Molecular evolution in the yeast transcriptional regulation network

2004 ◽  
Author(s):  
Annette M. Evangelisti ◽  
Andreas Wagner
Keyword(s):  
Transcriptional Regulation ◽  
Molecular Evolution ◽  
Regulation Network ◽  
Transcriptional Regulation Network

scholarly journals eRNAs and Superenhancer lncRNAs Are Functional in Human Prostate Cancer

2020 ◽  
Vol 2020 ◽  
pp. 1-17
Author(s):  
Xiaona Zhang ◽  
Panpan Pang ◽  
Min Jiang ◽  
Qunfa Cao ◽  
Huili Li ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Transcriptional Regulation ◽  
Target Genes ◽  
Open Chromatin ◽  
Medical Treatments ◽  
Binding Motifs ◽  
Therapy Targets ◽  
Regulation Network ◽  
New Perspective ◽  
Transcriptional Regulation Network

Prostate cancer (PCa) is one of the most commonly diagnosed cancers in males worldwide. lncRNAs (long noncoding RNAs) play a significant role in the occurrence and development of PCa. eRNAs (enhancer RNAs) and SE-lncRNAs (superenhancer lncRNAs) are important elements of lncRNAs, but the role of eRNAs and SE-lncRNAs in PCa remains largely unclear. In this work, we identified 681 eRNAs and 292 SE-lncRNAs that were expressed differentially in PCa using a microarray. We also found that eRNAs transcribed from active open chromatin had significantly higher expression than those from active closed chromatin, and SE-lncRNAs had a little higher expression than eRNAs. Next, we constructed a transcriptional regulation network that eRNA-related enhancer and the target genes shared the same TF-binding motifs. Further, we investigated whether CTCF played a role in mediating the transcriptional regulation network. eRNAs, especially those that regulate androgen response genes, may be candidates for prognostic biomarkers and therapy targets. Our work provides a new perspective for developing medical treatments and therapies for prostate cancer.

Plasticity of a transcriptional regulation network among alpha-proteobacteria is supported by the identification of CtrA targets in Brucella abortus

2002 ◽  
Vol 43 (4) ◽  
pp. 945-960 ◽  
Author(s):  
Anne-Flore Bellefontaine ◽  
Christophe E. Pierreux ◽  
Pascal Mertens ◽  
Jean Vandenhaute ◽  
Jean-Jacques Letesson ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Brucella Abortus ◽  
Regulation Network ◽  
Alpha Proteobacteria ◽  
Transcriptional Regulation Network

scholarly journals Post-GWAS functional studies reveal an RA-associated CD40 induced NF-kB signal transduction and transcriptional regulation network targeted by class II HDAC inhibitors

2021 ◽  
Author(s):  
Meijuan Zou ◽  
Danli Jiang ◽  
Ting Wu ◽  
Xiaoyu Zhang ◽  
Yihan Zhao ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Transcriptional Regulation ◽  
Target Identification ◽  
Hdac Inhibitors ◽  
Systemic Juvenile Idiopathic Arthritis ◽  
Published Data ◽  
Risk Genes ◽  
Functional Studies ◽  
Regulation Network ◽  
Transcriptional Regulation Network

Abstract Currently, it remains difficult to identify which SNPs identified by GWAS are functional, and how various functional SNPs (fSNPs) interact and contribute to disease susceptibility. GWAS have identified a CD40 locus that is associated with rheumatoid arthritis (RA). We previously used two techniques developed in our lab, SNP-seq and FREP-MS, to determine that the RA risk gene RBPJ regulates CD40 expression via a fSNP at the RA-associated CD40 locus. In the present work, by applying the same approach, we report the identification of 6 proteins that regulate RBPJ expression via binding to two fSNPs on the RA-associated RBPJ locus. Using these findings, together with published data, we constructed an RA-associated signal transduction and transcriptional regulation network (STTRN) that functionally connects multiple RA-associated risk genes via transcriptional regulation networks linked by CD40-induced NF-kB signaling. Remarkably, this STTRN provides insight into the potential mechanism of action for the histone deacetylase (HDAC) inhibitor givinostat, an approved therapy for systemic juvenile idiopathic arthritis (SJIA). Thus, generation of disease-associated STTRNs based on post-GWAS functional studies is demonstrated as a novel and effective approach to apply GWAS for mechanistic studies and target identification.

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