Computational analysis of transcriptomic alterations induced by stress granules in human cells

• Grant number: 16/25521-1
• Support Opportunities: Scholarships in Brazil - Master
• Effective date (Start): April 01, 2017
• Effective date (End): February 28, 2018
• Field of knowledge: Biological Sciences - Genetics - Human and Medical Genetics
• Acordo de Cooperação: Coordination of Improvement of Higher Education Personnel (CAPES)
• Principal Investigator: Katlin Brauer Massirer
• Grantee: Felipe Eduardo Ciamponi
• Host Institution: Centro de Biologia Molecular e Engenharia Genética (CBMEG). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil

Abstract

Stress granules are aggregates of proteins and RNAs found in the cytoplasm of cells, generally produced in response to a form of environmental stress. However, several neurodegenerative diseases, such as amyotrophic lateral sclerosis and Alzheimer's, have already been associated with pathogenic inclusions of these aggregates, which have deleterious consequences to the cell. Among the proteins present in the stress granule the G3BP1-CAPRIN1-USP10 complex is essential for the condensation of the granule and its association with ribosomal subunits, and the ectopic expression of CAPRIN1 is sufficient to induce the formation of granules. Although the molecular mechanisms associated with the granules are not completely elucidated, one of the main functions proposed for these structures is the reprogramming of the gene expression (transcriptome). One of the altered transcriptomic processes in stress situations is that of alternative splicing. The main consequence of such changes is the modification of the nucleotide sequence that will make up the final transcript by modifying the exonic regions used in the mRNA composition. The processes of alternative splicing have already been shown to be of vital importance in the process of stress response in various organisms. However, global scale assessments of these stress granule events are still lacking in human cell culture models. Preliminary results obtained from large-scale RNA sequencing (RNAseq), after ectopic expression of CAPRIN1, indicated the existence of 1058 alternative splicing events occurring in annotated transcripts. We also identified the existence of 12484 new isoforms and 875 unidentified transcripts that may represent novel genes associated with the formation of stress granules. Our work aims at the identification, characterization and annotation of these events found in the altered transcriptome of cells with induction of stress granules. For this we will evaluate the existence of enriched functional groups in the transcripts where alternative exons were identified, as well as the impact that these events may be causing in the transcript. Regarding the new isoforms, we will evaluate them as to their coding potential, presence of repetitive elements and alterations in the functional sequence. For the unknown transcripts, we will also perform a functional annotation step of the sequence. The present work presents the first proposal of a global characterization of transcriptome alteration events in human cells under induction of stress granules using RNAseq data. (AU)

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

WU, QIN; NIE, DAVID Y.; BA-ALAWI, WAIL; JI, YISHUAI; ZHANG, ZIWEN; CRUICKSHANK, JENNIFER; HAIGHT, JILLIAN; CIAMPONI, FELIPE E.; CHEN, JOCELYN; DUAN, SHILI; et al. PRMT inhibition induces a viral mimicry response in triple-negative breast cancer. Nature Chemical Biology, v. N/A, p. 22-pg., 2022-05-16. (15/25134-5, 20/02006-0, 16/25521-1, 14/50897-0)

SACHAMITR, PATTY; HO, JOLENE C.; CIAMPONI, FELIPE E.; BA-ALAWI, WAIL; COUTINHO, FIONA J.; GUILHAMON, PAUL; KUSHIDA, MICHELLE M.; CAVALLI, FLORENCE M. G.; LEE, LILIAN; RASTEGAR, NAGHMEH; et al. PRMT5 inhibition disrupts splicing and stemness in glioblastoma. NATURE COMMUNICATIONS, v. 12, n. 1, FEB 12 2021. (16/25521-1, 15/25134-5, 14/50897-0, 14/21704-9)