The functions of most long non-coding RNAs (lncRNAs) are unknown. In contrast to proteins, lncRNAs with similar functions often lack linear sequence homology; thus, the identification of function in one lncRNA rarely informs the identification of function in others. We developed a sequence comparison method to deconstruct linear sequence relationships in lncRNAs and evaluate similarity based on the abundance of short motifs called k-mers. We found that lncRNAs of related function often had similar k-mer profiles despite lacking linear homology, and that k-mer profiles correlated with protein binding to lncRNAs and with their subcellular localization. Using a novel assay to quantify Xist-like regulatory potential, we directly demonstrated that evolutionarily unrelated lncRNAs can encode similar function through different spatial arrangements of related sequence motifs. K-mer-based classification is a powerful approach to detect recurrent relationships between sequence and function in lncRNAs.
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We thank UNC colleagues for discussions, and J. Cheng for help with TETRIS cloning. This work was supported by National Institutes of Health (NIH) Grants UL1TR002489, GM121806, and GM105785, Basil O’Connor Award no. 5100683 from the March of Dimes Foundation, and funds from the Eshelman Institute for Innovation, the Lineberger Comprehensive Cancer Center and the UNC Department of Pharmacology (J.M.C.), the James S. McDonnell Foundation 21st Century Science Initiative–Complex Systems Scholar Award Grant no. 220020315 (P.J.M.), and NIH MIRA award R35 GM122532 (K.M.W.). J.M.K. is an NSF Graduate Research Fellow (Grant DGE-1650116) and was supported in part by an NIH training grant in bioinformatics and computational biology (T32 GM067553). D.M.L. was supported in part by an NIH training grant in genetics and molecular biology (T32 GM007092). M.J.S. was an NSF Graduate Research Fellow (Grant DGE-1144081) and was supported in part by an NIH training grant in molecular and cellular biophysics (Grant T32 GM08570).
The authors declare no competing interests.
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Supplementary Figures 1–11 and Supplementary Tables 2–6, 9, 10, 13–17 and 21
List of curated cis-regulatory lncRNAs in human and mouse
Human lncRNA community assignments and descriptions
Mouse lncRNA community assignments and descriptions
Human community k-mer profiles
Mouse community k-mer profiles
k-mer abundance in nuclear and cytosolic lncRNAs
Protein log-likelihood results comparing the predictive power of null versus full logistic regression models
Protein logistic regression (LR) precision and recall results
TETRIS-lncRNA fragment information
Oligonucleotide primers for the TETRIS assay
A library for counting small k-mer frequencies in nucleotide sequences
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Kirk, J.M., Kim, S.O., Inoue, K. et al. Functional classification of long non-coding RNAs by k-mer content. Nat Genet 50, 1474–1482 (2018). https://doi.org/10.1038/s41588-018-0207-8
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