A Potential Epigenetic Bookmarking Function for the Hematopoietic Transcription Factor GATA-1.

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 2601-2601
Author(s):  
Stephan Kadauke ◽  
Janine M Lamonica ◽  
Alan Lau ◽  
Margaret Chou ◽  
Gerd Blobel
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
High Throughput Sequencing ◽  
Conflicts Of Interest ◽  
Erythroid Differentiation ◽  
Regulatory Elements ◽  
Chromatin Binding ◽  
Erythroid Precursor ◽  
Lineage Stability ◽  
Mitotic Chromatin

Abstract Abstract 2601 Hematopoietic lineage choice decisions are stably maintained through many cell divisions. For example, erythroid precursor cells undergo several rounds of cell division during their maturation. During each mitosis, most transcription factors separate from chromatin causing transcription to cease globally. Mitosis therefore poses a challenge for transcription factors to re-associate with the appropriate target sites in chromatin of newborn cells. The epigenetic mechanisms that cement lineage stability and resist cell reprogramming during mitosis are poorly understood, although recent evidence supports the idea that “bookmarking” factors that remain associated with mitotic chromatin may play a role in this process. We therefore investigated whether the hematopoietic transcription factor GATA-1 might be retained at specific sites during mitosis. GATA-1 controls the expression of essentially all erythroid-specific genes and might therefore play a role in maintaining erythroid gene expression programs throughout the cell cycle. Surprisingly, we found that while a substantial fraction of GATA-1 dissociates from chromatin in mitosis, foci of high GATA-1 density are present within mitotic chromatin. To determine the exact locations of GATA-1 binding during mitosis, we developed a method to highly purify mitotic erythroid cells in sufficient quantities for chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq). These experiments revealed that a subset of sites bound by GATA-1 during interphase is occupied continuously throughout mitosis. Importantly, continuously GATA-1-occupied sites are enriched at promoters and cis-regulatory elements of genes coding for key developmental regulators of hematopoiesis (e.g., Fog1/Zfpm1, Gata2, Lyl1) but are notably absent at erythroid physiological and structural genes (e.g., Hba, Hbb, Epb4.9). To examine the importance of mitotic chromatin binding by GATA-1, we engineered a version of GATA-1 bearing a mitosis-specific degron that targets GATA-1 for degradation during mitosis but not interphase. Preliminary results show that mitotically degraded GATA-1 fails to induce differentiation when expressed in GATA-1-null erythroblasts. This suggests an important mitotic function for GATA-1. Current work focuses on delineating the mechanism by which continuous chromatin occupancy of GATA-1 throughout mitosis ensures proper erythroid differentiation. The results will be presented and discussed at the meeting. Disclosures: No relevant conflicts of interest to declare.

Lineage-Specific Mitotic Bookmarking by Hematopoietic Transcription Factor GATA1

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 547-547
Author(s):  
Stephan Kadauke ◽  
Jan M Pawlicki ◽  
Maheshi Udugama ◽  
Jordan C Achtman ◽  
Yong Cheng ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Target Genes ◽  
Confocal Imaging ◽  
Erythroid Precursor ◽  
Cell Divisions ◽  
A Genome ◽  
Target Sites ◽  
Lineage Stability ◽  
Mitotic Chromatin

Abstract Abstract 547 Hematopoietic lineage choice decisions are stably maintained throughout many cell divisions. For example, erythroid precursor cells undergo several rounds of cell division during their maturation. During each mitosis, most transcription factors separate from chromatin causing transcription to cease globally. Mitosis therefore poses a challenge for transcription factors to re-associate with the appropriate target sites in chromatin of newborn cells. The epigenetic mechanisms that cement lineage stability and resist cell reprogramming during mitosis are poorly understood, although recent evidence supports the existence of “bookmarking” factors that remain bound to mitotic chromatin. Since the hematopoietic transcription factor GATA1 controls the expression of essentially all erythroid-specific genes, we asked whether it might play a role in maintaining erythroid gene expression programs throughout the cell cycle. Live cell confocal imaging revealed that foci of high GATA1 density are present within mitotic chromatin. Using a novel approach that combines mitotic cell sorting with ChIP-Seq, we defined mitotic GATA1 binding sites on a genome-wide scale. Remarkably, whereas GATA1 vacated the great majority of its target sites during mitosis, including the archetypical GATA1 regulated genes α- and β-globin, those target sites where GATA1 was maintained during mitosis showed a strong tendency to reside near genes encoding key developmental regulators of hematopoiesis (e.g., Zfpm1, Nfe2, Klf1, Gata1, Gata2, Runx1). Tissue-specific GATA1 co-regulators such as FOG-1 and the SCL complex dissociated from GATA1-occupied elements during mitosis, suggesting that GATA1 persists at these sites to facilitate their spatially and temporally appropriate reassembly upon exit from mitosis. Consistent with the notion that GATA1 acts as a mitotic bookmark for its mitotic target genes, timed primary transcript analysis revealed that genes that are marked by GATA1 during mitosis re-activate more rapidly upon G1 entry than those that are not. To directly address the functional importance of mitotic chromatin binding, we developed a version of GATA1 that is selectively degraded during mitosis but remains stable during interphase. This strategy allowed us to prove, for the first time, that the presence of a transcription factor is required specifically during mitosis for timely reactivation of its mitotic target genes. In addition, mitotically disrupted GATA1 failed to fully repress markers of immature erythroid precursors (e.g., Kit, Lyl1), highlighting a potential role of mitotic GATA1 bookmarking for establishing and maintaining lineage- and developmental stage-specific transcriptional programs. Follow-up mechanistic experiments to define the mode by which GATA1 operates during mitosis are underway and will be discussed at the meeting. Together, these studies establish GATA1 as a bona fide mitotic bookmarking factor and provide a deeper understanding by which transcription programs are faithfully perpetuated through cell divisions to maintain lineage stability. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Genomic Retargeting of Tumor Suppressors p53 and CTCF Promotes Oncogenesis

2019 ◽  
Author(s):  
Michal Schwartz ◽  
Avital Sarusi Portugez ◽  
Bracha Zukerman Attia ◽  
Miriam Tannenbaum ◽  
Olga Loza ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Tumor Suppressors ◽  
Regulatory Network ◽  
Regulatory Elements ◽  
Cancer Development ◽  
Chromatin Binding ◽  
Transcriptional Reprogramming ◽  
Major Variation ◽  
Regulatory Landscape

AbstractGene transcription is substantially regulated by distant regulatory elements via combinatorial binding of transcription factors. It is more and more recognized that alterations in chromatin state and transcription factor binding in these distant regulatory elements may have key roles in cancer development. Here we focused on the first stages of oncogene induced carcinogenic transformation, and characterized the regulatory network underlying transcriptional reprogramming associated with this process. Using Hi-C data, we couple between differentially expressed genes and their differentially active regulatory elements and reveal two candidate transcription factors, p53 and CTCF, as major determinants of transcriptional reprogramming at early stages of HRas-induced transformation. Strikingly, the malignant transcriptional reprograming is promoted by redistribution of chromatin binding of these factors without major variation in their expression level. Our results demonstrate that alterations in the regulatory landscape have a major role in driving oncogene-induced transcriptional reprogramming.

scholarly journals Transcriptional Signaling Centers Govern Human Erythropoiesis and Harbor Genetic Variations of Red Blood Cell Traits

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 1277-1277
Author(s):  
Avik Choudhuri ◽  
Eirini Trompouki ◽  
Brian J. Abraham ◽  
Leandro Colli ◽  
William Mallard ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Blood Cell ◽  
Board Of Directors ◽  
Red Blood Cell ◽  
Erythroid Differentiation ◽  
Regulatory Elements ◽  
Advisory Committees ◽  
Equity Ownership

Abstract Single Nucleotide Polymorphisms (SNPs) identified through genome-wide association studies (GWAS) provide insight into the mechanism of human genetic diseases, and majority of functional GWAS mutations target genomic regulatory elements. During erythroid differentiation of human CD34+ cells, we mapped regulatory DNA elements (enhancers and open chromatin regions) by H3K27Ac ChIP-seq and ATAC-seq, and studied the SNPs that reside within these DNA regulatory elements. We followed genomic binding of lineage restricted GATA transcription factors and also chose to examine the binding of the BMP signal responsive transcription factor SMAD1 in CD34+ cells during erythropoiesis. By overlapping their genomic occupancy with stage-matched RNA-seq, we found that SMAD1, in association with GATA-factors, serves as marker of genes responsible for differentiation at every step of erythropoiesis. ChIP-seq for other crucial signaling transcription factors, such as WNT-responsive and TGFb-responsive factors (TCF7L2 and SMAD2, respectively) demonstrated a remarkable co-existence of such factors at GATA+SMAD1 co-bound regions nearby stage-specific genes. We defined such regions as "Transcriptional Signaling Centers (TSC)" where multiple signaling transcription factors converge with master transcription factors to determine optimum stage-specific gene expression in response to growth factors. Our bioinformatics-algorithms demonstrated that PU1 and FLI1 binding sites were present in progenitor-specific TSCs whereas KLF1 and NFE2 sites were enriched in TSCs of red blood cells. We performed CRISPR-CAS9 mediated perturbations of each of the PU1, GATA and SMAD1 motifs separately in a representative progenitor TSC in K562 and HUDEP2 cells. Similar to loss of PU1 and GATA motifs, loss of SMAD1 motif selectively inhibited expression of the associated gene and showed defects in erythroid differentiation, demonstrating that TSCs are important to provide optimum gene expression and proper erythroid differentiation. To determine if such TSCs are targeted by GWAS mutations, we have studied 1270 lead and additional 27,799 SNPs in linkage disequilibrium with lead SNPs that are associated with six critical red blood cell traits - hemoglobin concentration (Hb), hematocrit (Hct), mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC) and red blood cell count (RBC). Surprisingly, we observed that, out of the 3831 "functional" SNPs that fall within non-exonic H3K27Ac enhancers, while only 5% (188) of RBC-SNPs target only blood-master-transcription-factor motifs, at least 48% (1821) of them reside on various signaling pathway associated transcription factor motifs including SMADs (BMP/TGFb signaling), RXR/ROR (nuclear receptor signaling), FOXO/FOXA (FOX signaling), CREBs (cAMP signaling) and TCF7L2 (WNT signaling). Additionally, these RBC-trait-SNPs are specifically enriched in GATA+SMAD1 co-bound TSCs and fall within signaling factor binding sites. We validated such SNPs that target SMAD-motifs. The SNP rs9467664 is associated with the MCV-trait near HIST1H4A, a gene that increases in expression during differentiation. Using gel-shift assay, we found that SMAD1 binding is compromised when the major allele T changes to minor allele A under MCV-trait. Remarkably, eQTL analysis using microarray gene expression profiles of peripheral blood obtained from the Framingham Heart Studies revealed that expression of HIST1H4A is significantly more in a population with T-allele than that with A-allele. This demonstrates that inhibition of SMAD1 binding by the SNP causes a loss of allele-specific HIST1H4A expression. Another MCV-associated SNP rs737092 targets a SMAD motif within an erythroid-specific TSC near RBM38 gene. T-allele, in comparison with C-allele, that retains SMAD1 binding showed more expression in luciferase-based reporter assays specifically under BMP stimulation suggesting that rs737092 compromise BMP-responsiveness. Taken together, our study provides the first evidence that naturally occurring GWAS variations directly impact gene expression from signaling centers by modulating binding of signaling transcription factors under stimulation. Such aberrant signaling events over time could lead to "signalopathies", ultimately resulting in phenotypic variations of RBC traits. Disclosures Abraham: Syros Pharmaceuticals: Equity Ownership. Young:Omega Therapeutics: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Syros Pharmaceuticals: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Camp4 Therapeutics: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees.

scholarly journals Evolutionarily conserved transcription factors drive the oxidative stress response in Drosophila

2020 ◽  
Vol 223 (14) ◽  
pp. jeb221622
Author(s):  
Sarah M. Ryan ◽  
Kaitie Wildman ◽  
Briseida Oceguera-Perez ◽  
Scott Barbee ◽  
Nathan T. Mortimer ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Stress Responses ◽  
Binding Sites ◽  
Regulatory Elements ◽  
Genomic Locus ◽  
Biologically Relevant ◽  
Protein Levels ◽  
Putative Transcription Factor

ABSTRACTAs organisms are constantly exposed to the damaging effects of oxidative stress through both environmental exposure and internal metabolic processes, they have evolved a variety of mechanisms to cope with this stress. One such mechanism is the highly conserved p38 MAPK (p38K) pathway, which is known to be post-translationally activated in response to oxidative stress, resulting in the activation of downstream antioxidant targets. However, little is known about the role of p38K transcriptional regulation in response to oxidative stress. Therefore, we analyzed the p38K gene family across the genus Drosophila to identify conserved regulatory elements. We found that oxidative stress exposure results in increased p38K protein levels in multiple Drosophila species and is associated with increased oxidative stress resistance. We also found that the p38Kb genomic locus includes conserved AP-1 and lola-PT transcription factor consensus binding sites. Accordingly, over-expression of these transcription factors in D. melanogaster is sufficient to induce transcription of p38Kb and enhances resistance to oxidative stress. We further found that the presence of a putative lola-PT binding site in the p38Kb locus of a given species is predictive of the species' survival in response to oxidative stress. Through our comparative genomics approach, we have identified biologically relevant putative transcription factor binding sites that regulate the expression of p38Kb and are associated with resistance to oxidative stress. These findings reveal a novel mode of regulation for p38K genes and suggest that transcription may play as important a role in p38K-mediated stress responses as post-translational modifications.

scholarly journals The transcription factor TAL1 and miR-17-92 create a regulatory loop in hematopoiesis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Annekarin Meyer ◽  
Stefanie Herkt ◽  
Heike Kunze-Schumacher ◽  
Nicole Kohrs ◽  
Julia Ringleb ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Malignant Disease ◽  
Expression Patterns ◽  
Gene Activation ◽  
Erythroid Differentiation ◽  
Mature Micrornas ◽  
Gene Regulatory ◽  
Regulatory Loop ◽  
Transcriptional Complex

AbstractA network of gene regulatory factors such as transcription factors and microRNAs establish and maintain gene expression patterns during hematopoiesis. In this network, transcription factors regulate each other and are involved in regulatory loops with microRNAs. The microRNA cluster miR-17-92 is located within the MIR17HG gene and encodes six mature microRNAs. It is important for hematopoietic differentiation and plays a central role in malignant disease. However, the transcription factors downstream of miR-17-92 are largely elusive and the transcriptional regulation of miR-17-92 is not fully understood. Here we show that miR-17-92 forms a regulatory loop with the transcription factor TAL1. The miR-17-92 cluster inhibits expression of TAL1 and indirectly leads to decreased stability of the TAL1 transcriptional complex. We found that TAL1 and its heterodimerization partner E47 regulate miR-17-92 transcriptionally. Furthermore, miR-17-92 negatively influences erythroid differentiation, a process that depends on gene activation by the TAL1 complex. Our data give example of how transcription factor activity is fine-tuned during normal hematopoiesis. We postulate that disturbance of the regulatory loop between TAL1 and the miR-17-92 cluster could be an important step in cancer development and progression.

scholarly journals Identifying Transcription Regulatory Elements in the Human and Mouse Genomes Using Tissue-specific Gene Expression Profiles

2007 ◽  
Vol 4 (2) ◽  
pp. 1-23
Author(s):  
Amitava Karmaker ◽  
Kihoon Yoon ◽  
Mark Doderer ◽  
Russell Kruzelock ◽  
Stephen Kwek
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Binding Sites ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Tissue Specific Gene ◽  
Human And Mouse

Summary Revealing the complex interaction between trans- and cis-regulatory elements and identifying these potential binding sites are fundamental problems in understanding gene expression. The progresses in ChIP-chip technology facilitate identifying DNA sequences that are recognized by a specific transcription factor. However, protein-DNA binding is a necessary, but not sufficient, condition for transcription regulation. We need to demonstrate that their gene expression levels are correlated to further confirm regulatory relationship. Here, instead of using a linear correlation coefficient, we used a non-linear function that seems to better capture possible regulatory relationships. By analyzing tissue-specific gene expression profiles of human and mouse, we delineate a list of pairs of transcription factor and gene with highly correlated expression levels, which may have regulatory relationships. Using two closely-related species (human and mouse), we perform comparative genome analysis to cross-validate the quality of our prediction. Our findings are confirmed by matching publicly available TFBS databases (like TRANFAC and ConSite) and by reviewing biological literature. For example, according to our analysis, 80% and 85.71% of the targets genes associated with E2F5 and RELB transcription factors have the corresponding known binding sites. We also substantiated our results on some oncogenes with the biomedical literature. Moreover, we performed further analysis on them and found that BCR and DEK may be regulated by some common transcription factors. Similar results for BTG1, FCGR2B and LCK genes were also reported.

scholarly journals The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer–promoter communication

2021 ◽  
Author(s):  
Jonathan P. Karr ◽  
John J. Ferrie ◽  
Robert Tjian ◽  
Xavier Darzacq
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Regulatory Elements ◽  
Transcription Factor Activity ◽  
Factor Activity ◽  
New Model ◽  
Unresolved Question ◽  
Regulatory Information ◽  
Independent Mechanism ◽  
Coactivator P300

How distal cis-regulatory elements (e.g., enhancers) communicate with promoters remains an unresolved question of fundamental importance. Although transcription factors and cofactors are known to mediate this communication, the mechanism by which diffusible molecules relay regulatory information from one position to another along the chromosome is a biophysical puzzle—one that needs to be revisited in light of recent data that cannot easily fit into previous solutions. Here we propose a new model that diverges from the textbook enhancer–promoter looping paradigm and offer a synthesis of the literature to make a case for its plausibility, focusing on the coactivator p300.

scholarly journals The Histone Methyltransferase Setd8 Alters the Chromatin Landscape and Regulates the Expression of Key Transcription Factors during Erythroid Differentiation

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 2568-2568
Author(s):  
Jacquelyn Lillis ◽  
Jeffrey Malik ◽  
Tyler A Couch ◽  
Michael Getman ◽  
Laurie A. Steiner
Keyword(s):  
Transcription Factors ◽  
Progenitor Cells ◽  
Transcriptional Repression ◽  
Conflicts Of Interest ◽  
Large Fraction ◽  
Erythroid Differentiation ◽  
Cell Number ◽  
P Value ◽  
Histone H4 ◽  
And Control

Abstract Setd8 is the sole methyltransferase capable of mono-methylating histone H4, lysine 20. Setd8 mRNA is expressed ~10-fold higher in erythroid cells than any other cell type (biogps.org) and Setd8 protein levels increase in concert with GATA1 levels during erythroid differentiation of CD34+ HSPCs, suggesting Setd8 may have a role regulating the erythroid transcriptome. Consistent with this hypothesis, erythroid deletion of Setd8 is embryonic lethal by embryonic day 11.5 (E11.5) due to profound anemia and global transcriptomic analyses of sorted populations of E10.5 Sed8 null and control erythroblasts demonstrated a profound defect in transcriptional repression, with 340/345 differentially expressed genes (DEG) expressed at higher levels in the Setd8 null cells than controls (Malik Cell Reports 2017). Primitive erythroblasts mature and enucleate in a semi-synchronous manner in circulation. To better understand the function of Setd8 in regulating the erythroid transcriptome, we extended our transcriptomic analyses by performing RNA-seq in sorted E9.5 Sed8 null (EpoRCre+; Setd8 Δ/Δ) and control (EpoRCre+; Setd8 Δ/+) erythroblasts. The Setd8 null cells failed to repress 20/137 (15%) of the genes that are down regulated in control cells from E9.5 to E10.5. Although relatively few genes were impacted, those genes were enriched for the pathway "Oxidative Stress" (adjusted p-value 0.009) suggesting that Setd8 may regulate specific functions during terminal erythroid maturation. We next compared the DEG in Setd8 null erythroblasts to transcriptomic changes that occur as a cell transcends the hematopoietic hierarchy, gaining lineage specificity while suppressing the multi-lineage transcriptome (GSE14833). A large fraction, 105/345 (~30%), of genes up-regulated in Setd8 null erythroblasts, are also up-regulated in multipotent progenitors compared to proerythroblasts. In contrast, only 16/345 (5%) were also up-regulated in granulocyte-monocyte progenitors suggesting that Setd8 does not repress other lineage restricted signatures. Together, these results suggest that Setd8 regulates repression of the multi-lineage transcriptome during erythroid differentiation from multipotent progenitor cells. To gain insights into how Setd8 regulates the erythroid transcriptome, we performed ATAC-seq (Buenrostro Nature Methods 2013) on sorted populations of erythroblasts from E10.5 Sed8 null and control embryos. Cell number for the Setd8 null samples was limited due to anemia, with ~1000 cells used for each replicate. Setd8 and control replicates were aggregated and accessible regions were identified using MACS2. Regions more accessible in Setd8 null cells were identified by computing a log2 ratio between Setd8 null and control samples using deepTools bamCompare. In addition, we utilized ChIPmentation (Schmidl Nature Methods 2015) to assay H3K27me3 occupancy across the genome of WT E10.5 erythroblasts to identify regions of heterochromatin in maturing erythroblasts. Two replicates were performed using 2.5-5x105 cells per assay, and peak called was done using MACS2. A total of 157 genes were identified that had more accessible chromatin in Setd8 null cells and contained an enrichment for H3K27me3 in WT cells suggesting that these genes should be repressed during normal erythropoiesis. Among these were several DEG that were up-regulated in the Setd8 null cells including Hhex, Cd63, and Gata2. Genomic data integration also identified several additional transcriptional regulators that are active in earlier hematopoietic progenitors but typically silenced during erythroid differentiation including Notch1 and Cebpa. Pathway analysis of the 157 genes identified several stemness-related pathways including "Transcriptional regulation of pluripotent stem cells" and "OCT4, SOX2, NANOG repress genes related to differentiation" (adjusted p-values 0.005 and 0.008, respectively). The chromatin regions that were more accessible in the Setd8 null cells were enriched for the DNA binding motifs of the transcription factor ERG (p-value 1-257), SCL (p-value 1e-193), and NRF1 (p-value 1e-101). Taken together, these data suggest that Setd8 works in concert with erythroid transcription factors to repress the transcriptional network in stem and progenitor cells and establish appropriate patterns of gene expression during erythroid differentiation. Disclosures No relevant conflicts of interest to declare.

scholarly journals Predicting master transcription factors from pan-cancer expression data

2019 ◽  
Author(s):  
Jessica Reddy ◽  
Marcos A. S. Fonseca ◽  
Rosario I Corona ◽  
Robbin Nameki ◽  
Felipe Segato Dezem ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Regulatory Elements ◽  
Ca 125 ◽  
Tumor Type ◽  
Expression Data ◽  
Primary Tumors ◽  
Cancer Types ◽  
Tumor Types ◽  
Pan Cancer

The function of critical developmental regulators can be subverted by cancer cells to control expression of oncogenic transcriptional programs. These "master transcription factors" (MTFs) are often essential for cancer cell survival and represent vulnerabilities that can be exploited therapeutically. The current approaches to identify candidate MTFs examine super-enhancer associated transcription factor-encoding genes with high connectivity in network models. This relies on chromatin immunoprecipitation-sequencing (ChIP-seq) data, which is technically challenging to obtain from primary tumors, and is currently unavailable for many cancer types and clinically relevant subtypes. In contrast, gene expression data are more widely available, especially for rare tumors and subtypes where MTFs have yet to be discovered. We have developed a predictive algorithm called CaCTS (Cancer Core Transcription factor Specificity) to identify candidate MTFs using pan-cancer RNA-sequencing data from The Cancer Genome Atlas. The algorithm identified 273 candidate MTFs across 34 tumor types and recovered known tumor MTFs. We also made novel predictions, including for cancer types and subtypes for which MTFs have not yet been characterized. Clustering based on MTF predictions reproduced anatomic groupings of tumors that share 1-2 lineage-specific candidates, but also dictated functional groupings, such as a squamous group that comprised five tumor subtypes sharing 3 common MTFs. PAX8, SOX17, and MECOM were candidate factors in high-grade serous ovarian cancer (HGSOC), an aggressive tumor type where the core regulatory circuit is currently uncharacterized. PAX8, SOX17, and MECOM are required for cell viability and lie proximal to super-enhancers in HGSOC cells. ChIP-seq revealed that these factors co-occupy HGSOC regulatory elements globally and co-bind at critical gene loci including MUC16 (CA-125). Addiction to these factors was confirmed in studies using THZ1 to inhibit transcription in HGSOC cells, suggesting early down-regulation of these genes may be responsible for cytotoxic effects of THZ1 on HGSOC models. Identification of MTFs across 34 tumor types and 140 subtypes, especially for those with limited understanding of transcriptional drivers paves the way to therapeutic targeting of MTFs in a broad spectrum of cancers.

scholarly journals PML-Rara Drives Acute Promyelocytic Leukemia Genesis By Enhanceosome Depletion Leading to 3D Chromatin Reorganization

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 1554-1554
Author(s):  
Ping Wang ◽  
Zhonghui Tang ◽  
Hui Zhang ◽  
Yijun Ruan
Keyword(s):  
Transcription Factors ◽  
Conflicts Of Interest ◽  
Regulatory Elements ◽  
Myeloid Differentiation ◽  
Regulatory Interactions ◽  
3D Genome ◽  
Lineage Differentiation ◽  
Topology Changes ◽  
Distal Regulatory Elements ◽  
Target Promoters

Abstract Dynamic changes in chromatin looping structure are identified to reflect interactions of enhancers to target promoters. Such changes modulate hematopoietic lineage differentiation and are known to be mediated by some critical transcription factor, such as GATA1 and MYC. How chromatin topology changes in cancer such as leukemia is poorly understood on a global genomic view. Moreover, how oncogenic transcription factors, such as PML-RARA, AML1-ETO and others, manipulate gene regulation by globally altering the topology of chromatin, which contribute to leukemogenesis in acute myeloid leukemia (AML) remains to be described. Here we identified PML-RARA involved chromosomal interactions spanning hundreds of kilobases between promoters and distal regulatory elements. The RNAPII mediated chromatin connectivity between transcriptionally active genes and its distal regulatory elements were lost in the reorganized chromatin structure caused by PML-RARA, while the chromatin topological associated domain mediated by CTCF remained stable. PML-RARA mediated chromatin loops eliminated the occupancy of myeloid specific transcription factors (such as PU.1, IRF1 and CEBPB et al.) as well as coordinately general transcriptional factors (such as P300 and RNAPII) at the distal regulatory elements and respective promoters. Finally we show that interacting loci designated as super enhancers become depleted by PML-RARA looping to suppress myeloid differentiation regulomes. These distinct results based on 3D genome architecture uncover novel modes of how PML-RARA disrupts the regulome of myeloid differentiation to contribute to leukemogenesis. This study provides new insights and accessible tools to delineate the aberrant regulome originated from the chaotic gene regulatory interactions leading to cancer genesis. Disclosures No relevant conflicts of interest to declare.

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