Biology subjects

Lim, P. S. L.

Publications and source records attributed to Lim, P. S. L..

2 recordsLinked to original sources

bioRxiv2024

Distinct Roles for SETα and SETβ in Early Cell Fate Decisions

SET, the nuclear proto-oncogene, is primarily expressed as SET in embryonic stem cells. Upon pluripotency exit, a transcriptional switch driven by alternative promoters causes SET{beta} to largely replace SET expression. Functional distinctions between the two isoforms have been difficult to ascertain, partly due to the redundancy between SET and SET{beta} in their protein structure and activity. In this study, we use embryonic stem cells (ESCs) with inducible SET isoform-specific expression to investigate the differences between both SET isoforms. Time-course RNA-seq analyses in SET-KO backgrounds as well as isoform-specific ChIP-seq experiments reveal regulatory functions for SET and SET{beta}. Despite sharing many binding sites and binding partners, SET has unique regulatory functions on its target genes, while SET{beta} downregulates FGF4. As KLF5 specifically regulates SET, this implicates SET isoform switching at the KLF5/FGF signalling axis during primitive endoderm specification. Together, we propose a model of how distinct roles of SET and SET{beta} may regulate cell identity in the early blastocyst.

developmental biology↗

bioRxiv2023

Fluorescent protein lifetimes report increased local densities and phases of nuclear condensates during embryonic stem cell differentiation

Fluorescent proteins (FP) are frequently used for studying proteins inside cells. In advanced fluorescence microscopy, FPs can report on additional intracellular variables. One variable is the local density near FPs, which can be useful in studying densities within cellular bio-condensates. Here, we show that a reduction in fluorescence lifetimes of common monomeric FPs reports increased levels of local densities. We demonstrate the use of this fluorescence-based variable to report the distribution of local densities within heterochromatin protein 1 (HP1) in mouse embryonic stem cells (ESCs), before and after early differentiation. We find that local densities within HP1 condensates in pluripotent ESCs are heterogeneous and cannot be explained by a single liquid phase. Early differentiation, however, induces a change towards a more homogeneous distribution of local densities, which can be explained as a liquid-like phase. In conclusion, we provide a fluorescence-based method to report increased local densities and apply it to distinguish between homogeneous and heterogeneous local densities within bio-condensates.

biophysics↗