Biology subjects

Teves, S. S.

Publications and source records attributed to Teves, S. S..

7 recordsLinked to original sources

bioRxiv2025

Molecular determinants underlying functional divergence of TBP homologs

The TATA-box binding protein (TBP) is a highly conserved basal transcription factor and a core component of the pre-initiation complex (PIC) for all three eukaryotic RNA polymerases (RNA Pols). Despite this conservation, TBP function diverges across species. In yeast, TBP is required for all three RNA Pols, whereas in mammals, it is essential only for RNA Pol III, but not RNA Pol I or II. To examine the evolutionary divergence of TBP homologs in different species, we determined the ability of murine TBP and its paralogs to complement endogenous TBP in Saccharomyces cerevisiae. Despite their highly conserved DNA-binding domains, murine TBP homologs were unable to fully rescue the lethality caused by TBP inactivation in yeast. This incomplete complementation correlates with a failure to fully support binding by RNA Pols II and III. Furthermore, we show that the divergent N-terminal domain (NTD) of TBP contributes to species-specific activity and modulates RNA Pol II binding changes in stress-induced response. Lastly, we demonstrate a negative correlation between the length of the intrinsically disordered NTD of TBP family proteins and the gene density in different species, suggesting that the NTD may have contributed to increasingly complex gene regulation during evolution.

molecular biology↗

bioRxiv2024

Dynamic regulation of RNA Polymerase III transcription in mouse embryonic stem cells during heat shock stress

Cells respond to many different types of stresses by overhauling gene expression patterns, both at the transcriptional and translational level. Under heat stress, global transcription and translation are inhibited, while the expression of chaperone proteins are preferentially favored. As the direct link between mRNA transcription and protein translation, tRNA expression is intricately regulated during the stress response. Despite extensive research into the heat shock response (HSR), the regulation of tRNA expression by RNA Polymerase III (Pol III) transcription has yet to be fully elucidated in mammalian cells. Here, we examine the regulation of Pol III transcription during different stages of heat shock stress in mouse embryonic stem cells (mESCs). We observe that Pol III transcription is downregulated after 30 minutes of heat shock, followed by an overall increase in transcription after 60 minutes of heat shock. This effect is more evident in tRNAs, though other Pol III gene targets are also similarly affected. Notably, we show that the downregulation at 30 minutes of heat shock is independent of HSF1, the master transcription factor of the HSR, but that the subsequent increase in expression at 60 minutes requires HSF1. Taken together, these results demonstrate an adaptive RNA Pol III response to heat stress, and an intricate relationship between the canonical HSR and tRNA expression. Article SummaryThis study explores the regulation of RNA Polymerase III (Pol III) transcription during heat shock in mouse embryonic stem cells (mESCs). Results show that tRNA transcription is downregulated after 30 minutes of heat shock, but increases after 60 minutes, while other Pol III targets remain unaffected. Importantly, the initial downregulation is independent of heat shock factor 1 (HSF1), the key regulator of the heat shock response, but the subsequent increase in tRNA expression depends on HSF1. These findings reveal an adaptive mechanism of Pol III activity under heat stress, highlighting a complex interplay between heat shock response and tRNA expression.

molecular biology↗

bioRxiv2024

Functional divergence of TBP homologs through distinct DNA binding dynamics

The TATA box-binding protein (TBP) is an evolutionarily conserved basal transcription factor common in the pre-initiation complex of all three eukaryotic RNA polymerases (RNA Pols). Despite their high conservation, homologous TBPs exhibit species- and tissue-specific functions that may contribute to the increasingly complex gene expression regulation across evolutionary time. To determine the molecular mechanisms of species- and tissue-specificity for homologous TBPs, we examined the ability of yeast TBP and murine TBP paralogs to replace the endogenous TBP in mouse embryonic stem cells. We show that, despite the high conservation in the DNA binding domain among the homologs, they cannot fully rescue the lethality of TBP depletion in mESCs, largely due to their inability to support RNA Pol III transcription. Furthermore, we show that the homologs differentially support stress-induced transcription reprogramming, with the divergent N-terminal domain playing a role in modulating changes in transcriptional response. Lastly, we show that the homologs have vastly different DNA binding dynamics, suggesting a potential mechanism for the distinct functional behavior observed among the homologs. Taken together, these data show a remarkable balance between flexibility and essentiality for the different functions of homologous TBP in eukaryotic transcription.

molecular biology↗

bioRxiv2023

TBP facilitates RNA Polymerase I transcription following mitosis

The TATA-box binding protein (TBP) is the sole transcription factor common in the initiation complexes of the three major eukaryotic RNA Polymerases (Pol I, II, and III). Decades of research have shown that TBP is essential for proper transcription by the three RNA Pols, though the emergence of TBP paralogs throughout evolution have expanded the complexity in RNA Pol initiation. We have previously shown that acute TBP depletion in mouse embryonic stem cells led to a global decrease in Pol III activity, consistent with the requirement of TBP in Pol III inititation. In contrast, Pol II transcription remained unaffected in the absence of TBP and its paralogs. In this report, we show that, in contrast to Pol II-transcribed genes, the TBP paralog TRF2 does not bind to Pol I promoters, and therefore cannot functionally replace TBP upon depletion. Importantly, acute TBP depletion has no major effect on Pol I occupancy or activity on ribosomal RNA genes, but TBP binding in mitosis leads to efficient Pol I reactivation following cell division. These findings provide a more nuanced role for TBP in Pol I transcription in murine embryonic stem cells. SignificanceThe TATA-box binding protein (TBP) is a highly conserved and essential protein in eukaryotes. Decades of in vitro and yeast research have established its role in the initiation of the three main eukaryotic RNA polymerases. However, the ability to rapidly deplete proteins in vivo is revealing more nuance in the function of TBP in mammalian cells. Using this technology, we reassess the role of TBP in RNA Polymerase I (Pol I) transcription in mouse embryonic stem cells. We find that neither TBP nor its paralog TRF2 are required for Pol I recruitment or activity, but TBP binding during mitosis promotes efficient reactivation after cell division. Overall, these findings provide new evidence into the complex function of TBP in eukaryotic transcription.

molecular biology↗

bioRxiv2022

Distinct modes of heat shock transcription factor interactions with mitotic chromosomes

A large number of transcription factors have been shown to bind and interact with mitotic chromosomes, which may promote the efficient reactivation of transcriptional programs following cell division. Although the DNA-binding domain (DBD) contributes strongly to TF behavior, TFs from the same DBD family can display distinct binding behaviors during mitosis. To define the mechanisms governing TF behavior during mitosis in mouse embryonic stem cells, we examined two related TFs: Heat Shock Factor 1 and 2 (HSF1 and HSF2). We found that HSF2 maintains site-specific binding genome-wide during mitosis, whereas HSF1 binding is globally decreased. Surprisingly, live-cell imaging shows that both factors appear excluded from mitotic chromosomes, and are similarly more dynamic in mitosis than in interphase. Exclusion from mitotic DNA is not due to extrinsic factors like nuclear import and export mechanisms. Rather, we found that the HSF2 DBD alone can coat mitotic chromosomes, but is insufficient to promote HSF1 coating. These data further confirm that site-specific binding and chromosome coating are independent properties, and that for some TFs, mitotic behavior is largely determined by the non-DBD regions.

molecular biology↗

bioRxiv2021

A TBP-independent mechanism for RNA Polymerase II transcription

Transcription by RNA Polymerase II (Pol II) is initiated by the hierarchical assembly of the Pre-Initiation Complex onto promoter DNA. Decades of in vitro and yeast research have shown that the TATA-box binding protein (TBP) is essential to Pol II initiation by triggering the binding of other general transcription factors, and ensuring proper Pol II loading. Here, we report instead that acute depletion of TBP in mouse embryonic stem cells (mESCs) has no global effect on ongoing Pol II transcription. Surprisingly, Pol II transcriptional induction through the Heat Shock Response or cellular differentiation also occurs normally in the absence of TBP. In contrast, acute TBP depletion severely impairs initiation by RNA Polymerase III. Lastly, we show that a metazoan-specific paralog of TBP is expressed in mESCs and that it binds to promoter regions of active Pol II genes even in the absence of TBP. Taken together, our findings reveal an unexplored TBP-independent process in mESCs that points to a diversity in Pol II transcription initiation mechanisms.

molecular biology↗

bioRxiv2018

A stable mode of bookmarking by TBP recruits RNA Polymerase II to mitotic chromosomes

How a cell maintains transcriptional fidelity across mitosis has remained an enduring mystery in biology. One challenge arises during mitosis when chromatin becomes condensed and transcription is shut off. How do the daughter cells re-establish the original transcription program? Here, we report that the TATA-binding protein (TBP), a key component of the core transcriptional machinery, remains bound globally to active promoters in ES cells during mitosis. Using live-cell single-molecule imaging, we observed that TBP mitotic binding is highly stable, with an average residence time of minutes. This stable binding is in stark contrast to typical TFs with residence times of seconds. To test the functional effect of mitotic TBP binding, we used a drug-inducible degron system and found that TBP promotes the association of RNA Polymerase II with mitotic chromosomes, and facilitates transcriptional reactivation following mitosis. These results suggest that the core transcriptional machinery maintains global transcriptional memory during mitosis.

molecular biology↗