Microprotein-encoding RNA regulation in cells treated with pro-inflammatory and pro-fibrotic stimuli
Background Recent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of previously unannotated microprotein-coding small open reading frames (smORFs). Most functional microproteins were chosen for characterization because...
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| Published in | BMC genomics Vol. 25; no. 1; pp. 1034 - 21 |
|---|---|
| Main Authors | , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
BioMed Central
05.11.2024
BioMed Central Ltd Springer Nature B.V BMC |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1471-2164 1471-2164 |
| DOI | 10.1186/s12864-024-10948-1 |
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| Abstract | Background
Recent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of previously unannotated microprotein-coding small open reading frames (smORFs). Most functional microproteins were chosen for characterization because of their evolutionary conservation. However, one example of a non-conserved immunomodulatory microprotein in mice suggests that strict sequence conservation misses some intriguing microproteins.
Results
We examine the ability of gene regulation to identify human microproteins with potential roles in inflammation or fibrosis of the intestine. To do this, we collected ribosome profiling data of intestinal cell lines and peripheral blood mononuclear cells and used gene expression of microprotein-encoding transcripts to identify strongly regulated microproteins, including several examples of microproteins that are only conserved with primates.
Conclusion
This approach reveals a number of new microproteins worthy of additional functional characterization and provides a dataset that can be queried in different ways to find additional gut microproteins of interest. |
|---|---|
| AbstractList | Recent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of previously unannotated microprotein-coding small open reading frames (smORFs). Most functional microproteins were chosen for characterization because of their evolutionary conservation. However, one example of a non-conserved immunomodulatory microprotein in mice suggests that strict sequence conservation misses some intriguing microproteins.
We examine the ability of gene regulation to identify human microproteins with potential roles in inflammation or fibrosis of the intestine. To do this, we collected ribosome profiling data of intestinal cell lines and peripheral blood mononuclear cells and used gene expression of microprotein-encoding transcripts to identify strongly regulated microproteins, including several examples of microproteins that are only conserved with primates.
This approach reveals a number of new microproteins worthy of additional functional characterization and provides a dataset that can be queried in different ways to find additional gut microproteins of interest. Abstract Background Recent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of previously unannotated microprotein-coding small open reading frames (smORFs). Most functional microproteins were chosen for characterization because of their evolutionary conservation. However, one example of a non-conserved immunomodulatory microprotein in mice suggests that strict sequence conservation misses some intriguing microproteins. Results We examine the ability of gene regulation to identify human microproteins with potential roles in inflammation or fibrosis of the intestine. To do this, we collected ribosome profiling data of intestinal cell lines and peripheral blood mononuclear cells and used gene expression of microprotein-encoding transcripts to identify strongly regulated microproteins, including several examples of microproteins that are only conserved with primates. Conclusion This approach reveals a number of new microproteins worthy of additional functional characterization and provides a dataset that can be queried in different ways to find additional gut microproteins of interest. Recent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of previously unannotated microprotein-coding small open reading frames (smORFs). Most functional microproteins were chosen for characterization because of their evolutionary conservation. However, one example of a non-conserved immunomodulatory microprotein in mice suggests that strict sequence conservation misses some intriguing microproteins. We examine the ability of gene regulation to identify human microproteins with potential roles in inflammation or fibrosis of the intestine. To do this, we collected ribosome profiling data of intestinal cell lines and peripheral blood mononuclear cells and used gene expression of microprotein-encoding transcripts to identify strongly regulated microproteins, including several examples of microproteins that are only conserved with primates. This approach reveals a number of new microproteins worthy of additional functional characterization and provides a dataset that can be queried in different ways to find additional gut microproteins of interest. Background Recent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of previously unannotated microprotein-coding small open reading frames (smORFs). Most functional microproteins were chosen for characterization because of their evolutionary conservation. However, one example of a non-conserved immunomodulatory microprotein in mice suggests that strict sequence conservation misses some intriguing microproteins. Results We examine the ability of gene regulation to identify human microproteins with potential roles in inflammation or fibrosis of the intestine. To do this, we collected ribosome profiling data of intestinal cell lines and peripheral blood mononuclear cells and used gene expression of microprotein-encoding transcripts to identify strongly regulated microproteins, including several examples of microproteins that are only conserved with primates. Conclusion This approach reveals a number of new microproteins worthy of additional functional characterization and provides a dataset that can be queried in different ways to find additional gut microproteins of interest. Recent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of previously unannotated microprotein-coding small open reading frames (smORFs). Most functional microproteins were chosen for characterization because of their evolutionary conservation. However, one example of a non-conserved immunomodulatory microprotein in mice suggests that strict sequence conservation misses some intriguing microproteins.BACKGROUNDRecent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of previously unannotated microprotein-coding small open reading frames (smORFs). Most functional microproteins were chosen for characterization because of their evolutionary conservation. However, one example of a non-conserved immunomodulatory microprotein in mice suggests that strict sequence conservation misses some intriguing microproteins.We examine the ability of gene regulation to identify human microproteins with potential roles in inflammation or fibrosis of the intestine. To do this, we collected ribosome profiling data of intestinal cell lines and peripheral blood mononuclear cells and used gene expression of microprotein-encoding transcripts to identify strongly regulated microproteins, including several examples of microproteins that are only conserved with primates.RESULTSWe examine the ability of gene regulation to identify human microproteins with potential roles in inflammation or fibrosis of the intestine. To do this, we collected ribosome profiling data of intestinal cell lines and peripheral blood mononuclear cells and used gene expression of microprotein-encoding transcripts to identify strongly regulated microproteins, including several examples of microproteins that are only conserved with primates.This approach reveals a number of new microproteins worthy of additional functional characterization and provides a dataset that can be queried in different ways to find additional gut microproteins of interest.CONCLUSIONThis approach reveals a number of new microproteins worthy of additional functional characterization and provides a dataset that can be queried in different ways to find additional gut microproteins of interest. Background Recent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of previously unannotated microprotein-coding small open reading frames (smORFs). Most functional microproteins were chosen for characterization because of their evolutionary conservation. However, one example of a non-conserved immunomodulatory microprotein in mice suggests that strict sequence conservation misses some intriguing microproteins. Results We examine the ability of gene regulation to identify human microproteins with potential roles in inflammation or fibrosis of the intestine. To do this, we collected ribosome profiling data of intestinal cell lines and peripheral blood mononuclear cells and used gene expression of microprotein-encoding transcripts to identify strongly regulated microproteins, including several examples of microproteins that are only conserved with primates. Conclusion This approach reveals a number of new microproteins worthy of additional functional characterization and provides a dataset that can be queried in different ways to find additional gut microproteins of interest. Keywords: Small open reading frames (smORFs), Microproteins, Ribosome profiling, Inflammation, Fibrosis BackgroundRecent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of previously unannotated microprotein-coding small open reading frames (smORFs). Most functional microproteins were chosen for characterization because of their evolutionary conservation. However, one example of a non-conserved immunomodulatory microprotein in mice suggests that strict sequence conservation misses some intriguing microproteins.ResultsWe examine the ability of gene regulation to identify human microproteins with potential roles in inflammation or fibrosis of the intestine. To do this, we collected ribosome profiling data of intestinal cell lines and peripheral blood mononuclear cells and used gene expression of microprotein-encoding transcripts to identify strongly regulated microproteins, including several examples of microproteins that are only conserved with primates.ConclusionThis approach reveals a number of new microproteins worthy of additional functional characterization and provides a dataset that can be queried in different ways to find additional gut microproteins of interest. |
| ArticleNumber | 1034 |
| Audience | Academic |
| Author | Vaughan, Joan M. Pinto, Antonio M. Pai, Victor J. Gavva, Narender R. Saghatelian, Alan De Souza, Eduardo V. Diedrich, Jolene Donaldson, Cynthia Yu, Shan Garcia-Ruiz, Almudena Miller, Brendan Horman, Shane R. DeBoever, Christopher Lau, Calvin J. |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/39497054$$D View this record in MEDLINE/PubMed |
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| Keywords | Small open reading frames (smORFs) Microproteins Inflammation Ribosome profiling Fibrosis |
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| Snippet | Background
Recent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of... Recent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of previously... Background Recent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of... BackgroundRecent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of... Abstract Background Recent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of... |
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| Title | Microprotein-encoding RNA regulation in cells treated with pro-inflammatory and pro-fibrotic stimuli |
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