Identification of Novel Interspersed DNA Repetitive Elements in the Trypanosoma cruzi Genome Associated with the 3'UTRs of Surface Multigenic Families.

Simone Guedes Calderano,Maria Carolina Elias,Marcelo Da Silva Reis,Julia Pinheiro Chagas Da Cunha,Marjorie Marini,José Salvatore Leister Patané,Milton Yutaka Nishiyama Junior,José Franco Da Silveira,Nathan De Oliveira Nunes

doi:10.3390/genes11101235

Simone Guedes Calderano, Maria Carolina Elias + Show 7 more

Open Access

https://doi.org/10.3390/genes11101235

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Abstract

Trypanosoma cruzi is the etiological agent of Chagas disease, which affects millions of people in Latin America. No transcriptional control of gene expression has been demonstrated in this organism, and 50% of its genome consists of repetitive elements and members of multigenic families. In this study, we applied a novel bioinformatics approach to predict new repetitive elements in the genome sequence of T. cruzi. A new repetitive sequence measuring 241 nt was identified and found to be interspersed along the genome sequence from strains of different DTUs. This new repeat was mostly on intergenic regions, and upstream and downstream regions of the 241 nt repeat were enriched in surface protein genes. RNAseq analysis revealed that the repeat was part of processed mRNAs and was predominantly found in the 3′ untranslated regions (UTRs) of genes of multigenic families encoding surface proteins. Moreover, we detected a correlation between the presence of the repeat in the 3′UTR of multigenic family genes and the level of differential expression of these genes when comparing epimastigote and trypomastigote transcriptomes. These data suggest that this sequence plays a role in the posttranscriptional regulation of the expression of multigenic families.

Highlights

The protozoan T. cruzi is the causative agent of Chagas disease and affects approximately million people, mostly in Central and South America, where another 18 million people live at risk of infection [1]
The T. cruzi genome is composed of diverse repetitive elements that vary in size and copy number among different strains
We decided to start investigating both haplotypes (Esmeraldo like-S and non-Esmeraldo like-P) of the clone CL Brener genome sequence. This strain was used for the T. cruzi genome sequence project, and a considerable amount of information is available allowing future co-relation analysis

Summary

Introduction

The protozoan T. cruzi is the causative agent of Chagas disease and affects approximately million people, mostly in Central and South America, where another 18 million people live at risk of infection [1] This parasite exhibits a complex life cycle varying between the nonreplicative/infective form, known as the trypomastigote (bloodstream in mammalian host and metacyclic inside the vector), and the replicative forms, known as the amastigote (in the mammalian host) and. Other levels of gene expression regulation stand out, such as mRNA processing [6], translational repression [7,8,9], polysome recruitment [10], and codon adaptation [11,12]. In this scenario, noncoding DNA may be involved as a regulatory element in mRNA expression [10,11,12,13]

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