Özgen Deniz
YOU?
Author Swipe
View article: DNA methylation cooperates with genomic alterations during non-small cell lung cancer evolution
DNA methylation cooperates with genomic alterations during non-small cell lung cancer evolution Open
Aberrant DNA methylation has been described in nearly all human cancers, yet its interplay with genomic alterations during tumor evolution is poorly understood. To explore this, we performed reduced representation bisulfite sequencing on 2…
View article: Reawakening retrotransposons: immune modulation in normal and malignant hematopoiesis
Reawakening retrotransposons: immune modulation in normal and malignant hematopoiesis Open
Retrotransposons are mobile repetitive elements that constitute around 43% of the human genome. Normally silenced through epigenetic mechanisms, retrotransposons can become reactivated in response to various stimuli, producing immunogenic …
View article: Ph+B-ALL is defined by BCR::ABL1-induced enhancer reprogramming and hypersensitivity to enhancer-targeting drugs
Ph+B-ALL is defined by BCR::ABL1-induced enhancer reprogramming and hypersensitivity to enhancer-targeting drugs Open
Cancer is driven by genomic lesions and malignancy-promoting transcriptional programs. In blood cancers, both are often directly linked as lesions frequently affect transcription factor (TF) or epigenetic co-factor-encoding genes. Transcri…
View article: Transposable elements as genome regulators in normal and malignant haematopoiesis
Transposable elements as genome regulators in normal and malignant haematopoiesis Open
Transposable elements (TEs) constitute over half of the human genome and have played a profound role in genome evolution. While most TEs have lost the ability to transpose, many retain functional elements that serve as drivers of genome in…
View article: DEK::NUP214 acts as an XPO1-dependent transcriptional activator of essential leukemia genes
DEK::NUP214 acts as an XPO1-dependent transcriptional activator of essential leukemia genes Open
The t(6;9)(p22.3;q34.1) translocation/DEK::NUP214 fusion protein defines a distinct subgroup of younger AML patients classified as a separate disease entity by the World Health Organization. DEK is a nuclear factor with multifunctional rol…
View article: Unraveling BCR::ABL1-driven enhancer activation and transcriptional reprogramming in Ph B-ALL
Unraveling BCR::ABL1-driven enhancer activation and transcriptional reprogramming in Ph B-ALL Open
B-lineage acute-lymphoblastic leukemia (B-ALL) is driven by genomic lesions and distinct transcriptional programs. Both are often directly linked as most B-ALLs are caused by genetic lesions at transcription factor (TF)-encoding genes. TFs…
View article: Transposable Elements Shape Stemness in Normal and Leukemic Hematopoiesis
Transposable Elements Shape Stemness in Normal and Leukemic Hematopoiesis Open
Despite most acute myeloid leukemia (AML) patients achieving complete remission after induction chemotherapy, two-thirds will relapse with fatal disease within five years. AML is organized as a cellular hierarchy sustained by leukemia stem…
View article: TET2 Regulates the Neuroinflammatory Response in Microglia
TET2 Regulates the Neuroinflammatory Response in Microglia Open
Epigenomic mechanisms regulate distinct aspects of the inflammatory response in immune cells. Despite the central role for microglia in neuroinflammation and neurodegeneration, little is known about their epigenomic regulation of the infla…
View article: Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells
Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells Open
Transposable elements (TEs) are thought to have helped establish gene regulatory networks. Both the embryonic and extraembryonic lineages of the early mouse embryo have seemingly co-opted TEs as enhancers, but there is little evidence that…
View article: Author response: Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells
Author response: Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells Open
Article Figures and data Abstract eLife digest Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Transposable elements (TEs) a…
View article: Author response: Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells
Author response: Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells Open
Article Figures and data Abstract eLife digest Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Transposable elements (TEs) a…
View article: TET2 regulates the neuroinflammatory response in microglia
TET2 regulates the neuroinflammatory response in microglia Open
Summary Epigenetic mechanisms regulate distinct aspects of the inflammatory response in various immune cell types. Despite the central role for microglia, the resident macrophages of the brain, in neuroinflammation and neurodegeneration li…
View article: Functional evaluation of transposable elements as transcriptional enhancers in mouse embryonic and trophoblast stem cells
Functional evaluation of transposable elements as transcriptional enhancers in mouse embryonic and trophoblast stem cells Open
The recurrent invasion and expansion of transposable elements (TEs) throughout evolution brought with it a vast array of coding and non-coding sequences that can serve as substrates for natural selection. Namely, TEs are thought to have co…
View article: SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells
SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells Open
Our results demonstrate a novel and unexpected role for SETDB1 in protecting IAPs from TET2-dependent histone arginine demethylation.
View article: SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells
SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells Open
Background Endogenous retroviruses (ERVs), which are responsible for 10% of spontaneous mouse mutations, are kept under control via several epigenetic mechanisms. The H3K9 histone methyltransferase SETDB1 is essential for ERV repression in…