scholarly journals Gene Expression Correlation Analysis Reveals MYC-NAC Regulatory Network in Cotton Pigment Gland Development

2021 ◽  
Vol 22 (9) ◽  
pp. 5007
Author(s):  
Hailiang Cheng ◽  
Xiaoxu Feng ◽  
Dongyun Zuo ◽  
Youping Zhang ◽  
Qiaolian Wang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Correlation Analysis ◽  
Regulatory Network ◽  
Pigment Gland ◽  
Interaction Network ◽  
Nac Transcription Factors ◽  
Expression Correlation ◽  
Dna Binding Sites ◽  
Gene Expression Correlation ◽  
Gland Development

Plant NAC (NAM, ATAF1/2, and CUC2) family is involved in various development processes including Programmed Cell Death (PCD) associated development. However, the relationship between NAC family and PCD-associated cotton pigment gland development is largely unknown. In this study, we identified 150, 153 and 299 NAC genes in newly updated genome sequences of G. arboreum, G. raimondii and G. hirsutum, respectively. All NAC genes were divided into 8 groups by the phylogenetic analysis and most of them were conserved during cotton evolution. Using the vital regulator of gland formation GhMYC2-like as bait, expression correlation analysis screened out 6 NAC genes which were low-expressed in glandless cotton and high-expressed in glanded cotton. These 6 NAC genes acted downstream of GhMYC2-like and were induced by MeJA. Silencing CGF1(Cotton Gland Formation1), another MYC-coding gene, caused almost glandless phenotype and down-regulated expression of GhMYC2-like and the 6 NAC genes, indicating a MYC-NAC regulatory network in gland development. In addition, predicted regulatory mechanism showed that the 6 NAC genes were possibly regulated by light, various phytohormones and transcription factors as well as miRNAs. The interaction network and DNA binding sites of the 6 NAC transcription factors were also predicted. These results laid the foundation for further study of gland-related genes and gland development regulatory network.

scholarly journals Network Analysis Identifies Gene Regulatory Network Indicating the Role of RUNX1 in Human Intervertebral Disc Degeneration

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 771 ◽  
Author(s):  
Nazir M. Khan ◽  
Martha E Diaz-Hernandez ◽  
Steven M. Presciutti ◽  
Hicham Drissi
Keyword(s):  
Transcription Factors ◽  
Network Analysis ◽  
Intervertebral Disc ◽  
Disc Degeneration ◽  
Regulatory Network ◽  
Interaction Network ◽  
Functional Enrichment ◽  
Network Cluster ◽  
Chemokine Signaling

Intervertebral disc (IVD) degeneration (IDD) is a multifactorial physiological process which is often associated with lower back pain. Previous studies have identified some molecular markers associated with disc degeneration, which despite their significant contributions, have provided limited insight into the etiology of IDD. In this study, we utilized a network medicine approach to uncover potential molecular mediators of IDD. Our systematic analyses of IDD associated with 284 genes included functional annotation clustering, interaction networks, network cluster analysis and Transcription factors (TFs)-target gene network analysis. The functional enrichment and protein–protein interaction network analysis highlighted the role of inflammatory genes and cytokine/chemokine signaling in IDD. Moreover, sub-network analysis identified significant clusters possessing organized networks of 24 cytokine and chemokine genes, which may be considered as key modulators for IDD. The expression of these genes was validated in independent microarray datasets. In addition, the regulatory network analysis identified the role of multiple transcription factors, with RUNX1 being a master regulator in the pathogenesis of IDD. Our analyses highlighted the role of cytokine genes and interacting pathways in IDD and further improved our understanding of the genetic mechanisms underlying IDD.

scholarly journals A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors inArabidopsis thaliana

2014 ◽  
Vol 42 (12) ◽  
pp. 7681-7693 ◽  
Author(s):  
Søren Lindemose ◽  
Michael K. Jensen ◽  
Jan Van de Velde ◽  
Charlotte O'Shea ◽  
Ken S. Heyndrickx ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Network Analysis ◽  
Dna Binding ◽  
Binding Site ◽  
Regulatory Network ◽  
Nac Transcription Factors ◽  
Dna Binding Site

scholarly journals Networks of Splice Factor Regulation by Unproductive Splicing Coupled With Nonsense Mediated mRNA Decay

2020 ◽  
Author(s):  
Anna Desai ◽  
Zhiqiang Hu ◽  
Courtney E. French ◽  
James P. B. Lloyd ◽  
Steven E. Brenner
Keyword(s):  
Transcription Factors ◽  
Alternative Splicing ◽  
Regulatory Network ◽  
Mrna Decay ◽  
Current Knowledge ◽  
Interaction Network ◽  
Splicing Factor ◽  
Splicing Factors ◽  
Extensive Literature ◽  
Nonsense Mediated Mrna Decay

AbstractBackgroundNonsense mediated mRNA decay (NMD) is an RNA surveillance pathway that degrades aberrant transcripts harboring premature termination codons. This pathway, in conjunction with alternative splicing, regulates gene expression post-transcriptionally. Nearly all serine and arginine-rich (SR) proteins and many heterogeneous nuclear ribonucleoproteins (hnRNPs) produce isoforms that can be degraded by the NMD pathway. Many splicing factors have been reported to be regulated via alternative splicing coupled to NMD. However, it is still uncharacterized that to what extent NMD contributes to the regulation of splicing factors.ResultsHere, we characterized a regulatory network of splicing factors through alternative splicing coupled to NMD. Based upon an extensive literature search, we first assembled a network that encompasses the current knowledge of splice factors repressing or activating the expression of other splicing factors through alternative splicing coupled to NMD. This regulatory network is limited, including just a handful of well-studied splicing factors. To gain a more global and less biased overview, we examined the splicing factor-mRNA interactions from public crosslinking-immunoprecipitation (CLIP)-seq data, which provides information about protein–RNA interactions. A network view of these interactions reveals extensive binding among splicing regulators. We also found that splicing factors bind more frequently to transcripts of other splicing factors than to other genes. In addition, many splicing factors are targets of NMD, and might be regulated via alternative splicing coupled to NMD, which is demonstrated by the significant overlap between the experimental network and eCLIP-network. We found that hierarchy of the splicing-factor interaction network differs from the hierarchy observed for transcription factors.ConclusionThe extensive interaction between splicing factors and transcripts of other splicing factors suggests that the potential regulation via alternative splicing coupled with NMD is widespread. The splicing factor regulation is fundamentally different from that of transcription factors.

scholarly journals A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves

2013 ◽  
Vol 75 (1) ◽  
pp. 26-39 ◽  
Author(s):  
Richard Hickman ◽  
Claire Hill ◽  
Christopher A. Penfold ◽  
Emily Breeze ◽  
Laura Bowden ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Responses ◽  
Regulatory Network ◽  
Nac Transcription Factors

scholarly journals Revisiting floral fusion: the evolution and molecular basis of a developmental innovation

2020 ◽  
Vol 71 (12) ◽  
pp. 3390-3404 ◽  
Author(s):  
Heather R Phillips ◽  
Jacob B Landis ◽  
Chelsea D Specht
Keyword(s):  
Transcription Factors ◽  
Regulatory Network ◽  
Molecular Basis ◽  
Future Research ◽  
Complex Structures ◽  
Comprehensive Overview ◽  
Form Complex ◽  
Floral Organs ◽  
Nac Transcription Factors ◽  
Gene Regulatory

Abstract Throughout the evolution of the angiosperm flower, developmental innovations have enabled the modification or elaboration of novel floral organs enabling subsequent diversification and expansion into new niches, for example the formation of novel pollinator relationships. One such developmental innovation is the fusion of various floral organs to form complex structures. Multiple types of floral fusion exist; each type may be the result of different developmental processes and is likely to have evolved multiple times independently across the angiosperm tree of life. The development of fused organs is thought to be mediated by the NAM/CUC3 subfamily of NAC transcription factors, which mediate boundary formation during meristematic development. The goal of this review is to (i) introduce the development of fused floral organs as a key ‘developmental innovation’, facilitated by a change in the expression of NAM/CUC3 transcription factors; (ii) provide a comprehensive overview of floral fusion phenotypes amongst the angiosperms, defining well-known fusion phenotypes and applying them to a systematic context; and (iii) summarize the current molecular knowledge of this phenomenon, highlighting the evolution of the NAM/CUC3 subfamily of transcription factors implicated in the development of fused organs. The need for a network-based analysis of fusion is discussed, and a gene regulatory network responsible for directing fusion is proposed to guide future research in this area.

Comparative analysis of conservation and regulatory network on core transcription factors in mouse inner ear development

2013 ◽  
Vol 35 (10) ◽  
pp. 1198-1208
Author(s):  
Zhi-Qiang CHEN ◽  
Xin-Huan HAN ◽  
Qin-Jun WEI ◽  
Guang-Qian XING ◽  
Xin CAO
Keyword(s):  
Transcription Factors ◽  
Comparative Analysis ◽  
Inner Ear ◽  
Regulatory Network ◽  
Ear Development ◽  
Inner Ear Development
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