Biology subjects

Yuan, P.

Publications and source records attributed to Yuan, P..

41 records · Page 3Linked to original sources

bioRxiv2019

Non-Canonical Regulation of Phosphatidylserine Metabolism by a Phosphatidylinositol Transfer Protein and a Phosphatidylinositol 4-OH Kinase

The phosphatidylserine (PtdSer) decarboxylase Psd2 is proposed to engage in an endoplasmic reticulum (ER)-Golgi/endosome membrane contact site (MCS) that facilitates phosphatidylserine decarboxylation to phosphatidylethanomaine (PtdEtn) in Saccharomyces cerevisiae. While this MCS is envisioned to consist of Psd2, the Sec14-like phosphatidylinositol transfer protein (PITP) Sfh4, the Stt4 phosphatidylinositol (PtdIns) 4-OH kinase, the Scs2 tether, and at least one other uncharacterized protein, functional data that address key foundations of this model are sparse. We now report that Psd2, Sfh4 and Stt4 are the only components individually required for biologically sufficient Psd2-dependent PtdEtn production. Surprisingly, neither the PtdIns-transfer activity of Sfh4 nor its capacity to activate Stt4 is required to stimulate the Psd2 pathway. Instead, Sfh4 activates the Psd2 pathway via a specific Sfh4-Psd2 physical interaction. Whereas the data indicate an Sfh4-independent association of Stt4 with Psd2 as well, we find Stt4 also regulates Psd2 activity indirectly by influencing the PtdSer pool accessible to Psd2 for decarboxylation. These collective results demonstrate that the proposed ER-Golgi/endosomal MCS model fails to provide an accurate description of the Psd2 system in yeast, and provide an example where the biological function of a Sec14-like PITP is uncoupled from its canonical activity as a PtdIns transfer protein.

cell biology↗

bioRxiv2019

Atomistic basis of opening and conduction in mammalian inward rectifier potassium (Kir2.2) channels

Potassium ion conduction through open potassium channels is essential to control of membrane potentials in all cells. To elucidate the open conformation and hence the mechanism of K+ ion conduction in the classical inward rectifier Kir2.2, we introduced a negative charge (G178D) at the crossing point of the inner helix bundle (HBC), the location of ligand-dependent gating. This forced open mutation generated channels that were active even in the complete absence of phosphoinositol-4,5-bisphosphate (PIP2), an otherwise essential ligand for Kir channel opening. Crystal structures were obtained at a resolution of 3.6 [A] without PIP2 bound, or 2.8 [A] in complex with PIP2. The latter revealed a slight widening at the HBC, through backbone movement. Molecular dynamics (MD) simulations showed that subsequent spontaneous wetting of the pore through the HBC gate region allowed K+ ion movement across the HBC and conduction through the channel. Further simulations reveal atomistic details of the opening process and highlight the role of pore lining acidic residues in K+ conduction through Kir2 channels.

biophysics↗

bioRxiv2019

Leveraging Endogenous ADAR for Programmable Editing on RNA

Nucleic acid editing carries enormous potential for biological research and the development of therapeutics. Current tools for DNA or RNA editing rely on introducing exogenous proteins into living organisms, which is subject to potential risks or technical barriers due to possible aberrant effector activity, delivery limits and immunogenicity. Here, we report a programmable approach that employs a short RNA to leverage endogenous ADAR (Adenosine Deaminase Acting on RNA) proteins for targeted RNA editing. We engineered an RNA that is partially complementary to the target transcript to recruit native ADAR1 or ADAR2 to change adenosine to inosine at a specific site. We designated this new method as LEAPER (Leveraging Endogenous ADAR for Programmable Editing on RNA) and the ADAR-recruiting RNA as arRNA. arRNA, either expressed from plasmid or viral vector, or synthesized as an oligonucleotide, could achieve desirable editing. LEAPER has a manageable off-target rate on the targeted transcripts and rare global off-targets. We demonstrated that LEAPER could restore p53 function by repairing a specific cancer-relevant point mutation. Moreover, LEAPER could apply to a broad spectrum of cell types including multiple human primary cells, and it restored the -L-iduronidase catalytic activity in Hurler syndrome patient-derived primary fibroblasts without evoking innate immune responses. As a single molecule system akin to RNAi, LEAPER enables precise and efficient RNA editing, offering the transformative potential for basic research and therapeutics.

genomics↗

bioRxiv2018

Transcriptome Landscape of Human Oocytes and Granulosa Cells Throughout Folliculogenesis

Folliculogenesis is a highly regulated process that involves bidirectional interactions of the oocytes and surrounding granulosa cells (GCs). Little is unknown, however, about the transcriptomic profiles of human oocytes and GCs throughout folliculogenesis. Here we performed a high resolution RNA-Seq of human oocytes and GCs at each follicular stage, which revealed unique transcriptional profiles, stage-specific signature genes, oocyte- and GC-derived genes that reflect ovarian reserve. We identified reciprocal cell-to-cell interactions between oocytes and GCs, including NOTCH, TGF-{beta} signaling and gap junctions and determined the expression patterns of maternal-effect genes involved in folliculogenesis and early embryogenesis. Finally, we demonstrated robust differences between human and mice oocyte transcriptomes. This is the first comprehensive overview of the transcriptomic signatures governing the stepwise human folliculogenesis in-vivo that provides a valuable resource for basic and translational research in human reproductive biology.

cell biology↗

bioRxiv2017

The role of Cdx2 as a lineage specific transcriptional repressor for pluripotent network during trophectoderm and inner cell mass specification

The first cellular differentiation event in mouse development leads to the formation of the blastocyst consisting of the inner cell mass (ICM) and an outer functional epithelium called trophectoderm (TE). The lineage specific transcription factor CDX2 is required for proper TE specification, where it promotes expression of TE genes, and represses expression of Pou5f1 (OCT4) by inhibiting OCT4 from promoting its own expression. However its downstream network in the developing early embryo is not fully characterized. Here, we performed high-throughput single embryo qPCR analysis in Cdx2 null embryos to identify components of the CDX2-regulated network in vivo. To identify genes likely to be regulated by CDX2 directly, we performed CDX2 ChIP-Seq on trophoblast stem (TS) cells, derived from the TE. In addition, we examined the dynamics of gene expression changes using an inducible CDX2 embryonic stem (ES) cell system, so that we could predict which CDX2-bound genes are activated or repressed by CDX2 binding. By integrating these data with observations of chromatin modifications, we were able to identify novel regulatory elements that are likely to repress gene expression in a lineage-specific manner. Interestingly, we found CDX2 binding sites within regulatory elements of key pluripotent genes such as Pou5f1 and Nanog, pointing to the existence of a novel mechanism by which CDX2 maintains repression of OCT4 in trophoblast. Our study proposes a general mechanism in regulating lineage segregation during mammalian development.

cell biology↗