ◽  
Vladimir V. Kalinichenko
Keyword(s):  
Molecular Mechanisms ◽  
Cell Types ◽  
Early Embryo ◽  
Sequencing Data ◽  
Chronic Lung Diseases ◽  
Lung Morphogenesis ◽  
Pulmonary Cells ◽  
Mammalian Lung ◽  
Resolution Imaging ◽  
And Function

The unique architecture of the mammalian lung is required for adaptation to air breathing at birth and thereafter. Understanding the cellular and molecular mechanisms controlling its morphogenesis provides the framework for understanding the pathogenesis of acute and chronic lung diseases. Recent single-cell RNA sequencing data and high-resolution imaging identify the remarkable heterogeneity of pulmonary cell types and provides cell selective gene expression underlying lung development. We will address fundamental issues related to the diversity of pulmonary cells, to the formation and function of the mammalian lung, and will review recent advances regarding the cellular and molecular pathways involved in lung organogenesis. What cells form the lung in the early embryo? How are cell proliferation, migration, and differentiation regulated during lung morphogenesis? How do cells interact during lung formation and repair? How do signaling and transcriptional programs determine cell-cell interactions necessary for lung morphogenesis and function?

scholarly journals Emerging concepts in smooth muscle contributions to airway structure and function: implications for health and disease

2016 ◽  
Vol 311 (6) ◽  
pp. L1113-L1140 ◽  
Author(s):  
Y. S. Prakash
Keyword(s):  
Smooth Muscle ◽  
Cell Types ◽  
Structure And Function ◽  
Normal Lung ◽  
Future Research ◽  
Chronic Obstructive ◽  
Obstructive Pulmonary Disease ◽  
Health And Disease ◽  
Growth And Aging ◽  
And Function

Airway structure and function are key aspects of normal lung development, growth, and aging, as well as of lung responses to the environment and the pathophysiology of important diseases such as asthma, chronic obstructive pulmonary disease, and fibrosis. In this regard, the contributions of airway smooth muscle (ASM) are both functional, in the context of airway contractility and relaxation, as well as synthetic, involving production and modulation of extracellular components, modulation of the local immune environment, cellular contribution to airway structure, and, finally, interactions with other airway cell types such as epithelium, fibroblasts, and nerves. These ASM contributions are now found to be critical in airway hyperresponsiveness and remodeling that occur in lung diseases. This review emphasizes established and recent discoveries that underline the central role of ASM and sets the stage for future research toward understanding how ASM plays a central role by being both upstream and downstream in the many interactive processes that determine airway structure and function in health and disease.

scholarly journals Bi-fated tendon-to-bone attachment cells are regulated by shared enhancers and KLF transcription factors

2020 ◽  
Author(s):  
Shiri Kult ◽  
Tsviya Olender ◽  
Marco Osterwalder ◽  
Sharon Krief ◽  
Ronnie Blecher-Gonen ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Cell Fate ◽  
Single Molecule ◽  
Cell Types ◽  
Underlying Mechanism ◽  
Regulatory Elements ◽  
Transcriptional Enhancer ◽  
Molecular Identity ◽  
And Function

AbstractThe connection between different tissues is vital for the development and function of any organs and systems. In the musculoskeletal system, the attachment of elastic tendons to stiff bones poses a mechanical challenge that is solved by the formation of a transitional tissue, which allows the transfer of muscle forces to the skeleton without tearing. Here, we show that tendon-to-bone attachment cells are bi-fated, activating a mixture of chondrocyte and tenocyte transcriptomes, which is regulated by sharing regulatory elements with these cells and by Krüppel-like factors transcription factors (KLF).To uncover the molecular identity of attachment cells, we first applied high-throughput RNA sequencing to murine humeral attachment cells. The results, which were validated by in situ hybridization and single-molecule in situ hybridization, reveal that attachment cells express hundreds of chondrogenic and tenogenic genes. In search for the underlying mechanism allowing these cells to express these genes, we performed ATAC sequencing and found that attachment cells share a significant fraction of accessible intergenic chromatin areas with either tenocytes or chondrocytes. Epigenomic analysis further revealed transcriptional enhancer signatures for the majority of these regions. We then examined a subset of these regions using transgenic mouse enhancer reporter. Results verified the shared activity of some of these enhancers, supporting the possibility that the transcriptome of attachment cells is regulated by enhancers with shared activities in tenocytes or chondrocytes. Finally, integrative chromatin and motif analyses, as well as the transcriptome data, indicated that KLFs are regulators of attachment cells. Indeed, blocking the expression of Klf2 and Klf4 in the developing limb mesenchyme led to abnormal differentiation of attachment cells, establishing these factors as key regulators of the fate of these cells.In summary, our findings show how the molecular identity of bi-fated attachment cells enables the formation of the unique transitional tissue that connect tendon to bone. More broadly, we show how mixing the transcriptomes of two cell types through shared enhancers and a dedicated set of transcription factors can lead to the formation of a new cell fate that connects them.

scholarly journals Interplay of RFX transcription factors 1, 2 and 3 in motile ciliogenesis

2020 ◽  
Vol 48 (16) ◽  
pp. 9019-9036
Author(s):  
Sylvain Lemeille ◽  
Marie Paschaki ◽  
Dominique Baas ◽  
Laurette Morlé ◽  
Jean-Luc Duteyrat ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Transcriptional Control ◽  
Ex Vivo ◽  
Ependymal Cells ◽  
Clear Understanding ◽  
Animal Development ◽  
C Elegans ◽  
And Function ◽  
Redundant Functions

Abstract Cilia assembly is under strict transcriptional control during animal development. In vertebrates, a hierarchy of transcription factors (TFs) are involved in controlling the specification, differentiation and function of multiciliated epithelia. RFX TFs play key functions in the control of ciliogenesis in animals. Whereas only one RFX factor regulates ciliogenesis in C. elegans, several distinct RFX factors have been implicated in this process in vertebrates. However, a clear understanding of the specific and redundant functions of different RFX factors in ciliated cells remains lacking. Using RNA-seq and ChIP-seq approaches we identified genes regulated directly and indirectly by RFX1, RFX2 and RFX3 in mouse ependymal cells. We show that these three TFs have both redundant and specific functions in ependymal cells. Whereas RFX1, RFX2 and RFX3 occupy many shared genomic loci, only RFX2 and RFX3 play a prominent and redundant function in the control of motile ciliogenesis in mice. Our results provide a valuable list of candidate ciliary genes. They also reveal stunning differences between compensatory processes operating in vivo and ex vivo.

Long and small noncoding RNAs during oocyte-to-embryo transition in mammals

2017 ◽  
Vol 45 (5) ◽  
pp. 1117-1124 ◽  
Author(s):  
Petr Svoboda
Keyword(s):  
Noncoding Rna ◽  
Transcriptional Control ◽  
Noncoding Rnas ◽  
Rna Degradation ◽  
Early Embryo ◽  
Protein Coding ◽  
Small Noncoding Rnas ◽  
Major Genome ◽  
Silencing Pathways ◽  
And Function

Oocyte-to-embryo transition is a process during which an oocyte ovulates, is fertilized, and becomes a developing embryo. It involves the first major genome reprogramming event in life of an organism where gene expression, which gave rise to a differentiated oocyte, is remodeled in order to establish totipotency in blastomeres of an early embryo. This remodeling involves replacement of maternal RNAs with zygotic RNAs through maternal RNA degradation and zygotic genome activation. This review is focused on expression and function of long noncoding RNAs (lncRNAs) and small RNAs during oocyte-to-embryo transition in mammals. LncRNAs are an assorted rapidly evolving collection of RNAs, which have no apparent protein-coding capacity. Their biogenesis is similar to mRNAs including transcriptional control and post-transcriptional processing. Diverse molecular and biological roles were assigned to lncRNAs although most of them probably did not acquire a detectable biological role. Since some lncRNAs serve as precursors for small noncoding regulatory RNAs in RNA silencing pathways, both types of noncoding RNA are reviewed together.

scholarly journals Identification and functional characterization of circular RNAs in pericytes

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
S Glaser ◽  
A.W Heumueller ◽  
M Klangwart ◽  
A Wiederer ◽  
D John ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Transcription Factors ◽  
Cell Biology ◽  
Functional Characterization ◽  
Cell Types ◽  
Circular Rna ◽  
Circular Rnas ◽  
Funding Source ◽  
Factor Screening ◽  
And Function

Abstract Background Circular RNAs (circRNAs) are generated by back-splicing. They are known to be robustly expressed in a variety of mammalian cell types and organism and have been reported to influence cell biology by acting e.g. as microRNA sponges or regulating host gene expression. Recently, our group reported functionally relevant circRNA expression in endothelial cells. Despite their important role in the cardiovascular system, the expression and function of circRNAs in pericytes is not well studied. Pericytes are perivascular mural cells, important for vessel maturation and endothelial barrier function. Their recruitment towards endothelial cells is mainly meditated by platelet-derived growth factor (PDGF) signaling. However, a more precise understanding of the regulation of pericyte differentiation and survival is necessary. Objective Here, we analyse circRNA expression in pericytes and demonstrate biological relevance of the hypoxia regulated circular RNA PLOD2 (cPLOD2). Methods and results Using RNA Sequencing in ribosomal depleted RNA we characterized the expression of circRNAs in human pericytes under normoxic and hypoxic (1% O2, 48h) conditions. We identified several circular RNAs being regulated upon hypoxia. The identified circular RNAs demonstrated resistance towards RNase-R digestion and lacking of poly-adenylation. Some of them were found to be localized and in the cytosol, whereas others also occur in the nucleus of the cells. Especially cPLOD2 raised our attention since it is significantly upregulated and robustly expressed upon hypoxia. Silencing cPLOD2 by siRNA resulted in significant de-differentiation of pericytes that went along with a loss of cell viability. Mechanistically, transcription factor screening assays revealed that silencing of cPLOD2 enhances the activity of the transcription factors ELK1/SRF, which have been documented to result in de-differentiation of smooth muscle cells. Conclusion Here we characterize the expression pattern of circRNAs in human primary pericytes. Among others, cPLOD2 significantly regulates pericyte function. Our results indicate hypoxia as a major regulator of circRNA expression in pericytes and show that circRNAs are capable of regulating pericyte function by modulating activity of transcription factors. Funding Acknowledgement Type of funding source: Foundation. Main funding source(s): Deutsche Forschungsgesellschaft (DFG) - SFB834; Deutsche Gesellschaft für Herz-Kreislaufforschung (DZHK)

scholarly journals Retrotransposons as Drivers of Mammalian Brain Evolution

Life ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 376
Author(s):  
Roberto Ferrari ◽  
Nicole Grandi ◽  
Enzo Tramontano ◽  
Giorgio Dieci
Keyword(s):  
Cognitive Abilities ◽  
Large Scale ◽  
Transcriptional Control ◽  
Large Body ◽  
Three Dimensional ◽  
Brain Evolution ◽  
Cell Types ◽  
Brain Morphology ◽  
Mammalian Brain ◽  
And Function

Retrotransposons, a large and diverse class of transposable elements that are still active in humans, represent a remarkable force of genomic innovation underlying mammalian evolution. Among the features distinguishing mammals from all other vertebrates, the presence of a neocortex with a peculiar neuronal organization, composition and connectivity is perhaps the one that, by affecting the cognitive abilities of mammals, contributed mostly to their evolutionary success. Among mammals, hominids and especially humans display an extraordinarily expanded cortical volume, an enrichment of the repertoire of neural cell types and more elaborate patterns of neuronal connectivity. Retrotransposon-derived sequences have recently been implicated in multiple layers of gene regulation in the brain, from transcriptional and post-transcriptional control to both local and large-scale three-dimensional chromatin organization. Accordingly, an increasing variety of neurodevelopmental and neurodegenerative conditions are being recognized to be associated with retrotransposon dysregulation. We review here a large body of recent studies lending support to the idea that retrotransposon-dependent evolutionary novelties were crucial for the emergence of mammalian, primate and human peculiarities of brain morphology and function.

scholarly journals Pluripotency and differentiation of embryonic stem cells

2020 ◽  
Vol 185 ◽  
pp. 04034
Author(s):  
Yinyin Liu ◽  
Haibo Zhao ◽  
Liang Liang ◽  
Peilei Fan ◽  
Yujia Zhao ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Regenerative Medicine ◽  
Inner Cell Mass ◽  
Es Cells ◽  
Cell Mass ◽  
Embryonic Stem ◽  
Early Embryo ◽  
Self Renewal ◽  
Extracellular Signals ◽  
And Function

Mouse embryonic stem (ES) cells derive from the inner cell mass of an early embryo called blastocyst, making them promising resource for regenerative medicine. They possess two unique properties: self-renewal and pluripotency. Different ways can be used to assess which extracellular signal and factor inside ES cells has an impact on the pluripotency of ES cells. Nowadays, many extracellular signals and transcription factors have been identified, such as extracellular signals like LIF and transcription factors like Oct4. Studying the mechanism and function of these factors offers great insight and advance our understanding of pluripotency and self-renewal and thus shed light on regenerative medicine.

scholarly journals E3 ubiquitin ligase RFWD2 controls lung branching through protein-level regulation of ETV transcription factors

2016 ◽  
Vol 113 (27) ◽  
pp. 7557-7562 ◽  
Author(s):  
Yan Zhang ◽  
Shigetoshi Yokoyama ◽  
John C. Herriges ◽  
Zhen Zhang ◽  
Randee E. Young ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Ubiquitin Ligase ◽  
Protein Level ◽  
E3 Ubiquitin Ligase ◽  
Transcript Level ◽  
Branching Morphogenesis ◽  
Normal Lung ◽  
Lung Epithelium ◽  
E3 Ligases ◽  
Lung Branching

The mammalian lung is an elaborate branching organ, and it forms following a highly stereotypical morphogenesis program. It is well established that precise control at the transcript level is a key genetic underpinning of lung branching. In comparison, little is known about how regulation at the protein level may play a role. Ring finger and WD domain 2 (RFWD2, also termed COP1) is an E3 ubiquitin ligase that modifies specific target proteins, priming their degradation via the ubiquitin proteasome system. RFWD2 is known to function in the adult in pathogenic processes such as tumorigenesis. Here, we show that prenatal inactivation of Rfwd2 gene in the lung epithelium led to a striking halt in branching morphogenesis shortly after secondary branch formation. This defect is accompanied by distalization of the lung epithelium while growth and cellular differentiation still occurred. In the mutant lung, two E26 transformation-specific (ETS) transcription factors essential for normal lung branching, ETS translocation variant 4 (ETV4) and ETV5, were up-regulated at the protein level, but not at the transcript level. Introduction of Etv loss-of-function alleles into the Rfwd2 mutant background attenuated the branching phenotype, suggesting that RFWD2 functions, at least in part, through degrading ETV proteins. Because a number of E3 ligases are known to target factors important for lung development, our findings provide a preview of protein-level regulatory network essential for lung branching morphogenesis.

scholarly journals The Enigmatic HOX Genes: Can We Crack Their Code?

Cancers ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 323 ◽  
Author(s):  
Zhifei Luo ◽  
Suhn Rhie ◽  
Peggy Farnham
Keyword(s):  
Transcription Factors ◽  
Embryonic Development ◽  
Molecular Mechanisms ◽  
Hox Genes ◽  
Homeobox Genes ◽  
Large Family ◽  
Cell Types ◽  
Interacting Protein ◽  
Developmental Problems ◽  
And Function

Homeobox genes (HOX) are a large family of transcription factors that direct the formation of many body structures during early embryonic development. There are 39 genes in the subgroup of homeobox genes that constitute the human HOX gene family. Correct embryonic development of flies and vertebrates is, in part, mediated by the unique and highly regulated expression pattern of the HOX genes. Disruptions in these fine-tuned regulatory mechanisms can lead to developmental problems and to human diseases such as cancer. Unfortunately, the molecular mechanisms of action of the HOX family of transcription factors are severely under-studied, likely due to idiosyncratic details of their structure, expression, and function. We suggest that a concerted and collaborative effort to identify interacting protein partners, produce genome-wide binding profiles, and develop HOX network inhibitors in a variety of human cell types will lead to a deeper understanding of human development and disease. Within, we review the technological challenges and possible approaches needed to achieve this goal.

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