The role of genome and gene regulatory network canalization in the evolution of multi-trait polymorphisms and sympatric speciation

T-cell development from hematopoietic progenitors depends on multiple transcription factors, mobilized and modulated by intrathymic Notch signaling. Key aspects of T-cell specification network architecture have been illuminated through recent reports defining roles of transcription factors PU.1, GATA-3, and E2A, their interactions with Notch signaling, and roles of Runx1, TCF-1, and Hes1, providing bases for a comprehensively updated model of the T-cell specification gene regulatory network presented herein. However, the role of lineage commitment factor Bcl11b has been unclear. We use self-organizing maps on 63 RNA-seq datasets from normal and perturbed T-cell development to identify functional targets of Bcl11b during commitment and relate them to other regulomes. We show that both activation and repression target genes can be bound by Bcl11b in vivo, and that Bcl11b effects overlap with E2A-dependent effects. The newly clarified role of Bcl11b distinguishes discrete components of commitment, resolving how innate lymphoid, myeloid, and dendritic, and B-cell fate alternatives are excluded by different mechanisms.

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Functional role of hub molecules in miRNA and transcription factor mediated gene regulatory network of colorectal and lung cancer

Gene Reports ◽

10.1016/j.genrep.2021.101129 ◽

2021 ◽

Vol 23 ◽

pp. 101129

Author(s):

Zishan Ahmed ◽

Chittabrata Mal

Keyword(s):

Lung Cancer ◽

Transcription Factor ◽

Gene Regulatory Network ◽

Regulatory Network ◽

Functional Role ◽

Gene Regulatory

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Architecture and dynamics of the jasmonic acid gene regulatory network

10.1101/093682 ◽

2016 ◽

Cited By ~ 1

Author(s):

Richard J. Hickman ◽

Marcel C. Van Verk ◽

Anja J.H. Van Dijken ◽

Marciel Pereira Mendes ◽

Irene A. Vos ◽

...

Keyword(s):

Transcription Factors ◽

Jasmonic Acid ◽

Gene Regulatory Network ◽

Regulatory Network ◽

Network Modules ◽

Time Series Analyses ◽

Gene Regulatory ◽

Ja Signaling ◽

Signaling Components

ABSTRACTThe phytohormone jasmonic acid (JA) is a critical regulator of plant growth and defense. To significantly advance our understanding of the architecture and dynamics of the JA gene regulatory network, we performed high-resolution RNA-Seq time series analyses of methyl JA-treated Arabidopsis thaliana. Computational analysis unraveled in detail the chronology of events that occur during the early and later phases of the JA response. Several transcription factors, including ERF16 and bHLH27, were uncovered as early components of the JA gene regulatory network with a role in pathogen and insect resistance. Moreover, analysis of subnetworks surrounding the JA-induced transcription factors ORA47, RAP2.6L, and ANAC055 provided novel insights into their regulatory role of defined JA network modules. Collectively, our work illuminates the complexity of the JA gene regulatory network, pinpoints to novel regulators, and provides a valuable resource for future studies on the function of JA signaling components in plant defense and development.

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Reiterative AP2a activity controls sequential steps in the neural crest gene regulatory network

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1010740107 ◽

2010 ◽

Vol 108 (1) ◽

pp. 155-160 ◽

Cited By ~ 113

Author(s):

Noémie de Crozé ◽

Frédérique Maczkowiak ◽

Anne H. Monsoro-Burq

Keyword(s):

Transcription Factors ◽

Neural Crest ◽

Gene Regulatory Network ◽

Regulatory Network ◽

The Other ◽

Molecular Events ◽

Gene Regulatory ◽

Progenitor Domain ◽

Multifunctional Molecules

The neural crest (NC) emerges from combinatorial inductive events occurring within its progenitor domain, the neural border (NB). Several transcription factors act early at the NB, but the initiating molecular events remain elusive. Recent data from basal vertebrates suggest that ap2 might have been critical for NC emergence; however, the role of AP2 factors at the NB remains unclear. We show here that AP2a initiates NB patterning and is sufficient to elicit a NB-like pattern in neuralized ectoderm. In contrast, the other early regulators do not participate in ap2a initiation at the NB, but cooperate to further establish a robust NB pattern. The NC regulatory network uses a multistep cascade of secreted inducers and transcription factors, first at the NB and then within the NC progenitors. Here we report that AP2a acts at two distinct steps of this cascade. As the earliest known NB specifier, AP2a mediates Wnt signals to initiate the NB and activate pax3; as a NC specifier, AP2a regulates further NC development independent of and downstream of NB patterning. Our findings reconcile conflicting observations from various vertebrate organisms. AP2a provides a paradigm for the reiterated use of multifunctional molecules, thereby facilitating emergence of the NC in vertebrates.

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