DOI: 10.1101/482232Nov 29, 2018Paper

High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue-specificity

BioRxiv : the Preprint Server for Biology
Kaia MattioliJohn L Rinn

Abstract

Transcription initiates at both coding and non-coding genomic elements, including mRNA and long non-coding RNA (lncRNA) core promoters and enhancer RNAs (eRNAs). However, each class has different expression profiles with lncRNAs and eRNAs being the most tissue-specific. How these complex differences in expression profiles and tissue-specificities are encoded in a single DNA sequence, however, remains unresolved. Here, we address this question using computational approaches and massively parallel reporter assays (MPRA) surveying hundreds of promoters and enhancers. We find that both divergent lncRNA and mRNA core promoters have higher capacities to drive transcription than non-divergent lncRNA and mRNA core promoters, respectively. Conversely, lincRNAs and eRNAs have lower capacities to drive transcription and are more tissue-specific than divergent genes. This higher tissue-specificity is strongly associated with having less complex TF motif profiles at the core promoter. We experimentally validated these findings by testing both engineered single-nucleotide deletions and human single-nucleotide polymorphisms (SNPs) in MPRA. In both cases, we observe that single nucleotides associated with many motifs are important drivers of p...Continue Reading

Related Concepts

Gene Deletion
Genes
Nucleotides
Promoter Regions, Genetic
RNA
RNA, Messenger
Transcription Factor
Transcription, Genetic
Promoter
DNA Sequence

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