Project description:Single-cell RNA sequencing offers snapshots of whole transcriptomes but obscures the temporal RNA dynamics. Here we present single-cell metabolically labeled new RNA tagging sequencing (scNT-Seq), a method for massively parallel analysis of newly-transcribed and pre-existing mRNAs from the same cell. This droplet microfluidics-based method enables high-throughput chemical conversion on barcoded beads, efficiently marking newly-transcribed mRNAs with T-to-C substitutions. With scNT-Seq, we jointly profiled new and old transcriptomes in ~55,000 single cells. These data revealed time-resolved transcription factor activities and cell state trajectories at single-cell level in response to neuronal activation. We further determined rates of RNA biogenesis and decay to uncover RNA regulatory strategies during stepwise conversion between pluripotent and rare totipotent two-cell-embryo-like (2C-like) stem cell states. Finally, integrating scNT-Seq with genetic perturbation identifies DNA methylcytosine dioxygenases as an epigenetic barrier into 2C-like cell state. Time-resolved single-cell transcriptomic analysis thus opens new lines of inquiry regarding cell-type-specific RNA regulatory mechanisms.
Project description:This SuperSeries is composed of the following subset Series: GSE12019: Fine-scale mapping of copy-number alterations with massively parallel sequencing GSE13372: High-resolution mapping of copy-number alterations with massively parallel sequencing Refer to individual Series
Project description:Somatic cell nuclear transfer (SCNT) enables gaining of totipotency by reprogramming nuclei of terminally differentiated donor cell. Recent studies have clearly demonstrated that intervention of epigenetic networks can significantly elevate both in vitro and in vivo development potential of NT embryos. Specifically, trichostatin A (TSA), a kind of histone deacetylase inhibitors (HDACi), was proved to functionally works during cloning in various mammal systems. However, how it modulates histone acylation lacks careful illustration. Here, we systematically evaluate the effect and limitation of TSA during SCNT embryo development by generating genome-wide H3K9ac maps. In addition, a Dux-dependent 2-cell (2C) activation deficiency is observed in SCNT embryos as compared with their natural fertilized counterparts. Strikingly, a refined Dux supplement can successfully assist SCNT embryos in overcoming the 2C activation defect and further promotes the overall cloning efficiency. Together, our study for the first time reveals the regulation mechanism of histone marker H3K9ac in SCNT and provides the new insight of Dux during embryogenesis.
Project description:The activity of enhancers with dynamic P300 binding or mutagenized nuclear receptor motifs was assessed by massively parallel reporter assay during CM maturation.
Project description:A massively parallel reporter assay, MPRA, was conducted in mouse embryonic stem cells (mESC). Synthetic cis-regulatory elements comprised of binding sites for pluripotency transcription factors and genomic sequences with comparable binding sites configurations were used in the assay. Transcripts of dsRed were amplified via PCR from the end of the transcript to sequence 3' UTR barcodes.
Project description:Chimeric antigen receptor T cells (CAR-Ts) are transformative cellular therapies; however, current forms of CAR-T face multiple major hurdles. These include antigen loss, tumor microenvironment suppression, trafficking, proliferation, toxicity, and persistence. An efficient way to overcome these challenges is to engineer thousands of different CAR-T variants, and systematically select the best ones. To achieve this, we develop CLASH, a versatile platform that enables high-efficiency massively parallel CAR-T engineering. In CLASH, pooled AAVs mediate simultaneous gene editing and precise CAR knock-in via massively parallel homology-directed repair (HDR). Such library-scale HDR events produce a pool of stably integrated CAR-T variants each with targeted immune gene editing. In vitro or in vivo CLASH experiments using human CD8 and CD4 T cells subject the CAR-T pools to long-term co-culture or animal models of cancer, enabling unbiased selection of favorable CAR-T variants with enhanced cancer killing and persistence. Next-generation sequencing of genomic integrations deconvolves the time-course dynamics of knock-in CAR-T variants and identify winning CAR-Ts that survived specific selections. Validations of convergent top genes JADE1, PELI1, EHMT1, NLRP10, KDM4E, TET2 and PRDM1 show that their perturbations in CAR-Ts modulate T cell characteristics such as proliferation, exhaustion and memory phenotypes. A PRDM1 exon3-skip mutant CAR-T exhibits increased proliferation capacity, central memory cell phenotype and longevity, resulting in high-performance in vivo therapeutic efficacy in adoptive cell therapy models across multiple cancer models including solid tumor. Time-course transcriptomics and immune profiling and molecular interrogations demonstrate that PRDM1 exon3-skip CAR-Ts have multiple rewired gene expression patterns and immunological programs. Interrogations of the epigenetic mechanism via histone array, co-immunoprecipitation and genome-wide chromatin binding by Cut-and-Run reveal that deletion of exon-3 leads to disruption of histone H4 binding to the PR domain, thereby altering the regulation of critical downstream immune factors including SELL, CCR7, STAT1, STAT6, CDCA7 and IL7R. The versatility of CLASH is broadly applicable to the engineering of various desired CAR features in a wide range of cell therapies.
Project description:We performed a massively parallel screen in human HAP1 cells to identify loss-of-function missense variants in the key DNA mismatch repair factor MSH2. Resulting variant loss-of-function (LOF) scores are strongly concordant with previous functional evidence and available variant classification.