CIRDES: an efficient genome-wide method for in vivo RNA–RNA interactome analysis

The Analyst ◽  
2019 ◽  
Vol 144 (21) ◽  
pp. 6197-6206
Author(s):  
Yao-Ting Li ◽  
Nan Zhou ◽  
Wei-Xi Deng ◽  
Xue-Zhen Zeng ◽  
Xiao-Juan Wang ◽  
...  

Complex RNA–RNA interactions underlie fundamental biological processes.

2021 ◽  
Author(s):  
Sofia Archontidi ◽  
Corentine Marie ◽  
Beata Gyorgy ◽  
Justine Guegan ◽  
Marc Sanson ◽  
...  

Diffuse gliomas are primary brain tumors originating from the transformation of glial cells. In particular, oligodendrocyte precursor cells constitute the major tumor-amplifying population in the gliomagenic process. We previously identified the TCF12 gene, encoding a transcription factor of the E protein family, as being recurrently mutated in oligodendrogliomas. In this study, we sought to understand the function of TCF12 in oligodendroglial cells, the glioma lineage of origin. We first describe TCF12 mRNA and protein expression pattern in oligodendroglial development in the mouse brain. Second, by TCF12 genome wide chromatin profiling in oligodendroglial cells, we show that TCF12 binds active promoters of genes involved in proliferation, translation/ribosomes, and pathways involved in oligodendrocyte development and cancer. Finally, we perform OPC-specific Tcf12 inactivation in vivo and demonstrate by immunofluorescence and transcriptomic analyses that TCF12 is transiently required for OPC proliferation but dispensable for oligodendrocyte differentiation. We further show that Tcf12 inactivation results in deregulation of biological processes that are also altered in oligodendrogliomas. Together, our data suggest that TCF12 directly regulates transcriptional programs in oligodendroglia development that are relevant in a glioma context.


2019 ◽  
Vol 20 (20) ◽  
pp. 5014 ◽  
Author(s):  
Zelou Wei ◽  
Yalong Cheng ◽  
Chenchen Zhou ◽  
Dong Li ◽  
Xin Gao ◽  
...  

Extensive studies have shown that the MBW complex consisting of three kinds of regulatory proteins, MYB and basic helix–loop–helix (bHLH) transcription factors and a WD40 repeat protein, TRANSPARENT TESTA GLABRA1 (TTG1), acts in concert to promote trichome formation and flavonoid accumulation in Arabidopsis thaliana. TTG1 functions as an essential activator in these two biological processes. However, direct downstream targets of the TTG1-dependent MBW complex have not yet been obtained in the two biological processes at the genome-wide level in A. thaliana. In the present study, we found, through RNA sequencing and quantitative real-time PCR analysis, that a great number of regulatory and structural genes involved in both trichome formation and flavonoid accumulation are significantly downregulated in the young shoots and expanding true leaves of ttg1-13 plants. Post-translational activation of a TTG1-glucocorticoid receptor fusion protein and chromatin immunoprecipitation assays demonstrated that these downregulated genes are directly or indirectly targeted by the TTG1-dependent MBW complex in vivo during trichome formation and flavonoid accumulation. These findings further extend our understanding of the role of TTG1-dependent MBW complex in the regulation of trichome formation and flavonoid accumulation in A. thaliana.


2020 ◽  
Author(s):  
Sruti DebRoy ◽  
Victor Aliaga‐Tobar ◽  
Gabriel Galvez ◽  
Srishtee Arora ◽  
Xiaowen Liang ◽  
...  

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