Super-Enhancement and Control of Amh Expression

In previous work it was shown that mutation of site 1 in the downstream enhancer sequence (DE) led to ablation of enhancement. Mutation of the Wilms tumour factor element (Wt), situated in the Amh promoter between the tata box and the start of translation (TSS), also led to ablation of enhancement. This suggested that these sites may be the anchor points for a specific duplex factor bridging remote DNA elements to the promoter. Mutation analysis of the DNA sequence between sections 1 and 2 of DE was carried out by site directed mutagenesis. It is reported here that site 4 lying between DE1 and DE2, plays a key role in controlling the level of enhancement.

Genetic variant in a BaP-activated super-enhancer increases prostate cancer risk by promoting AhR-mediated FAM227A expression

Genetic variants in super-enhancers(SEs)are increasingly implicated as a disease risk-driving mechanism.Previous studies have reported an associations between benzo[a]pyrene(BaP)exposure and some malignant tumor risk.Currently,it is unclear whether BaP is involved in the effect of genetic variants in SEs on prostate cancer risk,nor the associated intrinsic molecular mechanisms.In the current study,by using logistic regression analysis,we found that rs5750581T>C in 22q-SE was significantly associated with prostate cancer risk(odds ratio=1.26,P=7.61×10^(-5)).We also have found that the rs6001092T>G,in a high linkage disequilibrium with rs5750581T>C(r^(2)=0.98),is located in a regulatory aryl hydrocarbon receptor(AhR)motif and may interact with the FAM227A promoter in further bioinformatics analysis.We then performed a series of functional and BaP acute exposure experiments to assess biological function of the genetic variant and the target gene.Biologically,the rs6001092-G allele strengthened the transcription factor binding affinity to AhR,thereby upregulating FAM227A,especially upon exposure to BaP,which induced the malignant phenotypes of prostate cancer.The current study highlights that AhR acts as an environmental sensor of BaP and is involved in the SE-mediated prostate cancer risk,which may provide new insights into the etiology of prostate cancer associated with the inherited SE variants under environmental carcinogen stressors.

Enhancer and super-enhancer: Positive regulators in gene transcription

Enhancer is a positive regulator for spatiotemporal development in eukaryotes. As a cluster, super-enhancer is closely related to cell identity- and fate-determined processes. Both of them function tightly depending on their targeted transcription factors, cofactors, and genes through distal genomic interactions. They have been recognized as critical components and played positive roles in transcriptional regulatory network or factory. Recent advances of next-generation sequencing have dramatically expanded our ability and knowledge to interrogate the molecular mechanism of enhancer and super-enhancer for transcription. Here, we review the history, importance, advances and challenges on enhancer and super-enhancer field.This will benefit our understanding of their function mechanism for transcription underlying precise gene expression.

Super-enhancer receives signals from the extracellular matrix to induce PD-L1-mediated immune evasion via integrin/ BRAF/TAK1/ERK/ETV4 signaling

Objective:PD-L1 and PD-L2 expression levels determine immune evasion and the therapeutic efficacy of immune checkpoint blockade.The factors that drive inducible PD-L1 expression have been extensively studied,but mechanisms that result in constitutive PD-L1 expression in cancer cells are largely unknown.Methods:DNA elements were deleted in cells by CRISPR/Cas9-mediated knockout.Protein function was inhibited by chemical inhibitors.Protein levels were examined by Western blot,mRNA levels were examined by real-time RT-PCR,and surface protein expression was determined by cellular immunofluorescence and flow cytometry.Immune evasion was examined by in vitro T cell-mediated killing.Results:We determined the core regions(chr9:5,496,378–5,499,663)of a previously identified PD-L1L2-super-enhancer(SE).Through systematic analysis,we found that the E26 transformation-specific(ETS)variant transcription factor(ETV4)bound to this core DNA region but not to DNA surrounding PD-L1L2SE.Genetic knockout of ETV4 dramatically reduced the expressions of both PD-L1 and PD-L2.ETV4 transcription was dependent on ERK activation,and BRAF/TAK1-induced ERK activation was dependent on extracellular signaling fromαvβ3 integrin,which profoundly affected ETV4 transcription and PD-L1/L2 expression.Genetic silencing or pharmacological inhibition of components of the PD-L1L2-SE-associated pathway rendered cancer cells susceptible to T cell-mediated killing.Conclusions:We identified a pathway originating from the extracellular matrix that signaled via integrin/BRAF/TAK1/ERK/ETV4 to PD-L1L2-SE to induce PD-L1-mediated immune evasion.These results provided new insights into PD-L1L2-SE activation and pathways associated with immune checkpoint regulation in cancer.

LncRNA Platr22 promotes super-enhancer activity and stem cell pluripotency

Super-enhancers(SEs)comprise large clusters of enhancers,which are co-occupied by multiple lineage-specific and master tran-scription factors,and play pivotal roles in regulating gene expression and cell fate determination.However,it is still largely un-known whether and how SEs are regulated by the noncoding portion of the genome.Here,through genome-wide analysis,wefound that tpng noncoding RNA(IncRNA)genes preferentially lie next to SEs.In mouse embryonic stem cells(mESCs),depletionof$E-associated IlncRNA transcripts dysregulated the activity of their nearby SEs.Specifically,we revealed a critical regulatoryrole of the IncRNA gene Platr22 in modulating the activity of a nearby SE and the expression of the nearby pluripotency regulatorZFP281.Through these regulatory events,Platr22 contributes to pluripotency maintenance and proper differentiation of mESCs.Mechanistically,Platr22 transcripts coat chromatin near the SE region and interact with DDX5 and hnRNP-L.DDX5 further recruitsp300 and other factors related to active transcription.We propose that these factors assemble into a transcription hub,thus pro-moting an open and active epigenetic chromatin state.0ur study highlights an unanticipated role for a class of lncRNAs in epige-netically controlling the activity and vulnerability to perturbation of nearby SEs for cell fate determination.

Differentiated super-enhancers in lung cancer cells

Super-enhancers(SEs) are regulatory elements with enriched accumulation of key transcription factors.Few studies were done investigating SEs in lung cancers.Here we analyzed epigenetic profiling data to identify SEs in lung cancer cell lines.Enhancers were classified as SEs and typical enhancers(TEs).Most of the TEs were overlapped between normal cell and cancer cells.A great portion of SEs were differentiated comparing these cells.Analysis of GO terms associated with SEs revealed SE remodeling(lost on some sites while gain on others) between normal and lung cancer cells.By comparing the average number of SEs in each GO term in cancer cells with the number in control cells,surprisingly,no GO terms with significantly increased SE number in cancer condition were observed.On the contrary,in aspects such as "cell-cell adhesion","receptor activity" and"negative regulation of canonical Wnt signaling pathway",the related SEs were significantly reduced in cancer cells.These findings suggest that in lung cancer,cells may not gain decisive gene expression in the related aspect,instead,they may have lost control of the fateful genes.Taken together,our work with the usability of omics data identified SEs in lung cancer cells and further showed cancer-specific features of SE-related terms.

PCGF6 regulates stem cell pluripotency as a transcription activator via super-enhancer dependent chromatin interactions

Polycomb group(PcG)ring finger protein 6(PCGF6),though known as a member of the transcription-re-pressing complexes,PcG,also has activation function in regulating pluripotency gene expression.However,the mechanism underlying the activation function of PCGF6 is poorly understood.Here,we found that PCGF6 co-localizes to gene activation regions along with pluripotency factors such as OCT4.In addition,PCGF6 was recruited to a subset of the super-enhancer(SE)regions upstream of cell cycle-associated genes by OCT4,and increased their expression.By combining with promoter capture Hi-C data,we found that PCGF6 activates cell cycle genes by regulating SE-promoter interactions via 3D chromatin.Our fin dings highlight a novel mechanism of PcG protein in regulating pluripotency,and provide a research basis for the therapeutic application of pluripotent stem cells.

RANKL-responsive epigenetic mechanism reprograms macrophages into bone-resorbing osteoclasts

Monocyte/macrophage lineage cells are highly plastic and can differentiate into various cells under different environmental stimuli. Bone-resorbing osteoclasts are derived from the monocyte/macrophage lineage in response to receptor activator of NF-κB ligand (RANKL). However, the epigenetic signature contributing to the fate commitment of monocyte/macrophage lineage differentiation into human osteoclasts is largely unknown. In this study, we identified RANKL-responsive human osteoclast-specific superenhancers (SEs) and SE-associated enhancer RNAs (SE-eRNAs) by integrating data obtained from ChIP-seq, ATAC-seq, nuclear RNA-seq and PRO-seq analyses. RANKL induced the formation of 200 SEs, which are large clusters of enhancers, while suppressing 148 SEs in macrophages. RANKL-responsive SEs were strongly correlated with genes in the osteoclastogenic program and were selectively increased in human osteoclasts but marginally presented in osteoblasts, CD4+ T cells, and CD34+ cells. In addition to the major transcription factors identified in osteoclasts, we found that BATF binding motifs were highly enriched in RANKL-responsive SEs. The depletion of BATF1/3 inhibited RANKL-induced osteoclast differentiation. Furthermore, we found increased chromatin accessibility in SE regions, where RNA polymerase II was significantly recruited to induce the extragenic transcription of SE-eRNAs, in human osteoclasts. Knocking down SE-eRNAs in the vicinity of the NFATc1 gene diminished the expression of NFATc1, a major regulator of osteoclasts, and osteoclast differentiation. Inhibiting BET proteins suppressed the formation of some RANKL-responsive SEs and NFATc1-associated SEs, and the expression of SE-eRNA:NFATc1. Moreover, SE-eRNA:NFATc1 was highly expressed in the synovial macrophages of rheumatoid arthritis patients exhibiting high-osteoclastogenic potential. Our genome-wide analysis revealed RANKL-inducible SEs and SE-eRNAs as osteoclast-specific signatures, which may contribute to the development of osteoclast-specific therapeutic interventions.

Enhancer RNAs: A missing regulatory layer in gene transcription

Enhancers and super-enhancers exert indispensable roles in maintaining cell identity through spatiotemporally regulating gene transcription.Meanwhile,active enhancers and super-enhancers also produce transcripts termed enhancer RNAs(eRNAs) from their DNA elements.Although enhancers have been identified for more than 30 years,widespread transcription from enhancers are just discovered by genome-wide sequencing and considered as the key to understand longstanding questions in gene transcription.RNA-transcribed enhancers are marked by histone modifications such as H3K4m1/2 and H3K27Ac,and enriched with transcription regulatory factors such as LDTFs,P300,CBP,BRD4 and MED1.Those regulatory factors might constitute a Mega-Trans-like complex to potently activate enhancers.Compared to mRNAs,eRNAs are quite unstable and play roles at local.Functionally,it has been shown that e RNAs promote formation of enhancer-promoter loops.Several studies also demonstrated that eRNAs help the binding of RNA polymerase II(RNAPII) or transition of paused RNAPII by de-association of the negative elongation factor(NELF) complex.Nevertheless,these proposed mechanisms are not universally accepted and still under controversy.Here,we comprehensively summarize the reported findings and make perspectives for future exploration.We also believe that super-enhancer derived RNAs(seRNAs) might be informative to understand the nature of super-enhancers.

Cyclin-dependent kinase 7 inhibitor THZ1 in cancer therapy

Current cancer therapies have encountered adverse response due to poor therapeutic efficiency,severe side effects and acquired resistance to multiple drugs.Thus,there are urgent needs for finding new cancer-targeted pharmacological strategies.In this review,we summarized the current understanding with THZ1,a covalent inhibitor of cyclin-dependent kinase 7(CDK7),which demonstrated promising anti-tumor activity against different cancer types.By introducing the anti-tumor behaviors and the potential targets for different cancers,this review aims to provide more effective approaches to CDK7 inhibitor-based therapeutic agents and deeper insight into the diverse tumor proliferation mechanisms.