Epigenetic Regulation of the Dendritic Cell Marker Gene MADDAM /ADAM19.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 4187-4187
Author(s):  
Marina Kreutz ◽  
Achim Ehrnsperger ◽  
Michael Rehli ◽  
Reinhard Andreesen
Keyword(s):  
Transcription Factors ◽  
Dendritic Cell ◽  
Binding Sites ◽  
Cpg Island ◽  
Trichostatin A ◽  
Proximal Promoter ◽  
Cell Type ◽  
Reporter Activity ◽  
Cell Type Specific ◽  
Specific Regulation

Abstract MADDAM (Metalloprotease And Disintegrin Dendritic Cell Antigen Marker, ADAM19), a human metalloprotease belonging to the ADAM-family, is strongly expressed during in vitro differentiation of monocytes into dendritic cells (DC), whereas differentiation of monocytes into macrophages (MAC) is associated with a loss of MADDAM transcription. To investigate the mechanisms underlying this cell-type specific expression pattern we defined the transcriptional start site and the proximal promoter of the MADDAM gene. Gene bank analysis of the CpG island promoter and first intron revealed putative binding sites for several transcription factors, including VDR, NF-kB and Sp1-family factors. EMSA demonstrated binding of Sp1, Sp3, NF-kB and VDR to their putative binding sites in the proximal promoter region and mutation of these elements led to a decreased reporter activity of the proximal promoter in luciferase assays. A minimal promoter construct of 150-bp showed weak reporter activity in primary monocyte-derived MAC and a threefold higher activity in monocyte-derived DC, indicating that differential binding of transcription factors contributes to the cell-type specific regulation of MADDAM. Transfection of monocytic THP-1 cells with the 150-bp fragment also resulted in significant reporter activity, despite the lack of endogenous MADDAM expression. Interestingly, Trichostatin A (TSA), a known inhibitor of histone deacetylation, lead to a dose dependent induction of MADDAM mRNA in THP-1 cells. Chromatin immunoprecipitation (ChIP) assays demonstrate increased levels of acetylated histones H3 and H4 in DC as compared to MAC, indicating an important role of histone acetylation in the cell-type specific regulation of the MADDAM gene.

scholarly journals DNA Methylation Repels Binding of HIF Transcription Factors to Maintain Tumour Immunotolerance

2020 ◽  
Author(s):  
Flora D’anna ◽  
Laurien Van Dyck ◽  
Jieyi Xiong ◽  
Hui Zhao ◽  
Rebecca V. Berrens ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Transcription Factors ◽  
Immune Checkpoint ◽  
Binding Sites ◽  
Dna Demethylation ◽  
Transcript Expression ◽  
Dependent Manner ◽  
Cell Type ◽  
Dna Hypomethylation ◽  
Cell Type Specific

AbstractBackgroundHypoxia is pervasive in cancer and other diseases. Cells sense and adapt to hypoxia by activating hypoxia-inducible transcription factors (HIFs), but it is still an outstanding question why cell types differ in their transcriptional response to hypoxia.ResultsHere, we report that HIFs fail to bind CpG dinucleotides that are methylated in their consensus binding sequence, both in in vitro biochemical binding assays and in vivo studies of differentially methylated isogenic cell lines. Based on in silico structural modelling, we show that 5-methylcytosine indeed causes steric hindrance in the HIF binding pocket. A model wherein cell-type-specific methylation landscapes, as laid-down by the differential expression and binding of other transcription factors under normoxia control cell-type-specific hypoxia responses is observed. We also discover ectopic HIF binding sites in repeat regions which are normally methylated. Genetic and pharmacological DNA demethylation, but also cancer-associated DNA hypomethylation, expose these binding sites, inducing HIF-dependent expression of cryptic transcripts. In line with such cryptic transcripts being more prone to cause double-stranded RNA and viral mimicry, we observe low DNA methylation and high cryptic transcript expression in tumours with high immune checkpoint expression, but not in tumours with low immune checkpoint expression, where they would compromise tumour immunotolerance. In a low-immunogenic tumour model, DNA demethylation upregulates cryptic transcript expression in a HIF-dependent manner, causing immune activation and reducing tumour growth.ConclusionsOur data elucidate the mechanism underlying cell-type specific responses to hypoxia, and suggest DNA methylation and hypoxia to underlie tumour immunotolerance.

scholarly journals Intragenic CpG islands play important roles in bivalent chromatin assembly of developmental genes

2017 ◽  
Vol 114 (10) ◽  
pp. E1885-E1894 ◽  
Author(s):  
Sun-Min Lee ◽  
Jungwoo Lee ◽  
Kyung-Min Noh ◽  
Won-Young Choi ◽  
Sejin Jeon ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Transcriptional Activation ◽  
Epigenetic Modification ◽  
Embryonic Stem ◽  
Housekeeping Genes ◽  
Regulation Of Transcription ◽  
Physical Interaction ◽  
Cell Type ◽  
Cell Type Specific ◽  
Specific Regulation

CpG, 5′-C-phosphate-G-3′, islands (CGIs) have long been known for their association with enhancers, silencers, and promoters, and for their epigenetic signatures. They are maintained in embryonic stem cells (ESCs) in a poised but inactive state via the formation of bivalent chromatin containing both active and repressive marks. CGIs also occur within coding sequences, where their functional role has remained obscure. Intragenic CGIs (iCGIs) are largely absent from housekeeping genes, but they are found in all genes associated with organ development and cell lineage control. In this paper, we investigated the epigenetic status of iCGIs and found that they too reside in bivalent chromatin in ESCs. Cell type-specific DNA methylation of iCGIs in differentiated cells was linked to the loss of both the H3K4me3 and H3K27me3 marks, and disruption of physical interaction with promoter regions, resulting in transcriptional activation of key regulators of differentiation such as PAXs, HOXs, and WNTs. The differential epigenetic modification of iCGIs appears to be mediated by cell type-specific transcription factors distinct from those bound by promoter, and these transcription factors may be involved in the hypermethylation of iCGIs upon cell differentiation. iCGIs thus play a key role in the cell type-specific regulation of transcription.

scholarly journals Shisa6 mediates cell-type specific regulation of depression in the nucleus accumbens

2021 ◽  
Author(s):  
Hee-Dae Kim ◽  
Jing Wei ◽  
Tanessa Call ◽  
Nicole Teru Quintus ◽  
Alexander J. Summers ◽  
...  
Keyword(s):  
Nucleus Accumbens ◽  
Molecular Mechanisms ◽  
Cell Types ◽  
Current Treatment ◽  
Specific Cell ◽  
Excitatory Synapses ◽  
Cell Type ◽  
Cell Type Specific ◽  
Specific Regulation ◽  
Circuit Function

AbstractDepression is the leading cause of disability and produces enormous health and economic burdens. Current treatment approaches for depression are largely ineffective and leave more than 50% of patients symptomatic, mainly because of non-selective and broad action of antidepressants. Thus, there is an urgent need to design and develop novel therapeutics to treat depression. Given the heterogeneity and complexity of the brain, identification of molecular mechanisms within specific cell-types responsible for producing depression-like behaviors will advance development of therapies. In the reward circuitry, the nucleus accumbens (NAc) is a key brain region of depression pathophysiology, possibly based on differential activity of D1- or D2- medium spiny neurons (MSNs). Here we report a circuit- and cell-type specific molecular target for depression, Shisa6, recently defined as an AMPAR component, which is increased only in D1-MSNs in the NAc of susceptible mice. Using the Ribotag approach, we dissected the transcriptional profile of D1- and D2-MSNs by RNA sequencing following a mouse model of depression, chronic social defeat stress (CSDS). Bioinformatic analyses identified cell-type specific genes that may contribute to the pathogenesis of depression, including Shisa6. We found selective optogenetic activation of the ventral tegmental area (VTA) to NAc circuit increases Shisa6 expression in D1-MSNs. Shisa6 is specifically located in excitatory synapses of D1-MSNs and increases excitability of neurons, which promotes anxiety- and depression-like behaviors in mice. Cell-type and circuit-specific action of Shisa6, which directly modulates excitatory synapses that convey aversive information, identifies the protein as a potential rapid-antidepressant target for aberrant circuit function in depression.

scholarly journals Promoter G-quadruplexes and transcription factors cooperate to shape the cell type-specific transcriptome

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sara Lago ◽  
Matteo Nadai ◽  
Filippo M. Cernilogar ◽  
Maryam Kazerani ◽  
Helena Domíniguez Moreno ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Binding Sites ◽  
Specific Gene ◽  
Open Chromatin ◽  
Rna Seq ◽  
Transcript Levels ◽  
Promoter Sequences ◽  
G Quadruplex ◽  
Cell Type Specific ◽  
Folding State

AbstractCell identity is maintained by activation of cell-specific gene programs, regulated by epigenetic marks, transcription factors and chromatin organization. DNA G-quadruplex (G4)-folded regions in cells were reported to be associated with either increased or decreased transcriptional activity. By G4-ChIP-seq/RNA-seq analysis on liposarcoma cells we confirmed that G4s in promoters are invariably associated with high transcription levels in open chromatin. Comparing G4 presence, location and transcript levels in liposarcoma cells to available data on keratinocytes, we showed that the same promoter sequences of the same genes in the two cell lines had different G4-folding state: high transcript levels consistently associated with G4-folding. Transcription factors AP-1 and SP1, whose binding sites were the most significantly represented in G4-folded sequences, coimmunoprecipitated with their G4-folded promoters. Thus, G4s and their associated transcription factors cooperate to determine cell-specific transcriptional programs, making G4s to strongly emerge as new epigenetic regulators of the transcription machinery.

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