Biology subjects

Aristizabal, M. J.

Publications and source records attributed to Aristizabal, M. J..

6 recordsLinked to original sources

bioRxiv2025

Molecular Dynamics-Guided All-Atom Reconstruction of Cryo-ET Maps Reveals Mechanisms of Histone Tail-Mediated Chromatin Compaction

Dynamics and physical state of chromatin are crucial in regulating gene expression, DNA replication, and repair. Intrinsically disordered histone tails were previously recognized as key modulators of chromatin states. However, detailed atomistic mechanisms by which histone tail dynamics are associated with chromatin compaction and higher-order chromatin organization remain poorly understood. In this work, we combine extensive all-atom molecular dynamics simulations of tri-nucleosomes with cryo-electron tomography (Cryo-ET) of native nucleosome arrays to investigate histone tail-mediated chromatin folding. Our approach offers distinct advantages as it elucidates realistic inter- and intra-nucleosomal interactions and DNA conformations derived from physics-based MD simulations, enabling a more accurate and physically grounded interpretation of Cryo-ET data. The results reveal that histone tails promote chromatin compaction and constrain tri-nucleosome unfolding via three major patterns: through histone-DNA interactions, histone H2A-H4 and H3-H4 tail-tail interactions. Notably, the distributions of MD-generated structural parameters of tri-nucleosomes with truncated histone tails were found to be in strong agreement with those of experimental open chromatin arrays with widely spaced nucleosomes, whereas the system with histone tails resembled more condensed chromatin. These findings provide mechanistic insights into how histone tails may mediate chromatin folding at the atomistic scale and underscore the dual role of histone tails in both structural compaction and inter-nucleosomal communication.

biophysics↗

bioRxiv2024

Cancer Histone Mutations Impact Binding and DNA Repair Processes, Leading to Increased Mutagenesis

Histones are key epigenetic factors for regulating the accessibility and compaction of eukaryotic genomes, affecting the replication, repair, and expression of DNA. Recent studies have demonstrated that histone missense mutations can perturb normal histone function, promoting the development of phenotypically distinguishable cancers. However, most histone mutations observed in cancer patients remain enigmatic in their potential to promote cancer development. To assess the oncogenic potential of histone missense mutations, we have gathered whole-exome sequencing data for the tumors of over 12,000 patients. Overall, histone mutations occurred in about 16% of cancer patients, although specific cancer types showed substantially higher rates. Using a combination of genomic, structural, and biophysical analyses, we found several predominant modes of action, where cancer missense mutations in histones affected acidic patches and protein binding interfaces in a cancer-specific manner and targeted interaction sites with specific DNA repair proteins. Consistent with this finding, we observed a high tumour mutational burden in patients with histone mutations affecting interactions of DNA repair proteins. We also identified potential cancer driver mutations in several histone genes, including histone H4-a highly conserved histone without previously documented driver mutations.

bioinformatics↗

bioRxiv2023

Rapid cold hardening modifies mechanisms of ion regulation to delay anoxia-induced spreading depolarization in the CNS of Locusta migratoria

Insects live in varied habitats and experience different kinds of environmental stresses. These stresses can impair neural performance, leading to spreading depolarization (SD) of nerve cells and neural shutdown underlying coma. The sensitivity of an insects nervous system to stress (e.g., anoxia) can be modulated by acute pre-treatment. Rapid cold hardening (RCH) is a form of preconditioning, in which a brief exposure to low temperature can enhance the stress tolerance of insects. SD is associated with a sudden loss of ion, notably K+, homeostasis. We used a pharmacological approach to investigate whether RCH affects anoxia-induced SD in the locust, L. migratoria, via one or more of the following homeostatic mechanisms: (1) Na+/K+-ATPase (NKA), (2) Na+/K+/2Cl- co-transporter (NKCC), and (3) voltage-gated K+ (Kv) channels. We also assessed abundance and phosphorylation of NKCC using immunoblotting. We found that inhibition of NKA or Kv channels delayed the onset of anoxia-induced SD in both control and RCH preparations. However, NKCC inhibition preferentially abrogated the effect of RCH. Additionally, we observed a higher abundance of NKCC in RCH preps but no statistical difference in its phosphorylation level, indicating the involvement of NKCC expression or degradation as part of the RCH mechanism.

physiology↗

bioRxiv2022

An important role for triglyceride in regulating spermatogenesis

Drosophila is a powerful model to study how lipids affect spermatogenesis. Yet, the contribution of neutral lipids, a major lipid group which resides in organelles called lipid droplets (LD), to sperm development is largely unknown. Emerging evidence suggests LD are present in the testis and that loss of neutral lipid- and LD-associated genes causes subfertility; however, key regulators of testis neutral lipids and LD remain unclear. Here, we show LD are present in early-stage somatic and germline cells within the Drosophila testis. We identified a role for triglyceride lipase brummer (bmm) in regulating testis LD, and found that whole-body loss of bmm leads to defects in sperm development. Importantly, these represent cell-autonomous roles for bmm in regulating testis LD and spermatogenesis. Because lipidomic analysis of bmm mutants revealed excess triglyceride accumulation, and spermatogenic defects in bmm mutants were rescued by genetically blocking triglyceride synthesis, our data suggest that bmm-mediated regulation of triglyceride influences sperm development. This identifies triglyceride as an important neutral lipid that contributes to Drosophila sperm development, and reveals a key role for bmm in regulating testis triglyceride levels during spermatogenesis.

developmental biology↗

bioRxiv2021

Cdk8 directly regulates glycolysis via phosphorylation of Gcr2

CDK8 encodes an evolutionarily conserved Mediator complex kinase subunit that functions in general and context-specific transcription regulation by phosphorylating core components of the transcription machinery and gene-specific transcription factors. To better understand the role Cdk8 in transcription regulation, we performed high-resolution gene expression time course analysis following nuclear depletion of Cdk8. Focusing on the earliest gene expression alterations revealed dysregulation of genes encoding glycolysis enzymes, suggesting a functional link to Gcr1 and Gcr2, key transcriptional activators of these genes. Consistently, we found that nuclear depletion of Cdk8 altered the mRNA levels of glycolysis genes as well as the promoter occupancy of Gcr2, but not Gcr1. Examination of the Gcr2 protein sequence revealed a putative Cdk8 phosphorylation site at serine 365, which we confirmed using in vitro and in vivo assays. Importantly, phospho-mutant GCR2 recapitulated the growth and gene expression defects of the GCR2 deletion mutant, effects not observed with a phospho mimetic mutant. As such, our work highlights Gcr2 as a new Cdk8 substrate, revealing that its phosphorylation is critical for the activation of genes encoding glycolysis enzymes.

molecular biology↗

bioRxiv2017

Conserved roles of RECQ-like helicases Sgs1 and BLM in preventing R-loop induced genome instability

Sgs1 is a yeast DNA helicase functioning in DNA replication and repair, and is the orthologue of the human Blooms syndrome helicase BLM. Here we analyze the mutation signature associated with SGS1 deletion in yeast, and find frequent copy number changes flanked by regions of repetitive sequence and high R-loop forming potential. We show that loss of SGS1 increases R-loop accumulation and sensitizes cells to replication-transcription collisions. Accordingly, in sgs1{Delta} cells the genome-wide distribution of R-loops shifts to known sites of Sgs1 action, replication pausing regions, and to long genes. Depletion of the orthologous BLM helicase from human cancer cells also increases R-loop levels, and R-loop-associated genome instability. In support of a direct effect, BLM is found physically proximal to DNA:RNA hybrids in human cells, and can efficiently unwind R-loops in vitro. Together our data describe a conserved role for Sgs1/BLM in R-loop suppression and support an increasingly broad view of DNA repair and replication fork stabilizing proteins as modulators of R-loop mediated genome instability.

cell biology↗