Molecular architecture of enhancer–promoter interaction

Hamamoto, Kota; Fukaya, Takashi

doi:10.1016/j.ceb.2022.01.003

Cited by 27 publications

(24 citation statements)

References 101 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Specific combinations of typically between three to five DNA-binding transcription factors execute the cis -regulatory grammar of any tissue-specific promoters and enhancers and lead to the formation of promoter-enhancer loops ( Fig. 4 ) and ultimately assembly of over 100 proteins/enzymes involved in transcriptional initiation and elongation (see Berger, 2007 ; Roeder, 2019 ; Hamamoto and Fukaya, 2022 ).…”

Section: Otx2 Pax6 Lhx2 Six3 and Six6: Model Transcription Factors An...mentioning

confidence: 99%

Cell fate decisions, transcription factors and signaling during early retinal development

Diacou

Nandigrami

Fiser

et al. 2022

Progress in Retinal and Eye Research

View full text Add to dashboard Cite

Section: Otx2 Pax6 Lhx2 Six3 and Six6: Model Transcription Factors An...mentioning

confidence: 99%

Cell fate decisions, transcription factors and signaling during early retinal development

Diacou

Nandigrami

Fiser

et al. 2022

Progress in Retinal and Eye Research

View full text Add to dashboard Cite

“…Cancers are associated with multiple aberrant biological processes, including sustained proliferation, immune escape and apoptosis prevention [ 59 , 60 ]. The aberrant expression of eRNA dysregulates cancer-related genes to promote cancer signaling pathways and results in abnormal cellular responses in tumorigenesis [ 45 , 61 , 62 ]. In this section, we summarize the contribution and mechanisms of eRNAs in different cancer types, as well as their potential clinical utility for cancer diagnosis and therapies.…”

Section: Role Of Ernas In Cancersmentioning

confidence: 99%

Enhancer RNA (eRNA) in Human Diseases

Wang

Zhang

Wang

et al. 2022

IJMS

View full text Add to dashboard Cite

Enhancer RNAs (eRNAs), a class of non-coding RNAs (ncRNAs) transcribed from enhancer regions, serve as a type of critical regulatory element in gene expression. There is increasing evidence demonstrating that the aberrant expression of eRNAs can be broadly detected in various human diseases. Some studies also revealed the potential clinical utility of eRNAs in these diseases. In this review, we summarized the recent studies regarding the pathological mechanisms of eRNAs as well as their potential utility across human diseases, including cancers, neurodegenerative disorders, cardiovascular diseases and metabolic diseases. It could help us to understand how eRNAs are engaged in the processes of diseases and to obtain better insight of eRNAs in diagnosis, prognosis or therapy. The studies we reviewed here indicate the enormous therapeutic potency of eRNAs across human diseases.

show abstract

“…Transcription factors (TFs) regulate gene expression through a tightly organized series of events, ultimately leading to the production of RNA by RNA Polymerase (RNAP). While all transcription requires a core group of general TFs to initiate transcription and guide RNAP to its target, many genes require additional cell-type specific TFs that bind to regions of DNA known as enhancers around the target gene to further stimulate or repress gene expression 1 , 2 . The activities of these TFs are tightly regulated by the cell.…”

Section: Introductionmentioning

confidence: 99%

Single molecule microscopy to profile the effect of zinc status on transcription factor dynamics

Damon

Aaron

Palmer

2022

Sci Rep

View full text Add to dashboard Cite

The regulation of transcription is a complex process that involves binding of transcription factors (TFs) to specific sequences, recruitment of cofactors and chromatin remodelers, assembly of the pre-initiation complex and recruitment of RNA polymerase II. Increasing evidence suggests that TFs are highly dynamic and interact only transiently with DNA. Single molecule microscopy techniques are powerful approaches for tracking individual TF molecules as they diffuse in the nucleus and interact with DNA. Here we employ multifocus microscopy and highly inclined laminated optical sheet microscopy to track TF dynamics in response to perturbations in labile zinc inside cells. We sought to define whether zinc-dependent TFs sense changes in the labile zinc pool by determining whether their dynamics and DNA binding can be modulated by zinc. We used fluorescently tagged versions of the glucocorticoid receptor (GR), with two C4 zinc finger domains, and CCCTC-binding factor (CTCF), with eleven C2H2 zinc finger domains. We found that GR was largely insensitive to perturbations of zinc, whereas CTCF was significantly affected by zinc depletion and its dwell time was affected by zinc elevation. These results indicate that at least some transcription factors are sensitive to zinc dynamics, revealing a potential new layer of transcriptional regulation.

show abstract

Molecular architecture of enhancer–promoter interaction

Cited by 27 publications

References 101 publications

Cell fate decisions, transcription factors and signaling during early retinal development

Cell fate decisions, transcription factors and signaling during early retinal development

Enhancer RNA (eRNA) in Human Diseases

Single molecule microscopy to profile the effect of zinc status on transcription factor dynamics

Contact Info

Product

Resources

About