Biology subjects

Ranish, J. A.

Publications and source records attributed to Ranish, J. A..

3 recordsLinked to original sources

bioRxiv2025

Trimodal Single-Cell Gene Regulatory Networks Reveal Principles of Stemness Loss and Cell Fate Acquisition in Human Hematopoiesis

Hematopoiesis requires the coordinated loss of stemness and acquisition of lineage identity, yet the regulatory logic and principles underlying these transitions has remained elusive. Single-cell studies suggest that hematopoietic stem and progenitor cells progress along continuous trajectories, but this view conflicts with the existence of discrete, functionally validated populations. Here, we establish the first dynamic, enhancer-based gene regulatory networks (eGRNs) that resolve the molecular programs underlying early human hematopoietic fate decisions. Built on a high-resolution trimodal framework generated with TEA-seq, these networks integrate simultaneously measured transcription factor abundance, enhancer and promoter accessibility, and gene expression within single-cell trajectories anchored to immunophenotypically defined populations. Our framework reveals that stemness loss and lineage acquisition are temporally and mechanistically uncoupled: stemness programs decline gradually through reduced TF abundance long before chromatin closure, whereas lineage identity emerges stepwise through enhancer reconfiguration and activation of lineage-defining eGRNs. This process generates discrete regulatory states that align with immunophenotypically defined populations. Together, these findings reconcile continuous and discrete models of hematopoiesis and establish eGRNs as a powerful framework for defining cell types by their regulatory logic. In addition, we provide an interactive web-based resource to facilitate further investigation of eGRNs and trajectories during early human hematopoiesis.

genomics↗

bioRxiv2020

Chromatin-associated protein complexes link DNA base J and transcription termination in Leishmania

Unlike most other eukaryotes, Leishmania and other trypanosomatid protozoa have largely eschewed transcriptional control of gene expression; relying instead on post-transcriptional regulation of mRNAs derived from polycistronic transcription units (PTUs). In these parasites, a novel modified nucleotide base ({beta}-D-glucopyranosyloxymethyluracil) known as J plays a critical role in ensuring that transcription termination occurs only at the end of each PTU, rather than at the polyadenylation sites of individual genes. To further understand the biology of J-associated processes, we used tandem affinity purification (TAP-tagging) and mass spectrometry to reveal proteins that interact with the glucosyltransferase performing the final step in J synthesis. These studies identified four proteins reminiscent of subunits in the PTW/PP1 complex that controls transcription termination in higher eukaryotes. Moreover, bioinformatic analyses identified the DNA-binding subunit of Leishmania PTW/PP1 as a novel J-binding protein (JBP3), which is also part of another complex containing proteins with domains suggestive of a role in chromatin modification/remodeling. Additionally, JBP3 associates (albeit transiently and/or indirectly) with the trypanosomatid equivalent of the PAF1 complex involved in regulation of transcription in other eukaryotes. Down-regulation of JBP3 expression levels in Leishmania resulted in a substantial increase in transcriptional read-through at the 3 end of most PTUs. We propose that JBP3 recruits one or more of these complexes to the J-containing regions at the end of PTUs, where they halt progression of the RNA polymerase. This de-coupling of transcription termination from splicing of individual genes enables the parasites unique reliance on polycistronic transcription and post-transcriptional regulation of gene expression. ImportanceLeishmania parasites cause a variety of serious human diseases, with no effective vaccine and emerging resistance to current drug therapy. We have previously shown that a novel DNA base called J is critical for transcription termination at the ends of the polycistronic gene clusters that are a hallmark of Leishmania and related trypanosomatids. Here, we describe a new J-binding protein (JBP3) associated with three different protein complexes that are reminiscent to those involved in control of transcription in other eukaryotes. However, the parasite complexes have been reprogrammed to regulate transcription and gene expression in trypanosomatids differently than in the mammalian hosts, providing new opportunities to develop novel chemotherapeutic treatments against these important pathogens.

molecular biology↗

bioRxiv2019

Absolute quantification of transcription factors reveals principles of gene regulation in erythropoiesis

Dynamic cellular processes such as differentiation are driven by changes in the abundances of transcription factors (TFs). Yet, despite years of studies we still do not know the protein copy number of TFs in the nucleus. Here, by determining the absolute abundances of 103 TFs and co-factors during the course of human erythropoiesis, we provide a dynamic and quantitative scale for TFs in the nucleus. Furthermore, we establish the first Gene Regulatory Network of cell fate commitment that integrates temporal protein stoichiometry data with mRNA measurements. The model revealed quantitative imbalances in TFs cross-antagonistic relationships that underlie lineage determination. Finally, we made the surprising discovery that in the nucleus, corepressors are dramatically more abundant than coactivators at the protein, but not at the RNA level, with profound implications for understanding transcriptional regulation. These analyses provide a unique quantitative framework to understand transcriptional regulation of cell differentiation in a dynamic context.

systems biology↗