scholarly journals EPEN-30. C11ORF95-RELA FUSION PROTEIN ENGAGES NOVEL GENOMIC LOCI TO DRIVE MURINE EPENDYMOMA GROWTH

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii314-iii314
Author(s):  
Amir Arabzade ◽  
Yanhua Zhao ◽  
Srinidhi Varadharajan ◽  
Hsiao-Chi Chen ◽  
Austin Stuckert ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Molecular Targets ◽  
Lead Target ◽  
Open Chromatin ◽  
Rna Seq ◽  
In Utero Electroporation ◽  
Pathway Activation ◽  
Mouse Cells ◽  
Shed Light

Abstract RATIONALE Over 70% of supratentorial (ST) ependymoma are characterized by an oncogenic fusion between C11ORF95 and RELA. C11ORF95-RELA fusion is frequently the sole genetic driver detected in ST ependymoma, thus ranking this genomic event as a lead target for therapeutic investigation. RELA is a transcription factor (TF) central to mediating NF-kB pathway activation in processes such as inflammation, cellular metabolism, and chemotaxis. HYPOTHESIS: We posited that C11ORF95-RELA acts as an oncogenic TF that aberrantly shapes the tumor epigenome to drive aberrant transcription. Approach: To this end we developed an in utero electroporation (IUE) mouse model of ependymoma to express C11ORF95-RELA during embryonic development. Our IUE approach allowed us to develop C11ORF95-RELA driven tumor models and cell lines. We comprehensively characterized the epigenome and transcriptome of C11ORF95-RELA fusion driven mouse cells by H3K27ac ChIP-seq, ATAC-seq, and RNA-seq. RESULTS This data revealed that: 1) C11ORF95-RELA directly engages ‘open’ chromatin and is enriched at regions with known RELA TF binding sites as well as novel genomic loci/motifs, 2) C11ORF95-RELA preferentially binds to both H3K27ac (active) enhancers and promoters, and 3) Bound C11ORF95-RELA promoter loci are associated with increased transcription of genes shared with human ependymoma. CONCLUSION Our findings shed light on the transcriptional mechanisms of C11ORF95-RELA, and reveal downstream targets that may represent cancer dependency genes and molecular targets.

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.

An evolutionary approach for identifying potential transcription factor binding sites: the renin gene as an example

2003 ◽  
Vol 284 (4) ◽  
pp. R1147-R1150 ◽  
Author(s):  
Ralf Mrowka ◽  
Karola Steinhage ◽  
Andreas Patzak ◽  
Pontus B. Persson
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Regulatory Region ◽  
Evolutionary Conservation ◽  
Binding Profile ◽  
Noncoding Sequences ◽  
Binding Characteristics ◽  
Renin Gene ◽  
Regulatory Dna ◽  
Shed Light

Evolutionary pressure has resulted in the conservation of certain nucleotide sequences. These conserved regions are potentially important for certain functions. Here we give an example of a comparison between noncoding sequences combined with other independent database information to shed light onto the regulation of the renin gene, a gene that has great importance for cardiovascular and renal homeostasis. To combine the information regarding conservation and weight matrices of transcription factor (TF) binding sites, an algorithm was developed (TFprofile). Notably, a local peak in the resulting binding profile coincides with a previously experimentally identified regulatory region for the renin gene. The existence of further peaks in the binding profile in the conserved 3.9-kb-long hRENc DNA block upstream of the renin gene suggests additional regions of potential importance for gene regulation. The algorithm TFprofile may be used to integrate information on cross-species evolutionary conservation and aspects of TF binding characteristics to provide putative regulatory DNA regions for experimental verification.

scholarly journals Integration of ATAC-seq and RNA-seq Unravels Chromatin Accessibility during Sex Reversal in Orange-Spotted Grouper (Epinephelus coioides)

2020 ◽  
Vol 21 (8) ◽  
pp. 2800 ◽  
Author(s):  
Xi Wu ◽  
Yang Yang ◽  
Chaoyue Zhong ◽  
Yin Guo ◽  
Tengyu Wei ◽  
...  
Keyword(s):  
Gene Expression ◽  
Binding Sites ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Sex Reversal ◽  
Open Chromatin ◽  
Specific Marker ◽  
Epinephelus Coioides ◽  
Rna Seq ◽  
Accessible Chromatin

Chromatin structure plays a pivotal role in maintaining the precise regulation of gene expression. Accessible chromatin regions act as the binding sites of transcription factors (TFs) and cis-elements. Therefore, information from these open regions will enhance our understanding of the relationship between TF binding, chromatin status and the regulation of gene expression. We employed an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and RNA-seq analyses in the gonads of protogynous hermaphroditic orange-spotted groupers during sex reversal to profile open chromatin regions and TF binding sites. We focused on several crucial TFs, including ZNF263, SPIB, and KLF9, and analyzed the networks of TF-target genes. We identified numerous transcripts exhibiting sex-preferred expression among their target genes, along with their associated open chromatin regions. We then investigated the expression patterns of sex-related genes as well as the mRNA localization of certain genes during sex reversal. We found a set of sex-related genes that—upon further study—might be identified as the sex-specific or cell-specific marker genes that trigger sex reversal. Moreover, we discovered the core genes (gnas, ccnb2, and cyp21a) of several pathways related to sex reversal that provide the guideposts for future study.

scholarly journals DNA motif analysis of shear stress responsive endothelial enhancers reveals differential association of KLF and ETV/ETS binding sites with gained and lost enhancers

2021 ◽  
Author(s):  
Arndt F Siekmann ◽  
Roman Tsaryk ◽  
Nora Yucel ◽  
Zoltan Arany ◽  
Olga Bondareva ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Shear Stress ◽  
Binding Sites ◽  
Regulatory Elements ◽  
Open Chromatin ◽  
Laminar Shear Stress ◽  
Rna Seq ◽  
Motif Analysis ◽  
Dna Motif ◽  
Laminar Shear

Endothelial cells (EC) lining blood vessels are exposed to mechanical forces, such as shear stress exerted by the flowing blood. These forces control many aspects of EC biology, including vascular tone, cell migration and proliferation in addition to cell size and shape. Despite a good understanding of the genes and signaling pathways responding to shear stress, our insights into the transcriptional regulation of these responses is much more limited. In particular, we do not know the different sets of regulatory elements (enhancers) that might control increases or decreases in gene expression. Here, we set out to study changes in the chromatin landscape of human umbilical vein endothelial cells (HUVEC) exposed to laminar shear stress. To do so, we performed ChIP-Seq for H3K27 acetylation, indicative of active enhancer elements and ATAC-Seq to mark regions of open chromatin in addition to RNA-Seq on HUVEC exposed to 6 hours of laminar shear stress. Our results show a correlation of gained and lost enhancers with up- and downregulated genes, respectively. DNA motif analysis revealed an over-representation of KLF transcription factor (TF) binding sites in gained enhancers, while lost enhancers contained more ETV/ETS motifs. We validated a subset of flow responsive enhancers using luciferase-based reporter constructs and CRISPR-Cas9 mediated genome editing. Lastly, we characterized shear stress responsive genes in ECs of zebrafish embryos using RNA-Seq. Together, our results reveal the presence of shear stress responsive DNA regulatory elements and lay the groundwork for the future exploration of these elements and the TFs binding to them in controlling EC biology.

Abstract 470: Computational Identification of NKX2-5 Binding Sites and Downstream Gene Targets Using Transcription Factor Motif and Human Heart-specific Experimental Data

2016 ◽  
Vol 119 (suppl_1) ◽  
Author(s):  
Nicholas Tan ◽  
Mina K Chung ◽  
Jonathan D Smith ◽  
David R Van Wagoner ◽  
John Barnard
Keyword(s):  
Experimental Data ◽  
Transcription Factor ◽  
Computational Methods ◽  
Pathway Analysis ◽  
Binding Sites ◽  
Human Heart ◽  
Rna Seq ◽  
Protein Coding ◽  
Transcription Factor Motif ◽  
Dnase Hypersensitivity

Background: While NKX2-5 plays pivotal roles in human cardiac development and disease, no ChIP-Seq studies of NKX2-5 in human cardiac tissues currently exist, resulting in an incomplete understanding of its direct gene targets. Modern computational methods which identify binding sites using transcription factor motif and tissue-specific experimental data can help to fill this knowledge gap. Objective: To use computational methods to identify likely NKX2-5 binding sites and downstream gene targets using human heart-specific experimental data. Methods: Human cardiomyocyte DNAse hypersensitivity data (2 replicates) were downloaded from the Encyclopedia of DNA Elements (ENCODE) database. The position weight matrix (PWM) representing the transcription factor motif of NKX2-5 was obtained from JASPAR. We applied the Protein Interaction Quantification (PIQ) algorithm to detect NKX2-5 binding sites using the PWM and DNAse hypersensitivity data as inputs. RNA-Seq data from 108 human heart-specific samples (atrial appendages and left ventricles) were downloaded from the Genotype-Tissue Expression (GTEx) database. Protein-coding genes significantly expressed in the heart (RPKM <= 1 based on the GTEx RNA-Seq data) that were within 100kb of the predicted binding sites were then identified. Pathway analysis of these genes was performed using Ingenuity Pathway Analysis (IPA). Results: 1283 binding sites for NKX2-5 were discovered by PIQ. Of 12698 protein-coding, heart-expressed genes, 625 were within 100kb of these binding sites. The identified genes were highly enriched in physiologic categories like “Vasculogenesis” and “Development of Cardiovascular Tissue” (p = 2.36x10-9 and 2.31x10-8 respectively). Notable genes included: cardiac transcription factors (MEF2A, TBX20); growth factors (TGFB2, BMP2); muscle and ion channel function (ACTA2, BIN1), and; calcium signaling (CALM2, CAMK2D). Conclusion: By using computational analyses of transcription factor motif and human heart-specific experimental data, we have identified candidate downstream targets of NKX2-5. Future work will include validation studies in an external cohort and analysis of associations between these candidate genes and cardiac disease.

Targeting NUPR1 for Cancer Treatment: A Risky Endeavor

2020 ◽  
Vol 20 (10) ◽  
pp. 768-778
Author(s):  
Salma M.A. Mansour ◽  
Sahar A. Ali ◽  
Shaira Nofal ◽  
Sameh H. Soror
Keyword(s):  
Transcription Factor ◽  
Cancer Treatment ◽  
Complex Network ◽  
Mechanism Of Action ◽  
Molecular Targets ◽  
Novel Therapies ◽  
Different Types ◽  
Shed Light

NUPR1 is a transcription factor that has attracted great attention because of its various roles in cancer. Several studies were carried out to determine its molecular targets and mechanism of action to develop novel therapies against cancer. Here, we shed light on the role of NUPR1 in different types of cancer. NUPR1 regulates a complex network of pathways that may be affected by its silencing, which can cause varying effects. Its role in some types of cancer has been reported but remains incompletely understood, whereas its roles in other types of cancers have not been reported yet. Therefore, targeting NUPR1 for cancer treatment remains challenging and risky.

scholarly journals Systems evaluation reveals novel transporter YohJK renders 3-hydroxypropionate tolerance in Escherichia coli

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Thuan Phu Nguyen-Vo ◽  
Seyoung Ko ◽  
Huichang Ryu ◽  
Jung Rae Kim ◽  
Donghyuk Kim ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Functional Analysis ◽  
Transcription Factor ◽  
Binding Sites ◽  
Deletion Mutant ◽  
Transmembrane Proteins ◽  
Rna Seq ◽  
Wild Type ◽  
Drastic Reduction ◽  
Functional Studies

Abstract Previously, we have reported that 3-hydroxypropionate (3-HP) tolerance in Escherichia coli W is improved by deletion of yieP, a less-studied transcription factor. Here, through systems analyses along with physiological and functional studies, we suggest that the yieP deletion improves 3-HP tolerance by upregulation of yohJK, encoding putative 3-HP transporter(s). The tolerance improvement by yieP deletion was highly specific to 3-HP, among various C2–C4 organic acids. Mapping of YieP binding sites (ChIP-exo) coupled with transcriptomic profiling (RNA-seq) advocated seven potential genes/operons for further functional analysis. Among them, the yohJK operon, encoding for novel transmembrane proteins, was the most responsible for the improved 3-HP tolerance; deletion of yohJK reduced 3-HP tolerance regardless of yieP deletion, and their subsequent complementation fully restored the tolerance in both the wild-type and yieP deletion mutant. When determined by 3-HP-responsive biosensor, a drastic reduction of intracellular 3-HP was observed upon yieP deletion or yohJK overexpression, suggesting that yohJK encodes for novel 3-HP exporter(s).

scholarly journals Identification and characteristic analysis of enhancers across 13 major cancer types

2021 ◽  
Author(s):  
Mingming Qian ◽  
Wenzhu Wang ◽  
Yana Zhang ◽  
Yi Zhao ◽  
Huige Quan ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Binding Sites ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Characteristic Analysis ◽  
Cancer Types ◽  
Highly Correlated ◽  
Functional Transcription Factor

Abstract Enhancers are often mutated and dysregulated in various diseases such as cancer. By integrating the FANTOM enhancers expression profiles and RNA-seq data from TCGA of 13 cancers and their corresponding para-cancerous tissues, we systematically identified a total of 4702 significantly differentially expressed enhancers (DE enhancers). Furthermore, a total of 1036 differentially expressed genes (DE genes) regulated by differentially expressed enhancers (DE enhancers) were identified. It was found that in these 13 cancers, most (61.13%) enhancers were ubiquitously expressed, whereas DE enhancers were more likely to be tissue-specific expressed, and the DE genes regulated by DE enhancers were significantly enriched in cancer-related pathways. Finally, it was manifested that 74 SNPs located in 37 DE enhancers, and these SNPs affected the gain and loss of functional transcription factor binding sites (TFBS) of 758 transcription factors, which had been shown to be highly correlated with tumorigenesis and development.

scholarly journals Neuroblast-specific chromatin landscapes allow integration of spatial and temporal cues to generate neuronal diversity in Drosophila

2018 ◽  
Author(s):  
Sonia Q Sen ◽  
Sachin Chanchani ◽  
Tony D Southall ◽  
Chris Q Doe
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Neuronal Diversity ◽  
Spatial Factors ◽  
Factor Binding ◽  
Temporal Cues ◽  
Spatial Factor ◽  
Early Neurogenesis

AbstractDuring early neurogenesis in flies and mice, spatial and temporal cues interact to specify neuronal diversity, yet in no organism is it known how spatial and temporal cues are integrated. We used Targeted DamID (TaDa) to identify the genomic binding sites of the temporal transcription factor Hunchback in two adjacent Drosophila neuroblasts (NB5-6 and NB7-4). Hunchback targets were different in each neuroblast. Profiling chromatin accessibility showed that each neuroblast had a distinct chromatin landscape: Hunchback-bound loci in NB5-6 were in open chromatin, but the same loci in NB7-4 were in closed chromatin. Moreover, binding of the spatial factor Gsb/Pax3, essential for NB5-6 specification, was correlated with open chromatin and Hunchback-enriched loci in NB5-6, but not NB7-4. We propose early-acting spatial factors establish a unique chromatin landscape in each neuroblast, thereby restricting temporal factor binding to different loci in each neuroblast, resulting in different neurons in each neuroblast lineage.Impact statementIntegration of spatial and temporal identity during Drosophila neurogenesis is due to spatial factors generating neuroblast-specific chromatin thereby biasing subsequent temporal transcription factor binding and producing neuroblast-specific neurons.

scholarly journals Identification of Transcription Factor Binding Sites using ATAC-seq

2018 ◽  
Author(s):  
Zhijian Li ◽  
Marcel H. Schulz ◽  
Martin Zenke ◽  
Ivan G. Costa
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Markov Models ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Variable Order ◽  
Open Chromatin ◽  
Factor Binding ◽  
Specific Protocol ◽  
Accessible Chromatin

1AbstractTransposase-Accessible Chromatin (ATAC) followed by sequencing (ATAC-seq) is a simple and fast protocol for detection of open chromatin. However, computational footprinting in ATAC-seq, i.e. search for regions with depletion of cleavage events due to transcription factor binding sites, has been poorly explored so far. We propose HINT-ATAC, a footprinting method that addresses ATAC-seq specific protocol artifacts. HINT-ATAC uses a probabilistic framework based on Variable-order Markov models to learn the complex sequence cleavage preferences of the transposase enzyme. Moreover, we observed specific strand specific cleavage patterns around the binding sites of transcription factors, which are determined by local nucleosome architecture. HINT-ATAC explores local nucleosome architecture to significantly outperform competing footprinting methods in predicting transcription factor binding sites by ChIP-seq. HINT-ATAC is an open source software and available online at www.regulatory-genomics.org/hint

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