The composition of untranslated regions in Trypanosoma cruzi genes

Brandão, Adeílton; Jiang, Taijiao

doi:10.1016/j.parint.2009.06.001

Cited by 15 publications

(10 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Visual inspection of the density (sequencing depth) of mapped reads suggests that several reads mapped on UTRs regions, predominantly on 3′UTR. It should be mentioned that T. cruzi UTR lengths vary according to the gene size, and have been estimated from experimentally mapped genes to range from 10-400 bp for 5′UTR and 17-2800 bp for 3′UTR (Brandao & Jiang, 2009), being 3′UTR 2-3 times longer than its corresponding 5′UTR (Ziccardi & Brandao, 2011). This result reinforces previous findings showing the relevance of 3′UTRs in the regulation of gene expression (Coughlin et al, 2000; Da Silva, Bartholomeu & Teixeira, 2006; Di Noia et al, 2000; Nozaki & Cross, 1995; Weston, La Flamme & Van Voorhis, 1999).…”

Section: Resultsmentioning

confidence: 99%

Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition inTrypanosoma cruzi

Berná

Chiribao

Greif

et al. 2017

PeerJ

View full text Add to dashboard Cite

American trypanosomiasis is a chronic and endemic disease which affects millions of people. Trypanosoma cruzi, its causative agent, has a life cycle that involves complex morphological and functional transitions, as well as a variety of environmental conditions. This requires a tight regulation of gene expression, which is achieved mainly by post-transcriptional regulation. In this work we conducted an RNAseq analysis of the three major life cycle stages of T. cruzi: amastigotes, epimastigotes and trypomastigotes. This analysis allowed us to delineate specific transcriptomic profiling for each stage, and also to identify those biological processes of major relevance in each state. Stage specific expression profiling evidenced the plasticity of T. cruzi to adapt quickly to different conditions, with particular focus on membrane remodeling and metabolic shifts along the life cycle. Epimastigotes, which replicate in the gut of insect vectors, showed higher expression of genes related to energy metabolism, mainly Krebs cycle, respiratory chain and oxidative phosphorylation related genes, and anabolism related genes associated to nucleotide and steroid biosynthesis; also, a general down-regulation of surface glycoprotein coding genes was seen at this stage. Trypomastigotes, living extracellularly in the bloodstream of mammals, express a plethora of surface proteins and signaling genes involved in invasion and evasion of immune response. Amastigotes mostly express membrane transporters and genes involved in regulation of cell cycle, and also express a specific subset of surface glycoprotein coding genes. In addition, these results allowed us to improve the annotation of the Dm28c genome, identifying new ORFs and set the stage for construction of networks of co-expression, which can give clues about coded proteins of unknown functions.

show abstract

Section: Resultsmentioning

confidence: 99%

Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition inTrypanosoma cruzi

Berná

Chiribao

Greif

et al. 2017

PeerJ

View full text Add to dashboard Cite

show abstract

“…Towards this goal, we carried out a global analysis using T. cruzi genomic data (El-Sayed et al, 2005). Since there is no information available for T. cruzi RNA-seq reads, noncoding sequences have been inferred from average lengths of 5′- and 3′-UTRs of T. cruzi published transcripts (Brandao & Jiang, 2009; Campos et al, 2008) and extracted from TriTrypDB () (Methods). These sequences were classified into functional categories in accordance to the KEGG pathway database (Kanehisa & Goto, 2000) ().…”

Section: Resultsmentioning

confidence: 99%

Genome-wide analysis of 3′-untranslated regions supports the existence of post-transcriptional regulons controlling gene expression in trypanosomes

Gaudenzi

Carmona

Agüero

et al. 2013

PeerJ

View full text Add to dashboard Cite

In eukaryotic cells, a group of messenger ribonucleic acids (mRNAs) encoding functionally interrelated proteins together with the trans-acting factors that coordinately modulate their expression is termed a post-transcriptional regulon, due to their partial analogy to a prokaryotic polycistron. This mRNA clustering is organized by sequence-specific RNA-binding proteins (RBPs) that bind cis-regulatory elements in the noncoding regions of genes, and mediates the synchronized control of their fate. These recognition motifs are often characterized by conserved sequences and/or RNA structures, and it is likely that various classes of cis-elements remain undiscovered. Current evidence suggests that RNA regulons govern gene expression in trypanosomes, unicellular parasites which mainly use post-transcriptional mechanisms to control protein synthesis. In this study, we used motif discovery tools to test whether groups of functionally related trypanosomatid genes contain a common cis-regulatory element. We obtained conserved structured RNA motifs statistically enriched in the noncoding region of 38 out of 53 groups of metabolically related transcripts in comparison with a random control. These motifs have a hairpin loop structure, a preferred sense orientation and are located in close proximity to the open reading frames. We found that 15 out of these 38 groups represent unique motifs in which most 3′-UTR signature elements were group-specific. Two extensively studied Trypanosoma cruzi RBPs, TcUBP1 and TcRBP3 were found associated with a few candidate RNA regulons. Interestingly, 13 motifs showed a strong correlation with clusters of developmentally co-expressed genes and six RNA elements were enriched in gene clusters affected after hyperosmotic stress. Here we report a systematic genome-wide in silico screen to search for novel RNA-binding sites in transcripts, and describe an organized network of several coordinately regulated cohorts of mRNAs in T. cruzi. Moreover, we found that structured RNA elements are also conserved in other human pathogens. These results support a model of regulation of gene expression by multiple post-transcriptional regulons in trypanosomes.

show abstract

“…5Ј upstream genomic sequences and 3Ј downstream genomic sequences were obtained using TcruziDB sequence retrieval tool. A length of 50 nt upstream to the coding sequences was used to obtain sequences resembling the 5ЈUTR, and 350 nt downstream to the coding sequences were used for 3ЈUTR, in agreement with previously reported data from trypanosomes (21)(22)(23).…”

Section: Methodsmentioning

confidence: 98%

Hyperosmotic Stress Induces Aquaporin-dependent Cell Shrinkage, Polyphosphate Synthesis, Amino Acid Accumulation, and Global Gene Expression Changes in Trypanosoma cruzi

Álvarez

Gaudenzi

et al. 2011

Journal of Biological Chemistry

View full text Add to dashboard Cite

Background: Trypanosoma cruzi is subjected to hyperosmotic stress during its life cycle. Results: The recovery from hyperosmotic stress involves the function of an aquaporin, amino acid accumulation, polyphosphate synthesis, and global gene regulation. Conclusion:The response to hyperosmotic stress is different from that observed in mammalian cells or yeasts. Significance: Learning the mechanism of osmoregulation is important for finding new drug targets.

show abstract

The composition of untranslated regions in Trypanosoma cruzi genes

Cited by 15 publications

References 35 publications

Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition inTrypanosoma cruzi

Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition inTrypanosoma cruzi

Genome-wide analysis of 3′-untranslated regions supports the existence of post-transcriptional regulons controlling gene expression in trypanosomes

Hyperosmotic Stress Induces Aquaporin-dependent Cell Shrinkage, Polyphosphate Synthesis, Amino Acid Accumulation, and Global Gene Expression Changes in Trypanosoma cruzi

Contact Info

Product

Resources

About