Discipline: Biological Sciences
Subcategory: Cell and Molecular Biology
Room: Exhibit Hall A
Helene Mantineo - Wheaton College MA
Co-Author(s): Benjamin L. King, Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME; Emily Robinson, Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME
The capacity to regenerate tissues after injury is not equal across vertebrates. Humans can regenerate some tissues whereas other vertebrates, such as the zebrafish (Danio rerio), can regenerate nearly any tissue after injury, including heart and caudal fin tissues. The long-term goal of this research is to discover the genetic factors that regulate regenerative capacity. One important class of regulatory genes are long non-coding RNA genes (lncRNAs). We hypothesize that lncRNAs function as pro-regenerative factors in tissue regeneration and that these lncRNAs are expressed in early stages of regeneration in multiple tissues. To begin to investigate our hypothesis, we analyzed high-throughput RNA sequencing gene expression data across multiple stages of adult zebrafish heart and caudal fin regeneration to identify lncRNAs that were differentially expressed in both tissues only during early stages of regeneration. The zebrafish heart regenerates in approximately 30 days following ventricular resection and we analyzed gene expression data for samples taken at 0, 1, 3, 7, 14, 21 and 30 days post ventricular resection (dpr). The caudal fin regenerates in approximately 14 days following amputation and we data characterized samples at 0, 2, 4, and 14 days post amputation (dpa). Trimmed RNA sequence data were mapped to the zebrafish GRCz11 genome assembly using HISAT2 and the resulting alignments and Ensembl (version 93) annotation were used to generate transcript models using StringTie. Read counts per transcript were generated for all samples using HTSeq and analyzed to find differentially expressed transcripts between timepoints in heart and caudal fin using the R/DESeq2 package. We found a total of 1,077 transcripts that were commonly differentially expressed between early stages of both heart (1 vs. 0 dpr and 3 vs. 0 dpr) and caudal fin (2 vs. 0 dpa and 4 vs. 0 dpa) regeneration. 637 of these transcripts were novel as they had not been annotated by Ensembl. Of the remaining 440 transcripts that matched existing annotation, 19 were from genes associated with heart regeneration based on literature and Gene Ontology annotations. Next, we searched for novel lncRNA transcripts with gene expression patterns that were highly correlated (|r2| > 0.75) with the set of 19 transcripts. One candidate lncRNA found on chromosome 5 was negatively correlated with anaphase promoting complex subunit 2 (anapc2), a cell cycle gene important in that also maps to chromosome 5. Cell cycle genes are important in the differentiation of cells during regeneration. This study found a set of 1,077 genes, including non-coding genes, that are commonly differentially expressed during early stages of heart and fin regeneration. These results suggest that these genes function together to initiate regeneration. A future direction would be including gene expression data of other regenerating tissues (e.g., muscle) to further refine the genes required for initiating regeneration.
Funder Acknowledgement(s): Research supported by REU Site: Accelerating New Environmental Workskills (NSF Award #1849802); RNA-Seq studies were conducted by the Voot Yin Laboratory and funded by NIH P20 GM103423.
Faculty Advisor: Benjamin L. King, firstname.lastname@example.org
Role: My part of the project was first analyzing the heart regeneration data. Then, I compared the early stages of heart and caudal fin regeneration data in which we found 1,077 transcripts that seem to act as pro-regenerative factors. After continuing to analyze these 1,077 transcripts, I found at least one potential long non-coding RNA that may regulate the anaphase promoting complex subunit 2.