Biology subjects

Mak, W.

Publications and source records attributed to Mak, W..

3 recordsLinked to original sources

bioRxiv2026

DNA methylation maintenance by DNMT1 is essential for human trophoblast stem cell homeostasis and differentiation

Proliferation of cytotrophoblasts (CTBs) and their differentiation into invasive extravillous trophoblasts (EVTs) are critical processes in early placental development. Defects in these processes are associated with adverse pregnancy outcomes, including recurrent pregnancy loss (RPL). There is evidence that reduced expression of the maintenance DNA methyltransferase DNMT1 in the placenta occurs in pregnancy loss and that RPL is associated with aberrant DNA methylation patterns. Therefore, we investigated the role of DNMT1 in human trophoblast growth and differentiation. Using human trophoblast stem cells (hTSCs), an in vitro analog to CTBs, we found that shRNA-mediated knockdown of DNMT1 led to decreased hTSC proliferation, genome-wide reductions in methylation, broad changes in gene expression, and impaired EVT differentiation. Transcriptome profiling of DNMT1-deficient hTSCs and hTSC-derived EVTs highlighted aberrant cytokine expression, drawing a connection to prior reports of immunological dysfunction in RPL. Finally, using a catalytic DNMT1 chemical inhibitor, we demonstrate the canonical methyltransferase activity of DNMT1 is essential for EVT differentiation and invasion. This study identifies new roles for DNMT1 in trophoblasts and addresses the molecular basis of the associations between DNMT1 expression, altered DNA methylation profiles, and RPL.

developmental biology↗

bioRxiv2019

Pumilio Proteins Exert Distinct Biological Functions and Multiple Modes of Post-Transcriptional Regulation in Embryonic Stem Cell Pluripotency and Early Embryogenesis

Gene regulation in embryonic stem cells (ESCs) has been extensively studied at the epigenetic-transcriptional levels, but not at the post-transcriptional levels. Pumilio (Pum) proteins are among the few known translational regulators required for stem cell maintenance in invertebrates and plants. Here we report the essential function of two murine Pum proteins, Pum1 and Pum2, in ESCs and early embryogenesis. Pum1/2 double mutants are developmentally delayed at the morula stage and lethal by embryonic day 8.5 (e8.5). Correspondingly, Pum1/2 double mutant ESCs display severely reduced self-renewal and differentiation, revealing the combined function of Pum1 and Pum2 in ESC pluripotency. Remarkably, Pum1-deficient ESCs show increased expression of pluripotency genes but not differentiation genes, indicating that Pum1 mainly promote differentiation; whereas Pum2-deficient ESCs show decreased expression of pluripotency genes and accelerated differentiation, indicating that Pum2 promotes self-renewal. Thus, Pum1 and Pum2 each uniquely contributes to one of the two complementary aspects of pluripotency. Furthermore, we show that Pum1 and Pum2 achieve ESC functions by forming a negative auto- and inter-regulatory feedback loop that directly regulates at least 1,486 mRNAs. Pum1 and Pum2 regulate target mRNAs not only by repressing translation as expected but also by promoting translation and enhancing or reducing mRNA stability of different target mRNAs. Together, these findings reveal the distinct roles of individual mammalian Pum proteins in ESCs and their collectively essential functions in ESC pluripotency and embryogenesis. Moreover, they demonstrate three novel modes of regulation of Pum proteins towards target mRNAs.\n\nSIGNIFICANCE STATEMENTThis report demonstrates the essential functions of mammalian Pumilio (Pum) proteins for embryonic stem cells (ESCs) pluripotency and embryogenesis. Moreover, it reveals the contrasting but complementary function of individual Pum proteins in regulating distinct aspects of ESC pluripotency, despite their largely overlapping expression and extremely high homology. Furthermore, it unravels a complex regulatory network in which Pum1 and Pum2 form a negative auto- and inter-regulatory feedback loop that regulates 1,486 mRNAs not only by translational repression as expected but also by promoting translation and enhancing or reducing stability of different target mRNAs, which reveals novel modes of post-transcriptional regulation mediated by Pum.

developmental biology↗

bioRxiv2018

Genetic Diversity and Distributional Pattern of Ammonia Oxidizing Archaea Lineages in the Global Oceans

In the study, we used miTAG approach to analyse the distributional pattern of the ammonium oxidizing archaea (AOA) lineages in the global oceans using the metagenomics datasets of the Tara Oceans global expedition (2009-2013). Using ammonium monooxygenase alpha subunit gene as biomarker, the AOA communities were obviously segregated with water depth, except the upwelling regions. Besides, the AOA communities in the euphotic zones are more heterogeneous than in the mesopelagic zones (MPZs). Overall, water column A clade (WCA) distributes more evenly and widely in the euphotic zone and MPZs, while water column B clade (WCB) and SCM-like clade mainly distribute in MPZ and high latitude waters, respectively. At fine-scale genetic diversity, SCM1-like and 2 WCA subclades showed distinctive niche separation of distributional pattern. The AOA subclades were further divided into ecological significant taxonomic units (ESTUs), which were delineated from the distribution pattern of their corresponding subclades. For examples, ESTUs of WCA have different correlation with depth, nitrate to silicate ratio and salinity; SCM1-like-A was negatively correlated with irradiation; the other SCM-like ESTUs preferred low temperature and high nutrient conditions, etc. Our study provides new insight to the genetic diversity of AOA in global scale and its connections with environmental factors.

ecology↗