scholarly journals Functional and genetic determinants of mutation rate variability in regulatory elements of cancer genomes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Christian A. Lee ◽  
Diala Abd-Rabbo ◽  
Jüri Reimand
Keyword(s):  
Binding Sites ◽  
Mutation Frequency ◽  
Scale Effects ◽  
Regulatory Elements ◽  
Ctcf Binding ◽  
Driver Gene ◽  
Open Chromatin ◽  
Genetic Determinants ◽  
Cancer Genomes ◽  
Mutational Processes

Abstract Background Cancer genomes are shaped by mutational processes with complex spatial variation at multiple scales. Entire classes of regulatory elements are affected by local variations in mutation frequency. However, the underlying mechanisms with functional and genetic determinants remain poorly understood. Results We characterise the mutational landscape of 1.3 million gene-regulatory and chromatin architectural elements in 2419 whole cancer genomes with transcriptional and pathway activity, functional conservation and recurrent driver events. We develop RM2, a statistical model that quantifies mutational enrichment or depletion in classes of genomic elements through genetic, trinucleotide and megabase-scale effects. We report a map of localised mutational processes affecting CTCF binding sites, transcription start sites (TSS) and tissue-specific open-chromatin regions. Increased mutation frequency in TSSs associates with mRNA abundance in most cancer types, while open-chromatin regions are generally enriched in mutations. We identify ~ 10,000 CTCF binding sites with core DNA motifs and constitutive binding in 66 cell types that represent focal points of mutagenesis. We detect site-specific mutational signature enrichments, such as SBS40 in open-chromatin regions in prostate cancer and SBS17b in CTCF binding sites in gastrointestinal cancers. Candidate drivers of localised mutagenesis are also apparent: BRAF mutations associate with mutational enrichments at CTCF binding sites in melanoma, and ARID1A mutations with TSS-specific mutagenesis in pancreatic cancer. Conclusions Our method and catalogue of localised mutational processes provide novel perspectives to cancer genome evolution, mutagenesis, DNA repair and driver gene discovery. The functional and genetic correlates of mutational processes suggest mechanistic hypotheses for future studies.

scholarly journals Functional and genetic determinants of mutation rate variability in regulatory elements of cancer genomes

2020 ◽  
Author(s):  
Christian A. Lee ◽  
Diala Abd-Rabbo ◽  
Jüri Reimand
Keyword(s):  
Binding Sites ◽  
Scale Effects ◽  
Regulatory Elements ◽  
Ctcf Binding ◽  
Mutation Rates ◽  
Driver Gene ◽  
Open Chromatin ◽  
Cancer Driver ◽  
Cancer Genomes ◽  
Mutational Processes

Localised variation of somatic mutation rates affects diverse functional sequence elements in cancer genomes through poorly understood mutational processes. Here, we characterise the mutational landscape of 640,000 gene regulatory and chromatin architectural elements in 2,421 whole cancer genomes using our new statistical model RM2. This method quantifies differential mutation rates and signatures in classes of genomic elements via genetic, trinucleotide and megabase-scale effects. We report a detailed map of localised mutational processes affecting CTCF binding sites, transcription start sites (TSS) and cancer-specific open-chromatin regions. This includes a pan-cancer indel depletion in open-chromatin sites, a TSS-specific mutational process correlated with mRNA abundance in core cellular and cancer-associated processes, a subset of hypermutated, constitutively active CTCF binding sites involved in chromatin architectural interactions, and an enrichment of signature SBS17b in CTCF sites in gastrointestinal cancers. We also detect genetic driver alterations potentially underlying localised mutation rates, including RAD21 amplifications and BRAF mutations associating with mutagenesis of CTCF binding sites, and SDHA amplifications indicative of frequent lung cancer mutations in open-chromatin sites. Our framework and the catalogue of localised mutational processes provide novel perspectives to cancer genome evolution and its implications for oncogenesis, tumor heterogeneity and cancer driver gene discovery.

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.

scholarly journals Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome

2021 ◽  
Author(s):  
Vera B Kaiser ◽  
Lana Talmane ◽  
Yatendra Kumar ◽  
Fiona Semple ◽  
Marie MacLennan ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Meiotic Recombination ◽  
Binding Sites ◽  
Evolutionary Process ◽  
Mutational Bias ◽  
Open Chromatin ◽  
Structural Variant ◽  
Regulatory Architecture ◽  
Mutational Processes ◽  
Regulatory Sites

Mutation in the germline is the ultimate source of genetic variation, but little is known about the influence of germline chromatin structure on mutational processes. Using ATAC-seq, we profile the open chromatin landscape of human spermatogonia, the most proliferative cell-type of the germline, identifying transcription factor binding sites (TFBSs) and PRDM9-binding sites, a subset of which will initiate meiotic recombination. We observe an increase in rare structural variant (SV) breakpoints at PRDM9-bound sites, implicating meiotic recombination in the generation of structural variation. Many germline TFBSs, such as NRF, are also associated with increased rates of SV breakpoints, apparently independent of recombination. Singleton short insertions (>=5 bp) are highly enriched at TFBSs, particularly at sites bound by testis active TFs, and their rates correlate with those of structural variant breakpoints. Short insertions often duplicate the TFBS motif, leading to clustering of motif sites near regulatory regions in this male-driven evolutionary process. Increased mutation loads at germline TFBSs disproportionately affect neural enhancers with activity in spermatogonia, potentially altering neurodevelopmental regulatory architecture. Local chromatin structure in spermatogonia is thus pervasive in shaping both evolution and disease.

scholarly journals Genetic determinants of chromatin reveal prostate cancer risk mediated by context-dependent gene regulation

2021 ◽  
Author(s):  
Sylvan C Baca ◽  
Cassandra Singler ◽  
Soumya Zacharia ◽  
Ji-Heui Seo ◽  
Tunc Morova ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Steady State ◽  
Binding Sites ◽  
Association Studies ◽  
Prostate Cancer Risk ◽  
Regulatory Elements ◽  
Genome Wide Association Studies ◽  
Genetic Determinants ◽  
Genome Wide ◽  
Context Dependent

Methods that link genetic variation to steady-state gene expression levels, such as expression quantitative trait loci (eQTLs), are widely used to functionally annotate trait-associated variants, but they are limited in identifying context-dependent effects on transcription. To address this challenge, we developed the cistrome-wide association study (CWAS), a framework for nominating variants that impact traits through their effects on chromatin state. CWAS associates the genetic determinants of cistromes (e.g., the genome-wide profiles of transcription factor binding sites or histone modifications) with traits using summary statistics from genome-wide association studies (GWAS). We performed CWASs of prostate cancer and androgen-related traits, using a reference panel of 307 prostate cistromes from 165 individuals. CWAS nominated susceptibility regulatory elements or androgen receptor (AR) binding sites at 52 out of 98 known prostate cancer GWAS loci and implicated an additional 17 novel loci. We functionally validated a subset of our results using CRISPRi and in vitro reporter assays. At 28 of the 52 risk loci, CWAS identified regulatory mechanisms that are not observable via eQTLs, implicating genes with complex or context-specific regulation that are overlooked by current approaches that relying on steady-state transcript measurements. CWAS genes include transcription factors that govern prostate development such as NKX3-1, HOXB13, GATA2, and KLF5. Moreover, CWAS boosts discovery power in modestly sized GWAS, identifying novel genetic associations mediated through AR binding for androgen-related phenotypes, including resistance to prostate cancer therapy. CWAS is a powerful and biologically interpretable paradigm for studying variants that influence traits by affecting context-dependent transcriptional regulation.

scholarly journals Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome

2021 ◽  
Author(s):  
Vera B. Kaiser ◽  
Lana Talmane ◽  
Yatendra Kumar ◽  
Fiona Semple ◽  
Marie MacLennan ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Meiotic Recombination ◽  
Binding Sites ◽  
Evolutionary Process ◽  
Mutational Bias ◽  
Open Chromatin ◽  
Structural Variant ◽  
Regulatory Architecture ◽  
Mutational Processes ◽  
Regulatory Sites

Mutation in the germline is the ultimate source of genetic variation, but little is known about the influence of germline chromatin structure on mutational processes. Using ATAC-seq, we profile the open chromatin landscape of human spermatogonia, the most proliferative cell type of the germline, identifying transcription factor binding sites (TFBSs) and PRDM9 binding sites, a subset of which will initiate meiotic recombination. We observe an increase in rare structural variant (SV) breakpoints at PRDM9-bound sites, implicating meiotic recombination in the generation of structural variation. Many germline TFBSs, such as NRF1, are also associated with increased rates of SV breakpoints, apparently independent of recombination. Singleton short insertions (≥5 bp) are highly enriched at TFBSs, particularly at sites bound by testis active TFs, and their rates correlate with those of structural variant breakpoints. Short insertions often duplicate the TFBS motif, leading to clustering of motif sites near regulatory regions in this male-driven evolutionary process. Increased mutation loads at germline TFBSs disproportionately affect neural enhancers with activity in spermatogonia, potentially altering neurodevelopmental regulatory architecture. Local chromatin structure in spermatogonia is thus pervasive in shaping both evolution and disease.

scholarly journals Dynamic CTCF binding directly mediates interactions among cis-regulatory elements essential for hematopoiesis

Blood ◽  
2020 ◽  
Author(s):  
Qian Qi ◽  
Li Cheng ◽  
Xing Tang ◽  
Yanghua He ◽  
Yichao Li ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Blood Cell ◽  
Binding Sites ◽  
Specific Binding ◽  
Regulatory Elements ◽  
Cell Development ◽  
Ctcf Binding ◽  
Cell Type ◽  
Dynamic Cell ◽  
Cell Type Specific

While constitutive CTCF-binding sites are needed to maintain relatively invariant chromatin structures, such as topologically associating domains, the precise roles of CTCF to control cell type-specific transcriptional regulation remain poorly explored. We examined CTCF occupancy in different types of primary blood cells derived from the same donor to elucidate a new role for CTCF in gene regulation during blood cell development. We identified dynamic, cell type-specific binding sites for CTCF that colocalize with lineage-specific transcription factors. These dynamic sites are enriched for single nucleotide polymorphisms that are associated with blood cell traits in different linages, and they coincide with the key regulatory elements governing hematopoiesis. CRISPR/Cas9-based perturbation experiments demonstrated that these dynamic CTCF-binding sites play a critical role in red blood cell development. Furthermore, precise deletion of CTCF-binding motifs in dynamic sites abolished interactions of erythroid genes, such as RBM38, with their associated enhancers and led to abnormal erythropoiesis. These results suggest a novel, cell type-specific function for CTCF in which it may serve to facilitate interaction of distal regulatory emblements with target promoters. Our study of the dynamic, cell type-specific binding and function of CTCF provides new insights into transcriptional regulation during hematopoiesis.

scholarly journals Deciphering essential cistromes using genome-wide CRISPR screens

2019 ◽  
Vol 116 (50) ◽  
pp. 25186-25195 ◽  
Author(s):  
Teng Fei ◽  
Wei Li ◽  
Jingyu Peng ◽  
Tengfei Xiao ◽  
Chen-Hao Chen ◽  
...  
Keyword(s):  
Predictive Models ◽  
Binding Sites ◽  
Regulatory Elements ◽  
High Accuracy ◽  
Essential Genes ◽  
Ctcf Binding ◽  
Prostate Cancer Cells ◽  
Regression Methods ◽  
Genome Wide ◽  
Breast And Prostate Cancer

Although millions of transcription factor binding sites, or cistromes, have been identified across the human genome, defining which of these sites is functional in a given condition remains challenging. Using CRISPR/Cas9 knockout screens and gene essentiality or fitness as the readout, we systematically investigated the essentiality of over 10,000 FOXA1 and CTCF binding sites in breast and prostate cancer cells. We found that essential FOXA1 binding sites act as enhancers to orchestrate the expression of nearby essential genes through the binding of lineage-specific transcription factors. In contrast, CRISPR screens of the CTCF cistrome revealed 2 classes of essential binding sites. The first class of essential CTCF binding sites act like FOXA1 sites as enhancers to regulate the expression of nearby essential genes, while a second class of essential CTCF binding sites was identified at topologically associated domain (TAD) boundaries and display distinct characteristics. Using regression methods trained on our screening data and public epigenetic profiles, we developed a model to predict essential cis-elements with high accuracy. The model for FOXA1 essentiality correctly predicts noncoding variants associated with cancer risk and progression. Taken together, CRISPR screens of cis-regulatory elements can define the essential cistrome of a given factor and can inform the development of predictive models of cistrome function.

scholarly journals A CTCF-Dependent Silencer Located in the Differentially Methylated Area May Regulate Expression of a Housekeeping Gene Overlapping a Tissue-Specific Gene Domain

2006 ◽  
Vol 26 (5) ◽  
pp. 1589-1597 ◽  
Author(s):  
Denis Klochkov ◽  
Héctor Rincón-Arano ◽  
Elena S. Ioudinkova ◽  
Viviana Valadez-Graham ◽  
Alexey Gavrilov ◽  
...  
Keyword(s):  
Gene Transcription ◽  
Globin Gene ◽  
Housekeeping Gene ◽  
Regulatory Elements ◽  
Ctcf Binding ◽  
Specific Gene ◽  
Open Chromatin ◽  
Erythroid Cells ◽  
Tissue Specific ◽  
In Erythroid Cells

ABSTRACT The tissue-specific chicken α-globin gene domain represents one of the paradigms, in terms of its constitutively open chromatin conformation and the location of several regulatory elements within the neighboring housekeeping gene. Here, we show that an 0.2-kb DNA fragment located ∼4 kb upstream to the chicken α-globin gene cluster contains a binding site for the multifunctional protein factor CTCF and possesses silencer activity which depends on CTCF binding, as demonstrated by site-directed mutagenesis of the CTCF recognition sequence. CTCF was found to be associated with this recognition site in erythroid cells but not in lymphoid cells where the site is methylated. A functional promoter directing the transcription of the apparently housekeeping ggPRX gene was found 120 bp from the CTCF-dependent silencer. The data are discussed in terms of the hypothesis that the CTCF-dependent silencer stabilizes the level of ggPRX gene transcription in erythroid cells where the promoter of this gene may be influenced by positive cis-regulatory signals activating α-globin gene transcription.

scholarly journals DNA hypohydroxymethylation in pediatric central nervous system tumors is associated with CTCF binding sites and reduced survival

2020 ◽  
Author(s):  
Nasim Azizgolshani ◽  
Curtis L. Petersen ◽  
Youdinghuan Chen ◽  
Lucas A. Salas ◽  
Laurent Perreard ◽  
...  
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Binding Sites ◽  
Regulatory Elements ◽  
Ctcf Binding ◽  
Central Nervous System Tumors ◽  
Nervous System Tumors ◽  
Model Based Clustering ◽  
Tumor Subtypes ◽  
Increased Risk

AbstractNucleotide-specific 5-hydroxymethylcytosine (5hmC) remains understudied in pediatric central nervous system tumors. We measured genome-scale 5hmC in glioma, ependymoma, and embryonal tumors from children, as well as control pediatric brain tissues using oxidative and bisulfite treatments. Tumor 5hmC localized to regulatory elements crucial to cell identity, including transcription factor binding sites and super-enhancers. A linear model tested the CpG-specific differences in 5hmC between tumor and non-tumor samples, as well as between tumor subtypes. Compared to non-tumor samples, tumors were hypohydroxymethylated across the epigenome. Differentially hydroxymethylated loci among tumor subtypes tended to be hypermethylated and disproportionally found in CTCF binding sites and genes related to posttranscriptional RNA regulation, such as DICER1. Model-based clustering results indicated that patients with low 5hmC patterns have poorer overall survival and increased risk of recurrence. These results have implications for emerging molecular neuropathology classification approaches and epigenetic therapeutic strategies in childhood brain tumors.

scholarly journals Genetic determinants of chromatin reveal prostate cancer risk mediated by context-dependent gene regulation

2021 ◽  
Author(s):  
Matthew Freedman ◽  
Sylvan Baca ◽  
Cassandra Singler ◽  
Soumya Zacharia ◽  
Ji-Heui Seo ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Steady State ◽  
Binding Sites ◽  
Association Studies ◽  
Prostate Cancer Risk ◽  
Regulatory Elements ◽  
Genome Wide Association Studies ◽  
Genetic Determinants ◽  
Genome Wide ◽  
Context Dependent

Abstract Methods that link genetic variation to steady-state gene expression levels, such as expression quantitative trait loci (eQTLs), are widely used to functionally annotate trait-associated variants, but they are limited in identifying context-dependent effects on transcription. To address this challenge, we developed the cistrome-wide association study (CWAS), a framework for nominating variants that impact traits through their effects on chromatin state. CWAS associates the genetic determinants of cistromes (e.g., the genome-wide profiles of transcription factor binding sites or histone modifications) with traits using summary statistics from genome-wide association studies (GWAS). We performed CWASs of prostate cancer and androgen-related traits, using a reference panel of 307 prostate cistromes from 165 individuals. CWAS nominated susceptibility regulatory elements or androgen receptor (AR) binding sites at 52 out of 98 known prostate cancer GWAS loci and implicated an additional 17 novel loci. We functionally validated a subset of our results using CRISPRi and in vitro reporter assays. At 28 of the 52 risk loci, CWAS identified regulatory mechanisms that are not observable via eQTLs, implicating genes with complex or context-specific regulation that are overlooked by current approaches that relying on steady-state transcript measurements. CWAS genes include transcription factors that govern prostate development such as NKX3-1, HOXB13, GATA2, and KLF5. Moreover, CWAS boosts discovery power in modestly sized GWAS, identifying novel genetic associations mediated through AR binding for androgen-related phenotypes, including resistance to prostate cancer therapy. CWAS is a powerful and biologically interpretable paradigm for studying variants that influence traits by affecting context-dependent transcriptional regulation.

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