4.7 Article

Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics

Journal

BMC GENOMICS
Volume 22, Issue 1, Pages -

Publisher

BMC
DOI: 10.1186/s12864-021-07474-9

Keywords

Comparative genomics; Structured ncRNAs; Human genomes; Animal genomes; Pipeline

Funding

  1. National Natural Science Foundation of China [31770882]
  2. Provincial Natural Science Foundation of Fujian province [2018 J01051]
  3. Project of Science and Technology of Quanzhou [2018C021]
  4. Xiamen Double-hundred Talent Project [Z1724069]
  5. Huaqiao University Talent Project [Z16Y0015]

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The researchers established a pipeline called CM-line to identify 11 classes of structured ncRNA candidates with significant covariations in the human genome. Functional analysis suggested that these ncRNAs may have variable functions, such as regulating circadian clock genes or the T-cell receptor signaling pathway. The pipeline can be applied to analyze structured ncRNAs and their functions in other large genomes as well.
BackgroundOnly 1.5% of the human genome encodes proteins, while large part of the remaining encodes noncoding RNAs (ncRNA). Many ncRNAs form structures and perform many important functions. Accurately identifying structured ncRNAs in the human genome and discovering their biological functions remain a major challenge.ResultsHere, we have established a pipeline (CM-line) with the following features for analyzing the large genomes of humans and other animals. First, we selected species with larger genetic distances to facilitate the discovery of covariations and compatible mutations. Second, we used CMfinder, which can generate useful alignments even with low sequence conservation. Third, we removed repetitive sequences and known structured ncRNAs to reduce the workload of CMfinder. Fourth, we used Infernal to find more representatives and refine the structure. We reported 11 classes of structured ncRNA candidates with significant covariations in humans. Functional analysis showed that these ncRNAs may have variable functions. Some may regulate circadian clock genes through poly (A) signals (PAS); some may regulate the elongation factor (EEF1A) and the T-cell receptor signaling pathway by cooperating with RNA binding proteins.ConclusionsBy searching for important features of RNA structure from large genomes, the CM-line has revealed the existence of a variety of novel structured ncRNAs. Functional analysis suggests that some newly discovered ncRNA motifs may have biological functions. The pipeline we have established for the discovery of structured ncRNAs and the identification of their functions can also be applied to analyze other large genomes.

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