Biology subjects

Chobirko, J. D.

Publications and source records attributed to Chobirko, J. D..

4 recordsLinked to original sources

bioRxiv2025

Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system

Transposable elements (TEs) make up about half of the human and mouse genomes and play important regulatory roles in immune responses. However, the cis-regulatory contribution of TEs to immune cell development is less characterized. Here, we analyzed hundreds of chromatin accessibility, gene expression, transcription factor occupancy and DNA-DNA contact datasets in diverse mouse and human immune cells. We identified two rodent-specific TE subfamilies, ORR1E and ORR1D2 (collectively, ODE) that have transformed into cell type-specific enhancers across the mouse immune system. ODE loci acquired mutations post-insertion that enable differential binding of lineage-specifying transcription factors. ODEs show evidence of evolutionary sequence constraint and contact promoters of hundreds of genes in immune cells. ODE-targeted genes show cell type-specific and mouse-specific increases in expression compared to concordant human cell types. Thus, a single TE family can undergo functionalization after its genomic spread to generate batteries of cell-specific enhancers supporting a complex developmental cascade.

genomics↗

bioRxiv2024

Deciphering gene regulatory programs underlying functionally divergent naive T cell subsets

Naive CD8+ T cells are a heterogeneous population, with different subsets possessing distinct functions and kinetics upon activation. However, the gene regulatory circuits differentiating these naive subsets are not well studied. In this work, we analyzed a large collection of public and newly generated RNA-seq and ATAC-seq profiles of different subsets of naive CD8+ T cells, revealing significant differences in the gene regulatory landscapes between subsets. We leveraged these data by employing a network inference algorithm, Inferelator, to identify the transcriptional regulatory circuits active in each subset. The predicted transcriptional network of the naive CD8+ T cell pool was validated by multiple orthogonal approaches, including CUT&Tag and Micro-C. Interestingly, our network analysis revealed a novel role for Eomes in promoting effector cell differentiation in specific cell subsets. Moreover, we uncovered multiple novel regulators across a variety of subsets and discovered several modules of genes that were co-regulated by shared sets of transcription factors in distinct subsets. Collectively, our data defines the gene regulatory programs differentiating naive CD8+ T cells and facilitates the identification of novel transcription factors that may alter the propensity of naive CD8+ T cells to become effector or memory cells after infection.

systems biology↗

bioRxiv2023

Regulatory Transposable Elements in the Encyclopedia of DNA Elements

Transposable elements (TEs) make up about half of the human genome and many have the biochemical hallmarks of tissue- or cell type-specific cis-regulatory elements. While some TEs have been rigorously documented to contribute directly to host gene regulation, we still have a very partial view of their regulatory landscape. Leveraging Phase 4 ENCODE data, we carried out the most comprehensive study to date of TE contributions to the regulatory genome. Here we investigated the sequence origins of candidate cis-regulatory elements (cCREs), showing that [~]25% of human cCREs comprising 236,181 elements are derived from TEs. Human-mouse comparisons indicate that over 90% of TE-derived cCREs are lineage-specific, accounting for 8-36% of lineage-specific cCREs across cCRE types. Next, we found that cCRE-associated transcription factor (TF) binding motifs in TEs originated from TE ancestral sequences significantly more than expected in all TE classes except for SINEs. Using both cCRE and TF binding data, we discovered that TEs providing cCREs and TF binding sites are closer in genomic distance to non-TE sites compared to other TEs, suggesting that TE integration site influences their later co-option as regulatory elements. We show that TEs have promoted TF binding site turnover events since human-mouse divergence, accounting for 3-56% of turnover events across 30 TFs examined. Finally, we demonstrate that TE-derived cCREs share similar features with non-TE cCREs, including massively parallel reporter assay activity and GWAS variant enrichment. Overall, our results substantiate the notion that TEs have played an important role in shaping the human regulatory genome.

genomics↗

bioRxiv2020

Ancestral class-promiscuity as a driver of functional diversity in the BAHD acyltransferase family in plants

Large enzyme families catalyze metabolic diversification by virtue of their ability to use diverse chemical scaffolds. How enzyme families attain such functional diversity is not clear. Here, we addressed this question using BAHD acyltransferases as a model, and identified the routes by which duplication, promiscuity and sequence changes influenced BAHD diversification. This fast-evolving family expanded drastically during land plant evolution from 1-5 copies in algae to [~]100 copies in diploid angiosperm genomes. In vitro characterization of fourteen BAHDs against a substrate panel and compilation of >160 published activities revealed the wide prevalence of promiscuity among BAHDs. Using phylogenetic analysis, we predicted the substrate classes that the ancestral enzymes were likely capable of using prior to land plant origins. While the anthocyanin acylation activity was fixed in BAHDs later near the origin of angiosperms, in vitro testing of BAHDs from non-seed plant lineages suggested that the ability to acylate anthocyanins likely existed promiscuously millions of years prior to its fixation. Motif enrichment analysis in anthocyanin-acylating BAHDs identified two motifs fixed in the largest anthocyanin acylating clade. Molecular dynamic simulations and enzyme kinetics revealed the important role of an active site tryptophan, whose bulkiness, hydrophobicity and aromaticity are critical for anthocyanin acylation. Our results thus describe the molecular processes in robust, evolvable enzymes that drive emergence of functional diversity in enzyme families. One sentence summaryUsing a combination of phylogenetics, biochemistry and protein structure analysis, we investigated how the BAHD acyltransferase family evolved to use a structurally diverse array of substrates.

plant biology↗