Biology subjects

Fong, Y. W.

Publications and source records attributed to Fong, Y. W..

3 recordsLinked to original sources

bioRxiv2026

Primer- and template-independent RNA polymerization by terminal nucleotidyltransferase TENT4B

RNA synthesis by eukaryotic polymerases requires existing polynucleotides to serve as templates or primers. Here, we describe primer- and template-free RNA generation by human terminal nucleotidyltransferase 4B (TENT4B) via de novo polymerization of free nucleotides. We observed that recombinant TENT4B (rTENT4B) consumes ATP to yield inorganic pyrophosphate in the absence of a primer or template, concurrent with the appearance of oligomeric poly-adenosine RNA products. Remarkably, 5 labels on {gamma}-phosphate-modified ATP or GTP are retained during polymerization in the presence of unlabeled nucleotide triphosphates (NTPs). These polymers are created at a similar efficiency irrespective of the inclusion of a primer, indicating robust RNA synthesis by rTENT4B from free NTPs. While canonical purine NTPs are favored, nucleotide diphosphates can also serve as substrates for rTENT4B-mediated de novo RNA polymerization. rTENT4B-mediated RNA synthesis using free adenosine nucleotides shows high processivity to generate 1000s-mers, whereas guanosine nucleotide polymerization is strongly and uniformly self-limited and yields a 3-exonuclease-resistant oligonucleotide. Interrogation of other RNA polymerases reveals potential capacity for de novo polymerization using free ATP, albeit at significantly higher substrate concentrations and lower efficiency compared to rTENT4B. Our data provide definitive evidence of efficient template-free de novo RNA synthesis by a eukaryotic polymerase.

molecular biology↗

bioRxiv2022

SOX15 regulates stem cell pluripotency and promotes neural fate during differentiation by activating Hes5

SOX2 and SOX15 are Sox family transcription factors enriched in embryonic stem cells (ESCs). The role of SOX2 in activating gene expression programs essential for stem cell self-renewal and acquisition of pluripotency during somatic cell reprogramming is well-documented. However, the contribution of SOX15 to these processes is unclear and often presumed redundant with SOX2 largely because overexpression of SOX15 can partially restore self-renewal in SOX2-deficient ESCs. Here, we show that SOX15 contributes to stem cell maintenance by cooperating with ESC-enriched transcriptional coactivators to ensure optimal expression of pluripotency-associated genes. We demonstrate that SOX15 depletion compromises reprogramming of fibroblasts to pluripotency which cannot be compensated by SOX2. Ectopic expression of SOX15 promotes the reversion of a post-implantation, epiblast stem cell state back to a pre-implantation, ESC-like identity even though SOX2 is expressed in both cell states. We also uncover a role of SOX15 in lineage specification, by showing that loss of SOX15 leads to defects in commitment of ESCs to neural fates. SOX15 promotes neural differentiation by binding to and activating a previously uncharacterized distal enhancer of a key neurogenic regulator, Hes5. Together, these findings identify a multifaceted role of SOX15 in induction and maintenance of pluripotency and neural differentiation.

cell biology↗

bioRxiv2020

ATP-binding cassette protein ABCF1 couples gene transcription with maintenance of genome integrity in embryonic stem cells

OCT4 and SOX2 confer pluripotency by recruiting coactivators to activate stem cell-specific gene expression programs. However, the composition of coactivator complexes and their roles in maintaining stem cell fidelity remain unclear. Here we report the identification of ATP-binding cassette subfamily F member 1 (ABCF1) as a critical coactivator for OCT4/SOX2. ABCF1 is required for pluripotency gene expression and stem cell self-renewal. ABCF1 binds co-dependent coactivators XPC and DKC1 via its intrinsically disordered region and stimulates transcription by linking SOX2 to the transcription machinery. Furthermore, in response to pathogen infection and DNA damage, ABCF1 binds intracellular DNAs accumulated in cells, concomitant with loss of SOX2 interaction and pluripotency gene transcription. This results in spontaneous differentiation of compromised stem cells and elimination from the self-renewing population. Thus, ABCF1 directly couples pluripotency gene transcription with sensing aberrant DNAs and acts as a checkpoint for self-renewal to safeguard stem cell fidelity and genome integrity.

biochemistry↗