teiser relies on calculating mutual information values between whole - genome measurements and millions of predefined structural motifs .
the decoy / scrambled experiments and sirna knock - downs were performed using lipofectamin 2000 reagent ( invitrogen ) . for hybridizations , we used human 444k whole - genome human arrays ( agilent ) . isolation and identification of rna - binding proteins were based on previously published protocols .
full methods and any associated references are available in the online version of the paper at www.nature.com/nature .
 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 efforts13 , 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 . 
Methods Summary
Supplementary Material