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Biology subjects

Perez, A. R.

Publications and source records attributed to Perez, A. R..

3 recordsLinked to original sources

TcBDF6 deficiency compromises intracellular amastigotes development and infectivity in Trypanosoma cruzi

Trypanosoma cruzi, the causative agent of Chagas disease, relies on complex gene regulatory mechanisms to adapt to its diverse host environments. In recent years, it has been established that epigenetics plays an essential role in these mechanisms via the regulation of chromatin structure. Bromodomain-containing factors (BDFs), known for recognizing acetylated lysines on histones, have emerged as key factors in chromatin remodeling complexes. Among the eight predicted BDFs in T. cruzi, BDF6 is part of a TINTIN-like complex with MRGx and MRGBP, homologous to components of the NuA4/TIP60 chromatin remodeling complex. We generated knockout (KO) parasites for bdf6 gene using CRISPR/Cas9 gene editing. BDF6-deficient epimastigotes exhibit normal morphology but decreased size and growth and the resulting metacyclic trypomastigotes displayed drastically reduced infectivity. Strikingly, once inside host cells, BDF6-deficient parasites differentiated into amastigotes but failed to replicate. This intracellular arrest was reversed by episomal complementation of BDF6. Consistently, BDF6-KO parasites also exhibited impaired infectivity in mice, a defect that was also rescued in the add back parasite strains. Our findings highlight BDF6 as a critical regulator of intracellular parasite development, operating in stages beyond epimastigotes where epigenetic plasticity is essential for host adaptation. This striking stage-specific phenotype of BDF6 KO underscores its functional importance and highlights the relevance of epigenetic regulators along T. cruzis life cycle.

microbiology↗

Interhelical E@g-N@a Interactions Modulate Coiled Coil Stability within a De Novo Set of Orthogonal Peptide Heterodimers

The designability of orthogonal coiled coil (CC) dimers, which draw on well-established design rules, plays a pivotal role in fueling the development of CCs as synthetically versatile assembly-directing motifs for the fabrication of bionanomaterials. Here, we aim to expand the synthetic CC toolkit through establishing a "minimalistic" set of orthogonal, de novo CC peptides that comprise 3.5 heptads in length and a single buried Asn to prescribe dimer formation. The designed sequences display excellent partner fidelity, confirmed via circular dichroism (CD) spectroscopy, and are corroborated in silico using molecular dynamics (MD) simulation. Detailed analysis of the MD conformational data highlights the importance of interhelical E@g-N@a interactions in coordinating an extensive 6-residue hydrogen bonding network that "locks" the interchain Asn-Asn contact in place. The enhanced stability imparted to the Asn-Asn bond elicits an increase in thermal stability of CCs up to [~]15{degrees}C and accounts for significant differences in stability within the collection of similarly designed orthogonal CC pairs. The presented work underlines the utility of MD simulation as a tool for constructing de novo, orthogonal CCs, and presents an alternative handle for modulating the stability of orthogonal CCs via tuning the number of interhelical E@g-N@a contacts. Expansion of CC design rules is a key ingredient for guiding the design and assembly of more complex, intricate CC-based architectures for tackling a variety of challenges within the fields of nanomedicine and bionanotechnology.

biochemistry↗

Correction of Off-Targeting in CRISPR Screens Uncovers Genetic Dependencies in Melanoma Cells

Off-target cleavage by Cas9 can confound measurements of cell proliferation/viability in CRISPR assays by eliciting a DNA-damage response that includes cell cycle arrest1-3. This gene-independent toxicity has been documented in large scale assays2-4 and shown to be a source of false-positives when libraries are populated by promiscuous guide RNAs (gRNAs)7. To address this, we developed CSC, a computational method to correct for the effect of specificity on gRNA depletion. We applied CSC to screening data from the Cancer Dependency Map and show that it significantly improves the specificity of CRISPR-Cas9 essentiality screens while preserving known gene essentialities even for genes targeted by highly pro-miscuous guides. We packaged CSC in a Python software to allow its seamless integration into current CRISPR analysis pipelines and improve the sensitivity of essentiality screens for repetitive genomic loci.

genomics↗