Biology subjects

Goh, S.-T.

Publications and source records attributed to Goh, S.-T..

3 recordsLinked to original sources

bioRxiv2020

The changing mouse embryo transcriptome at whole tissue and single-cell resolution

In mammalian embryogenesis differential gene expression gradually builds the identity and complexity of each tissue and organ system. We systematically quantified mouse polyA-RNA from embryo day E10.5 to birth, sampling 17 whole tissues, enhanced with single-cell measurements for the developing limb. The resulting developmental transcriptome is globally structured by dynamic cytodifferentiation, body-axis and cell-proliferation gene sets, characterized by their promoters transcription factor (TF) motif codes. We decomposed the tissue-level transcriptome using scRNA-seq and found that neurogenesis and haematopoiesis dominate at both the gene and cellular levels, jointly accounting for 1/3 of differential gene expression and over 40% of identified cell types. Integrating promoter sequence motifs with companion ENCODE epigenomic profiles identified a promoter de-repression mechanism unique to neuronal expression clusters and attributable to known and novel repressors. Focusing on the developing limb, scRNA-seq identified 25 known and candidate novel cell types, including progenitor and differentiating states with computationally inferred lineage relationships. We extracted cell type TF networks and complementary sets of candidate enhancer elements by de-convolving whole-tissue IDEAS epigenome chromatin state models. These ENCODE reference data, computed network components and IDEAS chromatin segmentations, are companion resources to the matching epigenomic developmental matrix, available for researchers to further mine and integrate.

developmental biology↗

bioRxiv2019

Dissecting the regulatory activity and key sequence elements of loci with exceptional numbers of transcription factor associations

DNA associated proteins (DAPs) classically regulate gene expression by binding to regulatory loci such as enhancers or promoters. As expanding catalogs of genome-wide DAP binding maps reveal thousands of loci that, unlike the majority of conventional enhancers and promoters, associate with dozens of different DAPs with apparently little regard for motif preference, an understanding of DAP association and coordination at such regulatory loci is essential to deciphering how these regions contribute to normal development and disease. In this study, we aggregated publicly available ChIP-seq data from 469 human DAPs assayed in three cell lines and integrated these data with an orthogonal dataset of 352 non-redundant, in vitro-derived motifs mapped to the genome within DNase hypersensitivity footprints in an effort to characterize regions of the genome that have exceptionally high numbers of DAP associations. We subsequently performed a massively parallel mutagenesis assay to search for sequence elements driving transcriptional activity at such loci and explored plausible biological mechanisms underlying their formation. We establish a generalizable definition for High Occupancy Target (HOT) loci and identify putative driver DAP motifs in HEPG2 cells, including HNF4A, SP1, SP5, and ETV4, that are highly prevalent and exhibit sequence conservation at HOT loci. The number of different DAPs associated with an element is positively associated with evidence of regulatory activity and, by systematically mutating 245 HOT loci, we localized regulatory activity to a central core region that depends on the motif sequences of our previously nominated driver DAPs. In sum, this work leverages the increasingly large number of DAP motif and ChIP-seq data publicly available to explore how DAP associations contribute to genome-wide transcriptional regulation.

genomics↗

bioRxiv2018

Occupancy patterns of 208 DNA-associated proteins in a single human cell type

Genome-wide occupancy maps of transcriptional regulators are important for understanding gene regulation and its effects on diverse biological processes, but only a small fraction of the >1,600 transcription factors (TFs) encoded in the human genome has been assayed. Here we present data and analyses of ChIP-seq experiments for 208 DNA-associated proteins (DAPs) in the HepG2 hepatocellular carcinoma line, spanning nearly a quarter of its expressed TFs, transcriptional co-factors, and chromatin regulator proteins. The DAP binding profiles classify into major groups associated predominantly with promoters or enhancers, or with both. We confirm and expand the current catalog of DNA sequence motifs; 77 factors showed similar motifs to those previously described using in vivo and/or in vitro methods, and 17 yielded novel motifs. We also describe motifs corresponding to other TFs that co-enrich with the primary ChIP target. FOX family motifs are, for example, significantly enriched in ChIP-seq peaks of 37 other DAPs. We show that promoters and enhancers can be discriminated based on motif content and occupancy patterns. This large catalog reveals High Occupancy Target (HOT) regions at which many DAPs associate, although each contains motifs for only a minority of the numerous associated DAPs. These analyses provide a deeper and more complete overview of the gene regulatory networks that define this cell type.

genomics↗