A genome-wide screen reveals new regulators of the 2-cell-like cell state Published: June, 2022 Abstract:
In mammals, only the zygote and blastomeres of the early embryo are fully totipotent. This totipotency is mirrored in vitro by mouse "2-cell-like cells" (2CLCs), which appear at low frequency in cultures of Embryonic Stem cells (ESCs). Because tot... Read more »
Comprehensive characterization of the epigenetic landscape in Multiple Myeloma Published: January, 2022 Abstract:
Background: Human multiple myeloma (MM) cell lines (HMCLs) have been widely used to understand themolecular processes that drive MM biology. Epigenetic modifications are involved in MM development,progression, and drug resistance. A comprehensive ... Read more »
Comprehensive characterization of the epigenetic landscape in Multiple
Myeloma Published: January, 2022 Abstract:
Background: Human multiple myeloma (MM) cell lines (HMCLs) have
been widely used to understand the molecular processes that drive MM
biology. Epigenetic modifications are involved in MM development,
progression, and drug resistance. A comprehensiv... Read more »
A Tumor Suppressor Enhancer of PTEN in T-cell development and leukemia Published: January, 2021 Abstract:
Long-range oncogenic enhancers play an important role in cancer. Yet, whether similar regulation of tumor suppressor genes is relevant remains unclear. Loss of expression of PTEN is associated with the pathogenesis of various cancers, including T-... Read more »
Histone H3.3G34-Mutant Interneuron Progenitors Co-opt PDGFRA for Gliomagenesis. Published: December, 2020 Abstract:
Histone H3.3 glycine 34 to arginine/valine (G34R/V) mutations drive deadly gliomas and show exquisite regional and temporal specificity, suggesting a developmental context permissive to their effects. Here we show that 50\% of G34R/V tumors (n&nbs... Read more »
SMaSH: Sample matching using SNPs in humans. Published: December, 2019 Abstract:
BACKGROUND: Inadvertent sample swaps are a real threat to data quality in any medium to large scale omics studies. While matches between samples from the same individual can in principle be identified from a few well characterized single nucleotid... Read more »
Methionine metabolism in health and cancer: a nexus of diet and precisionmedicine. Published: November, 2019 Abstract:
Methionine uptake and metabolism is involved in a host of cellular functions including methylation reactions, redox maintenance, polyamine synthesis and coupling to folate metabolism, thus coordinating nucleotide and redox status. Each of these fu... Read more »
Human mitochondrial DNA is extensively methylated in a non-CpG context Published: August, 2019 Abstract:
Mitochondrial dysfunction plays critical roles in cancer development and related therapeutic response; however, exact molecular mechanisms remain unclear. Recently, alongside the discovery of mitochondrial-specific DNA methyltransferases, global a... Read more »
Development and epigenetic plasticity of murine Müller glia. Published: July, 2019 Abstract:
The ability to regenerate the entire retina and restore lost sight after injury is found in some species and relies mostly on the epigenetic plasticity of Müller glia. To understand the role of mammalian Müller glia as a source of progen... Read more »
Guidelines for optimized gene knockout using CRISPR/Cas9 Published: May, 2019 Abstract:
CRISPR/Cas9 technology has evolved as the most powerful approach to generate genetic models both for fundamental and preclinical research. Despite its apparent simplicity, the outcome of a genome-editing experiment can be substantially impacted by... Read more »
TIP60: an actor in acetylation of H3K4 and tumor development in breast cancer. Published: November, 2018 Abstract:
AIM: The acetyltransferase TIP60 is reported to be downregulated in several cancers, in particular breast cancer, but the molecular mechanisms resulting from its alteration are still unclear. MATERIALS & METHODS: In breast tumors, H3K4ac enric... Read more »
A new metabolic gene signature in prostate cancer regulated by JMJD3 and EZH2. Published: May, 2018 Abstract:
Histone methylation is essential for gene expression control. Trimethylated lysine 27 of histone 3 (H3K27me3) is controlled by the balance between the activities of JMJD3 demethylase and EZH2 methyltransferase. This epigenetic mark has been shown ... Read more »
Molecular Signatures of Regression of the Canine Transmissible Venereal Tumor. Published: April, 2018 Abstract:
The canine transmissible venereal tumor (CTVT) is a clonally transmissible cancer that regresses spontaneously or after treatment with vincristine, but we know little about the regression mechanisms. We performed global transcriptional, methylatio... Read more »
The histone code reader Spin1 controls skeletal muscle development Published: November, 2017 Abstract:
While several studies correlated increased expression of the histone code reader Spin1 with tumor formation or growth, little is known about physiological functions of the protein. We generated Spin1M5 mice with ablation of Spin1 in myoblast precu... Read more »
FOXF1 transcription factor promotes lung regeneration after partial pneumonectomy Published: September, 2017 Abstract:
FOXF1, a member of the forkhead box family of transcription factors, has been previously shown to be critical for lung development, homeostasis, and injury responses. However, the role of FOXF1 in lung regeneration is unknown. Herein, we performed... Read more »
Global analysis of H3K27me3 as an epigenetic marker in prostate cancer progression Published: April, 2017 Abstract:
BACKGROUND:
H3K27me3 histone marks shape the inhibition of gene transcription. In prostate cancer, the deregulation of H3K27me3 marks might play a role in prostate tumor progression.
METHODS:
We investigated genome-wide H3K27me3 histone methy... Read more »
Crebbp loss cooperates with Bcl2 over-expression to promote lymphoma in mice Published: March, 2017 Abstract:
CREBBP is targeted by inactivating mutations in follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL). Here, we provide evidence from transgenic mouse models that Crebbp deletion results in deficits in B-cell development and can coope... Read more »
Rapid Recall Ability of Memory T cells is Encoded in their Epigenome Published: January, 2017 Abstract:
Even though T-cell receptor (TCR) stimulation together with co-stimulation is sufficient for the activation of both naïve and memory T cells, the memory cells are capable of producing lineage specific cytokines much more rapidly than the na&i... Read more »
Genome-wide epigenomic profiling for biomarker discovery Published: November, 2016 Abstract:
A myriad of diseases is caused or characterized by alteration of epigenetic patterns, including changes in DNA methylation, post-translational histone modifications, or chromatin structure. These changes of the epigenome represent a highly interes... Read more »
Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells Published: November, 2016 Abstract:
Characterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human genetics and medicine. We carried out high-resolution genetic, epigenetic, and transcriptomic profiling in thr... Read more »
RNA polymerase II promoter-proximal pausing in mammalian long non-coding genes Published: August, 2016 Abstract:
Mammalian genomes encode a large number of non-coding RNAs (ncRNAs) that greatly exceed mRNA genes. While the physiological and pathological roles of ncRNAs have been increasingly understood, the mechanisms of regulation of ncRNA expression are le... Read more »
Epigenetic dynamics of monocyte-to-macrophage differentiation Published: July, 2016 Abstract:
BACKGROUND:
Monocyte-to-macrophage differentiation involves major biochemical and structural changes. In order to elucidate the role of gene regulatory changes during this process, we used high-throughput sequencing to analyze the complete tran... Read more »
Characterization of the replication timing program of 6 human model cell lines Published: July, 2016 Abstract:
During the S-phase, the DNA replication process is finely orchestrated and regulated by two programs: the spatial program that determines where replication will start in the genome (Cadoret et al. (2008 Oct 14), Cayrou et al. (2011 Sep), Picard et... Read more »
Genome-wide non-CpG methylation of the host genome during M. tuberculosis infection Published: April, 2016 Abstract:
A mammalian cell utilizes DNA methylation to modulate gene expression in response to environmental changes during development and differentiation. Aberrant DNA methylation changes as a correlate to diseased states like cancer, neurodegenerative co... Read more »
Standardizing chromatin research: a simple and universal method for ChIP-seq Published: December, 2015 Abstract:
Here we demonstrate that harmonization of ChIP-seq workflows across cell types and conditions is possible when obtaining chromatin from properly isolated nuclei. We established an ultrasound-based nuclei extraction method (Nuclei Extraction b... Read more »
Loss of BAP1 function leads to EZH2-dependent transformation Published: October, 2015 Abstract:
The tumor suppressors BAP1 and ASXL1 interact to form a polycomb deubiquitinase complex that removes monoubiquitin from histone H2A lysine 119 (H2AK119Ub). However, BAP1 and ASXL1 are mutated in distinct cancer types, consistent with independent r... Read more »
Bacterial Infection Remodels the DNA Methylation Landscape of Human Dendritic Cells Published: March, 2015 Abstract:
DNA methylation is thought to be robust to environmental perturbations on a short time scale. Here, we challenge that view by demonstrating that the infection of human dendritic cells (DCs) with a pathogenic bacteria is associated with rapid chang... Read more »
Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Published: July, 2014 Abstract:
Alternative splicing (AS) of pre-mRNA represents a major mechanism underlying increased transcriptome and proteome complexity. Here, we show that the nuclear speckle RNA-binding protein (NSR) and the AS competitor long noncoding RNA (or ASCO-lncRN... Read more »
