Project description:X chromosome reactivation (XCR) occurs over a prolonged period during genome-wide reprogramming in female germ cells, initiating soon after primordial germ cell specification. The kinetics of XCRs remain poorly understood, as previous studies of XCR were based on a few genes. For a global appraisal of the regulation of XCR dynamics, we performed matched CUT&RUN for H3K27me3 and H2AK119ub1 on F1 female (XX(Xist∆)) germ cells at E13.5 and E16.5 stages during embryonic development.
Project description:CUT&RUN was performed for Sox2 on ex-vivo dissected visual thalamic nuclei from P0 mice, revealing context specific activity of Sox2 binding in differentiated neurons.
Project description:The Wnt/β-catenin signaling pathway plays crucial roles in nearly all parts of embryonic development and adult stem cell homeostasis. Its aberrant activation has been linked to many diseases such as developmental irregularities and various severe forms of cancer, with colorectal cancer (CRC) as a prime example. While much work has been dedicated to uncovering effective therapeutics to block oncogenic Wnt signaling, such interventions have not proven trivial because of the broad activity of Wnt throughout the adult body and the difficulty in finding suitable molecular targets. We have previously identified the developmental transcription factor TBX3 as a participant of the Wnt-mediated transcriptional regulation. Here we examine the genome-wide binding pattern of TBX3 in the human CRC cells lines HCT116 (25 replicates), DLD1 (2 replicates) and SW620 (2 replicates), by employing CUT&RUN (C&R) with Low-Volume and Urea (LoV-U; Zambanini et al., 2022).
Project description:STAT1 and IRF1 transcription factor enrichment by CUT&RUN. HeLa cells were primed with IFNγ for 24 hours, followed with IFNγ washout. After 48h, naïve and primed cells were induced by IFNγ for 1h and 3h. Cells were harvested at indicated time points and processed for CUT&RUN
Project description:We performed high numbers of replicates of CUT&RUN LoV-U against H3K4me3, β-catenin, and the negative control IgG in human colorectal cancer HCT116 cells over two independent rounds of experiments to discover the complete set of binding events.
Project description:H2A.Z-nucleosomes participate in both euchromatic and heterochromatic scenarios and it has proven difficult to reveal correlation of the disparate roles with the stability features imparted by H2A.Z on the nucleosomes. Using a robust in situ assay of nucleosome stability and cell lines expressing only engineered forms of the variant we show that a major fraction of H2A.Z is released from the nucleosomes of peripheral heterochromatin at unusually high salt concentration, an observation reproduced with reconstituted nucleosomes. In cells expressing H2A.Z lacking its C-terminal tail, or upon addition of the tail peptide to control nuclei, canonical stability features are restored, the peripheral heterochromatin becomes dispersed and an increase of nuclease sensitivity, mainly at lamina-associated domains, ensues. Binding of the peptide to nucleosomes was detected by fluorescence correlation spectrometry. The peptide, when introduced into live cells, also induces reorganization of chromatin and decreases MYC expression, offering means for targeted epigenetic modulation.
Project description:The epigenetic mechanisms established by histone modifications may affect the transcriptional silencing of HIV-1 and viral latency. A systematic epigenome profiling could be applicable to develop new epigenetic diagnostic markers for detecting HIV-1 latency. In this study, histone modification profiles of HIV-1 latency cell lines were compared with those of uninfected CD4+ T cell line. The HIV-1 latency gave rise to differential histone modification regions. The differential enrichment patterns helped us to define potential effector genes leading to the viral latency. The histone H3K4me3 and H3K9ac profiles were obtained from the HIV-1 latency cell lines (NCHA1, NCHA2, and ACH2) and control CD4+ T cell line (A3.01)
Project description:This experiment aimed at investigating how O-GlcNac occupancy sites are impacted by RNA Polymerase II removal upon doxycycline stimulation. These human colon adenocarcinoma DLD-1 cells express OsTIR and a cassette encoding mini-AID (mAID) and fluorescent protein mClover (mAID+mClover) at the initiation site of the endogenous Rpb1 gene locus (POLR2A) (Nagashima 2019).
Project description:We employ multi-step affinity purification followed by high-throughput sequencing to determine the location of EJC complexes assembled on a cellular transcriptome in Drosophila S2 cells, finding 6% of the intron-containing genes were not associated with EJCs, and within genes with multiple introns, only specific exon-exon junctions assembled an EJC. RIP-Seq, 3 samples
Project description:The experiment aim to show where COUPTFII is binding in Human cells as HUDEP21/2. The cells do not naturally express COUPTFII so we overexpressed it. We do then a comparison between the cells in which is not expressed and the on in which it is (and we compare the binding profile in HIDEP1 and HUDEP2)