Systematic discovery of structural elements governing stability of mammalian messenger RNAs

Abstract

Decoding post-transcriptional regulatory programs in RNA is a critical step in the larger goal to develop predictive dynamical models of cellular behavior. Despite recent efforts1–3, the vast landscape of RNA regulatory elements remain largely uncharacterized. A longstanding obstacle is the contribution of local RNA secondary structure in defining 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 (e.g. 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. We have developed 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 behavior. The application of this framework to genome-wide mammalian mRNA stability data revealed eight highly significant elements with substantial structural information, for the strongest of which we showed a major role in global mRNA regulation. Through biochemistry, mass-spectrometry, and in vivo binding studies, we identified HNRPA2B1 as the key regulator that binds this element and stabilizes a large number of its target genes. Ultimately, 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 can also be employed to reveal the structural elements that modulate other aspects of RNA behavior.

Frac-seq reveals isoform-specific recruitment to polyribosomes

“…RNA secondary structures can also regulate translational control of mRNA isoforms (Bonnal et al 2003;Goodarzi et al 2012). A prime example of this type of regulation occurs during the localization of the Oskar mRNA to the posterior pole of the Drosophila oocyte.…”

An RNA matchmaker protein regulates the activity of the long noncoding RNA HOTAIR

“…Several binding motifs have been proposed for the hnRNP A2/B1 proteins: hnRNP A2/B1 preferentially bind the telomeric ssDNA repeat TTAGGG, in addition to the RNA UUAGGG motif (McKay and Cooke 1992). Recently, A2/ B1 were found to bind a 19-mer AU-rich motif (Goodarzi et al 2012), and also to bind N 6 -methyladenosine-modified (m6A) transcripts and affect microRNA processing (Alarcón et al 2015). We analyzed recently published m6A CLIP data (Linder et al 2015) that provides single-nucleotide resolution of the m6A modifications in the HEK293 transcriptome.…”

RNA-ID, a highly sensitive and robust method to identify cis-regulatory sequences using superfolder GFP and a fluorescence-based assay

“…Second, regulatory elements in RNAs are sometimes difficult to distinguish by computational methods since the essential features of an RNA regulatory element may be either its direct sequence or the RNA structure that it forms, either in the presence or absence of protein cofactors (Macdonald and Kerr 1998;Rabani et al 2008;Goodarzi et al 2012). For example, both distinct structural motifs and linear sequence motifs are important for the RNA localization of the zebrafish squint/nodal-related 1 RNA (Gilligan et al 2011), as well as for human mRNA stability (Goodarzi et al 2012).…”

“…For example, both distinct structural motifs and linear sequence motifs are important for the RNA localization of the zebrafish squint/nodal-related 1 RNA (Gilligan et al 2011), as well as for human mRNA stability (Goodarzi et al 2012). In fact, discovery of cis-elements involved in human mRNA stability required not only two different computational analyses to find the sequence and structural elements, but also a correlation with experimentally derived whole-genome mRNA decay measurements (Goodarzi et al 2012).…”