The Plant-Specific Dof Transcription Factors Family: New Players Involved in Vascular System Development and Functioning in Arabidopsis

We review the molecular basis of several transcription factors (Eya1, Sox2), including the three related genes coding basic helix–loop–helix (bHLH; see abbreviations) proteins (Neurog1, Neurod1, Atoh1) during the development of spiral ganglia, cochlear nuclei, and cochlear hair cells. Neuronal development requires Neurog1, followed by its downstream target Neurod1, to cross-regulate Atoh1 expression. In contrast, hair cells and cochlear nuclei critically depend on Atoh1 and require Neurod1 expression for interactions with Atoh1. Upregulation of Atoh1 following Neurod1 loss changes some vestibular neurons’ fate into “hair cells”, highlighting the significant interplay between the bHLH genes. Further work showed that replacing Atoh1 by Neurog1 rescues some hair cells from complete absence observed in Atoh1 null mutants, suggesting that bHLH genes can partially replace one another. The inhibition of Atoh1 by Neurod1 is essential for proper neuronal cell fate, and in the absence of Neurod1, Atoh1 is upregulated, resulting in the formation of “intraganglionic” HCs. Additional genes, such as Eya1/Six1, Sox2, Pax2, Gata3, Fgfr2b, Foxg1, and Lmx1a/b, play a role in the auditory system. Finally, both Lmx1a and Lmx1b genes are essential for the cochlear organ of Corti, spiral ganglion neuron, and cochlear nuclei formation. We integrate the mammalian auditory system development to provide comprehensive insights beyond the limited perception driven by singular investigations of cochlear neurons, cochlear hair cells, and cochlear nuclei. A detailed analysis of gene expression is needed to understand better how upstream regulators facilitate gene interactions and mammalian auditory system development.

Download Full-text

Gene Trap, Gene Knockout, Gene Knock-In, and Transgenics in Vascular Development

Thrombosis and Haemostasis ◽

10.1055/s-0037-1615924 ◽

1999 ◽

Vol 82 (08) ◽

pp. 865-869 ◽

Cited By ~ 4

Author(s):

Thomas Sato

Keyword(s):

Animal Models ◽

Molecular Mechanisms ◽

Vascular System ◽

System Development ◽

Gene Knockout ◽

Vascular Development ◽

Branching Morphogenesis ◽

Abnormal Development ◽

Organ Systems ◽

Almost All

IntroductionThe vascular system is one of the first organ systems to develop in our bodies. Normal development and maturation of the physiological functions of almost all of the other organs are critically dependent on the accurate and tightly controlled establishment of the vascular system. Our understanding of the mechanisms underlying the formation of the vascular system during development is still in its infancy. With further understanding of these mechanisms, we may eventually be able to correct the abnormal development and the malfunctioning of many organs by therapeutically modulating the morphology and/or physiological function of the vascular system.Our further understanding of the vascular development can, in part, be achieved by discovering the molecules that play critical roles in this process. We could also achieve this goal by learning more about the functions of previously identified molecules in the vascular system. Discovery of new processes underlying the development of the vascular system will also contribute to further understanding of these molecular mechanisms.Recent advances, using the whole genome approach, have resulted in a flood of new information. This trend will continue, and fortunately, a number of molecular reagents will become available. Therefore, the field will likely experience an exponential growth in terms of novel biological insights and discovering the mechanisms of vascular system development.Occasionally, reductionistic approaches help to systematically address a number of biological problems, including the problems associated with vascular system development. One such approach is to choose an organism that allows us to systematically address these biological questions. The choice of animal models that are well-suited for the study of a particular question has led to a large number of discoveries. To address questions in vascular system development, current research has focused on animal models, including fish, frog, bird, and mouse, and also studies involving humans. It is also worthwhile to note that the branching morphogenesis of the fly trachea system has been utilized to address fundamental questions of vascular morphogenesis.This chapter will summarize the genomic manipulation of the murine vascular system to address questions regarding vascular development. In addition, the advances that have been made in this field using such methods will be summarized.

Download Full-text

Genome-wide identification of Dof transcription factors possibly associated with internal browning of postharvest pineapple fruits

Scientia Horticulturae ◽

10.1016/j.scienta.2019.03.007 ◽

2019 ◽

Vol 251 ◽

pp. 80-87 ◽

Cited By ~ 1

Author(s):

Keqian Hong ◽

Jiewen Xian ◽

Zhiwei Jia ◽

Xiaowan Hou ◽

Lubin Zhang

Keyword(s):

Transcription Factors ◽

Genome Wide ◽

Internal Browning ◽

Dof Transcription Factors

Download Full-text

Phylogenetic comparative and expression analysis of genes encoding dof transcription factors from Eucalyptus grandis

BMC Proceedings ◽

10.1186/1753-6561-5-s7-p159 ◽

2011 ◽

Vol 5 (S7) ◽

Author(s):

Gabriel d'Almeida ◽

Michèle Breton ◽

Sandro Camargo ◽

Jeverson Frazzon ◽

Giancarlo Pasquali

Keyword(s):

Transcription Factors ◽

Expression Analysis ◽

Eucalyptus Grandis ◽

Genes Encoding ◽

Dof Transcription Factors

Download Full-text

Regulation and function of homeodomain proteins in the embryonic and adult vascular systemsThis paper is one of a selection of papers published in this Special Issue, entitled Young Investigators' Forum.

Canadian Journal of Physiology and Pharmacology ◽

10.1139/y06-091 ◽

2007 ◽

Vol 85 (1) ◽

pp. 55-65 ◽

Cited By ~ 15

Author(s):

Josette M. Douville ◽

Jeffrey T. Wigle

Keyword(s):

Transcription Factors ◽

Target Genes ◽

Vascular System ◽

Homeobox Genes ◽

Tube Formation ◽

Binding Motif ◽

Homeodomain Proteins ◽

Downstream Target ◽

Endothelial Tube Formation ◽

And Function

During embryonic development, the cardiovascular system first forms and then gives rise to the lymphatic vascular system. Homeobox genes are essential for both the development of the blood and lymphatic vascular systems, as well as for their maintenance in the adult. These genes all encode proteins that are transcription factors that contain a well conserved DNA binding motif, the homeodomain. It is through the homeodomain that these transcription factors bind to the promoters of target genes and regulate their expression. Although many homeodomain proteins have been found to be expressed within the vascular systems, little is known about their downstream target genes. This review highlights recent advances made in the identification of novel genes downstream of the homeodomain proteins that are necessary for regulating vascular cellular processes such as proliferation, migration, and endothelial tube formation. Factors known to regulate the functions of vascular cells via modulating the expression of homeobox genes will be discussed. We will also review current methods used to identify and characterize downstream target genes of homeodomain proteins.

Download Full-text

From Blood Islands to Blood Vessels: Morphologic Observations and Expression of Key Molecules during Hyaloid Vascular System Development

Investigative Opthalmology & Visual Science ◽

10.1167/iovs.12-10140 ◽

2012 ◽

Vol 53 (13) ◽

pp. 7912 ◽

Cited By ~ 20

Author(s):

D. Scott McLeod ◽

Takuya Hasegawa ◽

Takayuki Baba ◽

Rhonda Grebe ◽

Ines Galtier d'Auriac ◽

...

Keyword(s):

Blood Vessels ◽

Vascular System ◽

System Development

Download Full-text

Decoding molecular markers and transcriptional circuitry of naive and primed states of human pluripotency

10.1101/2020.04.17.046037 ◽

2020 ◽

Author(s):

Arindam Ghosh ◽

Anup Som

Keyword(s):

Transcription Factors ◽

Molecular Mechanisms ◽

System Development ◽

Enrichment Analysis ◽

Pathway Enrichment Analysis ◽

List Type ◽

Metabolic Processes ◽

Primed State

ABSTRACTPluripotent stem cells (PSCs) have been observed to occur in two distinct states — naive and primed. Both naive and primed state PSCs can give rise to tissues of all the three germ layers in vitro but differ in their potential to generate germline chimera in vivo. Understanding the molecular mechanisms that govern these two states of pluripotency in human can open up a plethora of opportunities for studying early embryonic development and in biomedical applications. In this work, we use weighted gene co-expression network (WGCN) approach to identify the key molecular makers and their interactions that define the two distinct pluripotency states. Signed-hybrid WGCN was reconstructed from transcriptomic data (RNA-seq) of naive and primed state pluripotent samples. Our analysis revealed two sets of genes that are involved in establishment and maintenance of naive (4791 genes) and primed (5066 genes) states. The naive state genes were found to be enriched for biological processes and pathways related to metabolic processes while primed state genes were associated with system development. Further, we identified the top 10% genes by intra-modular connectivity as hubs and the hub transcription factors for each group, thus providing a three-tier list of genes associated with naive and primed states of pluripotency in human.HIGHLIGHTSWeighted gene co-expression network analysis (WGCNA) identified 4791 and 5066 genes to be involved in naive and primed states of human pluripotency respectively.Functional and pathway enrichment analysis revealed the naive genes were mostly related to metabolic processes and primed genes to system development.The top 10% genes based on intra-modular connectivity from each group were defined as hubs.Identified 52 and 33 transcription factors among the naive and primed module hubs respectively.The transcription factors might play a switch on-off mechanism in induction of the two pluripotent states.

Download Full-text