Introduction

NcPEPs are mainly identified by computational prediction software for potential ORFs, and out of many predicted ncPEPs, only a handful of them have been characterized by MS and techniques such as western blotting, immunohistochemistry, and ribosome profiling. Moreover, functional characterization of ncPEP is difficult and limiting and more effective techniques for functional validation are warranted to expand this field. Only a few experimentally discovered ncPEPs have been functionally characterized in last decade to understand their role in ncRNA-associated pathology and in tissue homeostasis. The biologically active short ncPEPs are functionally distinct from peptides translated from highly conserved messenger RNAs (mRNAs) or short peptides generated through the breakdown of large proteins. For example, human smORFs are not always conserved beyond primates while several human proteins are highly conserved across species. Regarding the function of human ncPEPs, they are mostly involved in rapidly changing adaptive processes such as immunity and tumorigenesis.

Studies reporting ncPEPs using indirect (in silico analyses and peptide sequencing data without molecular validation) and predictive methods need more characterization and cannot be argued to be functional. Therefore, in 2020 we have put together the first database of functional ncRNA-encoded peptides (FuncPEP) including only ncPEPs validated by experimental methods and functionally characterized. As proteomics technologies significantly developed, we hypothesized that in the last years the discovery of ncPEPs escalated and, therefore we performed an update of our previous database version. This revised version of the database (FuncPEP v2.0) includes the new functional ncPEPs published in the last 3 years along with the categorization of the host ncRNA from which they are derived.

Citation

Dragomir MP, Manyam GC, Ott LF, Berland L, Knutsen E, Ivan C, Lipovich L, Broom BM, Calin GA. FuncPEP: A Database of Functional Peptides Encoded by Non-Coding RNAs. Noncoding RNA. 2020 Sep 23;6(4):41. doi: 10.3390/ncrna6040041. PMID: 32977531; PMCID: PMC7712257.
Swati M, Anik B, Paola R, Manyam GC, Broom BM, Calin GA. FuncPEP 2.0: A Database of Functional Peptides Encoded by Non-Coding RNAs. Noncoding RNA (in submission)

Contact

George Calin Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.