Biology subjects

Pires, D. d. S.

Publications and source records attributed to Pires, D. d. S..

3 recordsLinked to original sources

bioRxiv2024

Integrating tDNA Epigenomics and Expression with Codon Usage Unravel an Intricate Connection with Protein Expression Dynamics in Trypanosoma cruzi

Codon usage bias impacts protein expression across all kingdoms of life, including trypanosomatids. These protozoa, such as the Trypanosoma cruzi, primarily regulate their protein-coding genes through posttranscriptional mechanisms. Here, we integrated analyses of codon usage with multiple high-throughput sequencing data to investigate whether codon usage bias is present into surface virulence factors (disruptive compartment), conserved housekeeping proteins (core compartment), and proteins involved in the developmental stages of T. cruzi. For the first time in trypanosomatids, tRNA sequencing was employed to reveal coadaptation between codon usage and anticodon availability. Despite notable differences in the proteomes of infective and non-infective forms, they exhibited similar pools of tRNAs and similar codon usage preferences. We observed that open chromatin levels of tRNA genes correlate with tRNA expression in non-infective forms, but not in infective forms, suggesting chromatin states do not control the tRNA pool in the latter. Our analysis also revealed a relationship between anticodon:codon pairing modes and protein abundance. Highly expressed mRNAs favored Watson- Crick base pairing, whereas less expressed mRNAs displayed more wobble base pairing. Overall, our findings suggest that protein expression in T. cruzi is influenced by a combination of codon usage bias, tRNA abundance, and anticodon:codon pairing modes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/602108v2_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@1f63f77org.highwire.dtl.DTLVardef@1c0abf8org.highwire.dtl.DTLVardef@5a4988org.highwire.dtl.DTLVardef@1918f49_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2024

Hidden origami in Trypanosoma cruzi nuclei highlights its nonrandom 3D genomic organization

The protozoan Trypanosoma cruzi, the causative agent of Chagas disease, exhibits polycistronic transcription and unidimensional genome compartmentalization of core (conserved) and disruptive (virulence factors from multigenic families) genes. Approximately 50% of its genome is repetitive, mainly virulence factor genes. Genomic sequences, including repeats, motifs of architectural proteins, and noncoding RNA loci are crucial for genome folding. Here, we evaluated the genomic features associated with higher-order chromatin organization in T. cruzi through extensive computational processing of high-throughput chromosome conformation capture (Hi-C) data, accounting for repetitive regions and improvements in genome annotation. Our study revealed that repetitive DNA (multimapped reads) influences 3D chromatin folding, particularly in determining the boundaries of topologically associated domains (TAD)-like structures. Virulence factor genes, unlike core genes, form shorter and more compact TAD-like structures enriched in loops, suggesting a gene expression regulatory mechanism. We found nonprotein-coding RNA loci (e.g., tRNAs) and transcription termination sites preferentially located at the boundaries of the TAD-like structures, while pseudogenes and multigenic family genes located in unstructured genomic regions. Our data indicate 3D clustering of tRNA loci, likely optimizing transcription by RNA polymerase III, and a complex interaction between spliced-leader RNA and 18S rRNA loci. Our findings provide insights into 3D genome organization in T. cruzi, contributing to the understanding of supranucleosome-level chromatin organization and suggesting possible links between 3D architecture and gene expression. We draw an analogy to the art of origami (e.g., papers folded into various shapes) resembling the DNA packed in chromatin fibers assuming distinct folds within the nucleus. ImportanceDespite the knowledge about the linear genome sequence and the identification of numerous virulence factors in the protozoan parasite Trypanosoma cruzi, there has been a limited understanding of how these genomic features are spatially organized within the nucleus and how this organization impacts gene regulation and pathogenicity. By providing a detailed analysis of the three-dimensional chromatin architecture in T. cruzi, our study contributed to filling this gap. We deciphered part of the origami structure hidden in the T. cruzi nucleus, showing the unidimensional genomic features are nonrandomly organized in the nuclear 3D landscape. We revealed the possible role of non-protein-coding RNA loci (e.g., tRNAs, SL-RNA, and 18S RNA) in shaping the genomic architecture. These findings provide insights into an additional epigenetic layer that may influence gene expression. Graphical abstractThe spatial organization of chromatin within the nuclei of T. cruzi and its resemblance to origami art. A. Identification of the 3D nuclear architectures within T. cruzi nuclei: topologically associating domains (TADs) and their boundaries; chromatin loops; and 3D networks. Inter- and intrachromosomal interactions reflect DNA-DNA contacts on the same (cis) and between different (trans) chromosomes. B. Resemblance between origami art and chromatin folding. Steps "a" to "l" show the process of folding a flat piece of paper from its unidimensional view up to its 3D boat form. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/601582v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1ca38b4org.highwire.dtl.DTLVardef@150bc99org.highwire.dtl.DTLVardef@18de8a9org.highwire.dtl.DTLVardef@1a5efa4_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2021

{-}{-} Histone H2B.V demarcates strategic regions in the Trypanosoma cruzi genome, associates with a bromodomain factor and affects parasite differentiation and host cell invasion

Histone variants play a crucial role in chromatin structure organization and gene expression. Trypanosomatids have an unusual H2B variant (H2B.V) that is known to dimerize with the variant H2A.Z generating unstable nucleosomes. Previously, we found that H2B.V protein is enriched in nonreplicative life forms of Trypanosoma cruzi, suggesting that this variant may contribute to the differences in chromatin structure and global transcription rates observed among parasite life forms. Here, we performed the first genome-wide profiling of histone localization in T. cruzi using replicative and nonreplicative life forms, and we found that H2B.V was preferentially located at the edges of divergent switch regions, which encompass putative transcriptional start regions; at some tDNA loci; and between the conserved and disrupted genome compartments, mainly at trans-sialidase, mucin and MASP genes. Remarkably, the chromatin of nonreplicative forms was depleted of H2B.V-enriched peaks in comparison to replicative forms. Interactome assays indicated that H2B.V associated specifically with H2A.Z, bromodomain factor 2, nucleolar proteins and a histone chaperone, among others. Parasites expressing reduced H2B.V levels were associated with higher rates of parasite differentiation and mammalian cell infectivity. Taken together, H2B.V demarcates critical genomic regions and associates with regulatory chromatin proteins, suggesting a scenario wherein local chromatin structures associated with parasite differentiation and invasion are regulated during the parasite life cycle. Author SummaryTrypanosomatids have to adapt to different environmental conditions, changing their morphology, gene expression and metabolism. These organisms have many unique features in terms of gene expression regulation. The genomic organization includes polycistronic regions with the absence of well-defined transcription start sites. In T. brucei, histone variants mark the start and ending sites of transcription; however, little is known about whether these proteins change their genome location, expression levels and interactors along life forms and what the impact is of these changes on parasite differentiation and infection. In T. cruzi, the causative agent of Chagas disease, we previously found that the histone variant of H2B is enriched in nonreplicative and infective forms, suggesting that this variant may contribute to the differences in chromatin structure and global transcription rates observed among these life forms. Here, we aimed to go one step further and performed the first histone ChIP-seq analysis in T. cruzi, in which we found that H2B.V was enriched at divergent strand switch regions, some tDNA loci and other critical genomic regions associated with T. cruzi genome compartments. We found that H2B.V interacts with a bromodomain factor, suggesting an intricate network involving chromatin acetylation around H2B.V enriched sites. Moreover, parasites expressing reduced H2B.V levels were associated with higher rates of differentiation and mammalian cell infectivity.

microbiology↗