Bacterial Transcriptional Regulation and Computational Epigenomics Lab
PhD. in Integrative Genomics, Universidad Mayor, Chile.
victor.aliaga@umayor.cl
Our research focuses on understanding bacterial transcriptional regulation through integrative bioinformatic approaches, with a current emphasis on bacterial epigenomics
The laboratory focuses on the study of bacterial transcriptional regulation in pathogenic species under adverse conditions. At present, we are investigating the transcriptional response to variations in iron availability. Why iron? Because it is an essential metal for cells, yet it represents a double-edged sword: while indispensable, excessive levels can be toxic. Therefore, bacteria have evolved intricate mechanisms to regulate iron acquisition and utilization, maintaining iron homeostasis to avoid toxicity.
In a pathogenic context, bacteria within the host encounter dynamic iron availability. Host cells tightly sequester iron, limiting its free form and thus creating a condition of iron deficiency. Conversely, when bacteria deploy strategies to acquire iron, they may face iron overload. From a transcriptional perspective, the bacterial response to iron is particularly compelling, as cells must rapidly and precisely modulate gene expression to survive both iron scarcity and excess.
Our research uses Enterococcus faecalis as a model organism. E. faecalis is a Gram-positive commensal bacterium and a frequent resident of the gastrointestinal tract. In recent years, it has drawn increasing attention due to its remarkable adaptability to environmental stressors, particularly its rapid acquisition of antibiotic resistance.
We explore transcriptional regulation as a multilayered process, currently focusing on three regulatory layers:
i) Non-coding RNAs (ncRNAs)
Using previously generated transcriptomic data (RNA-seq), we are identifying regulatory ncRNAs present in the total RNA repertoire of E. faecalis. Our goal extends beyond cataloging; we aim to understand the identities and potential functions of these ncRNAs in bacterial physiology.
ii) Transcription Factors (TFs)
In collaboration with Dr. Mauricio Latorre at the Universidad de O’Higgins (see Collaborators for more information), we are examining transcriptional regulation mediated by TFs through systems biology approaches. Specifically, we analyze how transcriptional regulatory networks respond to environmental stimuli.
iii) Epigenomics
This recently incorporated regulatory layer addresses how bacterial DNA methylation impacts gene expression in E. faecalis. We are investigating how epigenetic modifications influence transcriptional responses under varying iron conditions.
Dr. Victor Aliaga-Tobar earned his Ph.D. in Integrative Genomics from Universidad Mayor, conducting his doctoral research under the supervision of Dr. Vinicius Maracaja-Coutinho. His thesis focused on the identification of non-coding RNAs associated with biofilm formation in extremophilic archaea, combining bioinformatic approaches with experimental validation.
After completing his Ph.D., Dr. Aliaga-Tobar joined the Integrative Bioinformatics Laboratory at the University of Chile as a Researcher, where he contributed to studies on non-coding RNAs in humans and mouse models, under the guidance of Dr. Vinicius Maracaja-Coutinho. He later expanded his research to bacterial transcriptional regulation, working under the supervision of Dr. Mauricio Latorre at the Institute of Engineering Sciences (ICI) at Universidad de O'Higgins. In this context, he deepened his study of bacterial transcriptional networks composed of non-coding RNAs and transcription factors.
In 2022, Dr. Aliaga-Tobar was awarded a postdoctoral fellowship from ANID, focused on bacterial epigenomics, specifically investigating epigenetic modifications that influence gene expression in bacteria.
Since 2024, Dr. Aliaga-Tobar has served as an Assistant Professor at the Center for Genomics and Bioinformatics at Universidad Mayor, where he leads his own research group. His current work centers on the study of the bacterial epigenome and epitranscriptome, as well as the functional characterization of non-coding RNAs in medically relevant bacterial species.
