Biology subjects

Saldivar, J. C.

Publications and source records attributed to Saldivar, J. C..

5 recordsLinked to original sources

bioRxiv2026

Anoxia Tolerant DNA Replication is Supported by ATR Kinase in the Annual Killifish Austrofundulus limnaeus

Hypoxia and anoxia are known to suppress cell proliferation due to an increase in replication stress and activation of DNA damage checkpoints. Embryos of the annual killifish Austrofundulus limnaeus show a strong tolerance to extended anoxic exposure, indicating an improved genomic stability under oxygen starvation. Here we investigate the cell cycle regulation of the anoxia tolerant killifish embryonic cell line PSU-AL-WS40NE during anoxic exposure. Live cell imaging confirms continued cell proliferation of WS40NE cells for the first 24 hours of anoxic exposure with minimal cell death. Fluorescent imaging shows that cells begin to accumulate in G1 after the first day in anoxia with a pronounced and rapid entry into the S phase upon reoxygenation. Pharmacological inhibition tests show that this response appears to be reliant more on ATR signaling then ATM, suggesting that increased {gamma}H2AX levels are driven by increased replication stress instead of DNA damage. This conclusion is further supported by an apparent lack of induction of a G2 checkpoint in these cells suggesting that DNA damage during anoxic replication is minimal. Maintaining cellular proliferation during initial exposure to anoxia and accumulating cells in the G1 phase for extended anoxic exposure is likely one way that embryos of the annual killifish are able to survive prolonged anoxia and provides insight into mechanisms that enable cells to proliferate under metabolic stress.

cell biology↗

bioRxiv2026

ATR enforcement of the S/G2 checkpoint prevents premature S phase shutdown and genome instability

The ATR-enforced S/G2 checkpoint activates during DNA replication to restrain CDK1-dependent phosphorylation of FOXM1 and subsequent transactivation of the G2/M gene network until the end of S phase. However, the extent to which this checkpoint ensures the completion of DNA replication and whether it safeguards genomic integrity has remained unknown. Here, we induce S/G2 checkpoint failure throughout S phase in non-malignant human epithelial cells using multiple ATR pathway inhibitors. Consequently, the mitotic kinase complex cyclin B1-CDK1 prematurely shuts-down the DNA replication program, preventing the completion of genome duplication. In turn, this leads to the retention of inactive replisomes on chromatin and unfired origins into the G2 phase, which induce subsequent accumulation of pan-nuclear {gamma}H2AX and mitotic failure. Collectively, these findings indicate the S/G2 checkpoint ensures replication completion and genome stability.

molecular biology↗

bioRxiv2026

G2-to-G0 cell cycle exit underlies sensitivity to ATR inhibition via the p53-p21-RB1 axis

Ataxia-telangiectasia and Rad3-related (ATR) is an essential DNA damage response kinase that protects genome integrity by controlling cell cycle checkpoints, regulating origin firing, stabilizing replication forks, and signaling DNA repair. Due to hyper-proliferation, cancer cells depend on ATR for survival, implicating ATR inhibitors as promising therapeutics. However, variable tumor responses to ATR inhibitors highlights the need to uncover the determinants of cell fate. Here, we show breast cancer sensitivity to ATR inhibition correlates with the appearance of pan-nuclear DNA damage. The fate of these cells is driven by a p53-p21-RB1 axis that triggers a G2-to-G0-like cell cycle exit and is buffered by the p53 inhibitor MDM2. MDM2 inhibition lowers the DNA damage threshold for cell cycle exit and robustly targets ATR inhibitor-resistant cells. Our work reveals cell cycle plasticity as a mechanism determining cell fate during ATR inhibition and identifies MDM2 as a target for increasing ATR inhibitor efficacy.

molecular biology↗

bioRxiv2024

A phosphorylation code coordinating transcription condensate dynamics with DNA replication

Chromatin is organized into compartments enriched with functionally-related proteins driving non-linear biochemical activities. Some compartments, e.g. transcription foci, behave as liquid condensates. While the principles governing the enrichment of proteins within condensates are being elucidated, mechanisms that coordinate condensate dynamics with other nuclear processes like DNA replication have not been identified. We show that at the G1/S cell cycle transition, large transcription condensates form at histone locus bodies (HLBs) in a cyclin-dependent kinase 1 and 2 (CDK1/2)-dependent manner. As cells progress through S phase, ataxia-telangiectasia and Rad3-related (ATR) accumulates within HLBs and dissolves the associated transcription condensates. Integration of CDK1/2 and ATR signaling creates a phosphorylation code within the intrinsically-disordered region of mediator subunit 1 (MED1) coordinating condensate dynamics with DNA replication. Disruption of this code results in imbalanced histone biosynthesis, and consequently, global DNA damage. We propose the spatiotemporal dynamics of transcription condensates are actively controlled via phosphorylation and essential for viability of proliferating cells.

molecular biology↗

bioRxiv2017

DNA Replication Modulates R-loop Levels to Maintain Genome Stability

Conflicts between transcription and replication are a potent source of DNA damage. The transcription machinery has the potential to aggravate such conflicts by generating co-transcriptional R-loops as an additional barrier to replication fork progression. Here, we investigate the influence of conflict orientation and R-loop formation on genome stability in human cells using a defined episomal system. This approach reveals that head-on (HO) and co-directional (CD) conflicts induce distinct DNA damage responses. Unexpectedly, the replisome acts as an orientation-dependent regulator of R-loop levels, reducing R-loops in the CD orientation but promoting their formation in the HO orientation. Replication stress and deregulated origin firing increase the number of HO collisions leading to genome-destabilizing R-loops. Our findings not only uncover an intrinsic function of the replisome in R-loop homeostasis, but also suggest a mechanistic basis for genome instability associated with deregulated DNA replication, which is observed in many disease states, including cancer.

cell biology↗