Biology subjects

Newberry, K. M.

Publications and source records attributed to Newberry, K. M..

3 recordsLinked to original sources

bioRxiv2025

KOLF2.1J iTF-Microglia: A standardized platform to studymicroglial transcriptional regulatory networks in CNS disease

Understanding transcriptional regulatory networks (TRNs) in microglia is key to uncovering mechanisms driving central nervous system (CNS) disorders. Human iPSC-derived models offer a tractable system for studying microglia, yet variability between lines has limited reproducibility. Here, we use the standardized KOLF2.1J iTF line to rapidly generate microglia-like cells (iTF-Microglia) and profile TRNs under homeostatic and inflammatory conditions. iTF-Microglia closely resemble primary brain microglia at both transcriptomic and epigenomic levels. Integrative analyses reveal microglia-enriched candidate cis-regulatory elements (cCREs) and dynamic enhancer remodeling upon differentiation and LPS+IFNG stimulation, involving key transcription factors (TFs) including NF-{kappa}B, IRF, and STAT families. TRNs active in iTF-Microglia are enriched for genetic variants linked to Alzheimers disease and other CNS disorders. These findings establish KOLF2.1J iTF-Microglia as a reproducible and genetically tractable platform for studying human microglial gene regulation and provide mechanistic insight into how TRN remodeling may contribute to CNS disease risk.

genomics↗

bioRxiv2020

Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands

Massively parallel reporter assays (MPRAs) are useful tools to discover and characterize regulatory elements in human genomes. Partly because enhancer function is assumed to be orientation independent with respect to each strand of the DNA helix, most reported MPRA results ignore stranded information. However, we find pervasive strand asymmetry of MPRA signals in datasets from multiple reporter configurations and in both published and newly reported data. These effects are reproducible across different cell types and in different treatments within a cell type, and are observed both within and outside of annotated regulatory elements. From elements in gene bodies, MPRA strand asymmetry favors the sense strand, suggesting that biological function related to endogenous transcription is driving the phenomenon. Similarly, within Alu mobile element insertions, we find that strand asymmetry favors the transcribed strand of the ancestral retrotransposon. The effect is consistent across the multiplicity of Alu elements in human genomes, and is more pronounced in younger, less diverged Alu elements. We find sequence features driving MPRA strand asymmetry and demonstrate its prediction from sequence alone. We see some evidence for both RNA stabilization and transcriptional activation mechanisms, and hypothesize that the effect is driven by natural selection favoring efficient transcription. Our results indicate that strand asymmetry, as a pervasive and reproducible feature, should be accounted for in analysis of MRPA data. More importantly, the fact that MPRA asymmetry favors naturally transcribed strands suggests that it stems from preserved biological functions that have a substantial, global impact on gene and genome evolution.

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↗