Decoding post-transcriptional regulatory programs in RNA is a critical step towards the larger goal of developing predictive dynamical models of cellular behaviour. Despite recent efforts1, 2, 3, the vast landscape of RNA regulatory elements remains largely uncharacterized. A long-standing obstacle is the contribution of local RNA secondary structure to the definition of interaction partners in a variety of regulatory contexts, including—but not limited to—transcript stability3, alternative splicing4 and localization3. There are many documented instances where the presence of a structural regulatory element dictates alternative splicing patterns (for example, human cardiac troponin T) or affects other aspects of RNA biology5. Thus, a full characterization of post-transcriptional regulatory programs requires capturing information provided by both local secondary structures and the underlying sequence3, 6. Here we present a computational framework based on context-free grammars3, 7 and mutual information2 that systematically explores the immense space of small structural elements and reveals motifs that are significantly informative of genome-wide measurements of RNA behaviour. By applying this framework to genome-wide human mRNA stability data, we reveal eight highly significant elements with substantial structural information, for the strongest of which we show a major role in global mRNA regulation. Through biochemistry, mass spectrometry and in vivo binding studies, we identified human HNRPA2B1 (heterogeneous nuclear ribonucleoprotein A2/B1, also known as HNRNPA2B1) as the key regulator that binds this element and stabilizes a large number of its target genes. We created a global post-transcriptional regulatory map based on the identity of the discovered linear and structural cis-regulatory elements, their regulatory interactions and their target pathways. This approach could also be used to reveal the structural elements that modulate other aspects of RNA behaviour.
At a glance
Gene Expression Omnibus
- High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA 14, 1959–1972 (2008) et al.
- A universal framework for regulatory element discovery across all genomes and data types. Mol. Cell 28, 337–350 (2007) , &
- Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes. Proc. Natl Acad. Sci. USA 105, 14885–14890 (2008) , &
- Deciphering the splicing code. Nature 465, 53–59 (2010) et al.
- Understanding the transcriptome through RNA structure. Nature Rev. Genet. 12, 641–655 (2011) , , , &
- RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences. Nucleic Acids Res. 32, 3258–3269 (2004) , , &
- The language of genes. Nature 420, 211–217 (2002)
- Secondary structure prediction for aligned RNA sequences. J. Mol. Biol. 319, 1059–1066 (2002) , &
- Genome-wide measurement of RNA secondary structure in yeast. Nature 467, 103–107 (2010) et al.
- Revealing global regulatory perturbations across human cancers. Mol. Cell 36, 900–911 (2009) , &
- Global quantification of mammalian gene expression control. Nature 473, 337–342 (2011) et al.
- Silencing or knocking out eukaryotic gene expression by oligodeoxynucleotide decoys. Crit. Rev. Eukaryot. Gene Expr. 16, 23–30 (2006) &
- Isolation of specific RNA-binding proteins using the streptomycin-binding RNA aptamer. Nature Protocols 1, 637–640 (2006) &
- Two homologous genes, originated by duplication, encode the human hnRNP proteins A2 and A1. Nucleic Acids Res. 22, 1996–2002 (1994) , , , &
- The cap-to-tail guide to mRNA turnover. Nature Rev. Mol. Cell Biol. 2, 237–246 (2001) , &
- Antagonistic role of hnRNP A1 and KSRP in the regulation of let-7a biogenesis. Nature Struct. Mol. Biol. 17, 1011–1018 (2010) &
- Systematic variation in gene expression patterns in human cancer cell lines. Nature Genet. 24, 227–235 (2000) et al.
- CLIP: crosslinking and immunoprecipitation of in vivo RNA targets of RNA-binding proteins. Methods Mol. Biol. 488, 85–98 (2008) &
- RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nature Protocols 1, 302–307 (2006) , &
- HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature 456, 464–469 (2008) et al.
- An integrated ChIP-seq analysis platform with customizable workflows. BMC Bioinformatics 12, 277–294 (2011) &
- Predicting gene expression from sequence. Cell 117, 185–198 (2004) &
- RNA secondary structure in mutually exclusive splicing. Nature Struct. Mol. Biol. 18, 159–168 (2011) et al.
- Nuclear import of histone deacetylase 5 by requisite nuclear localization signal phosphorylation. Mol. Cell Proteomics 10, M110.004317 (2011) , , &
- Universal sample preparation method for proteome analysis. Nature Methods 6, 359–362 (2009) , , &
- Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460, 479–486 (2009) , , &
- Supplementary Information (2.5M)
This file contains Supplementary Figures 1-15, Supplementary Tables 1-2 and additional references.