As the human genome harbors a large amount of similar Alu-derived regulatory elements, it suggests that their potential interaction with these trans-acting factors may represent a widespread phenomenon with effect on pre-mRNA processing and alternative splicing regulation. Genomic variants that affect splicing regulatory elements can alter the normal pattern of splicing and consequently cause or modify the severity of human diseases. Their effect depends on the complex interplay between cis-acting elements, which reside both in exonic and intronic regions, and trans-acting factors that they interact with. However, the function of intronic sequences in modulation of pre-mRNA splicing is poorly understood so the analyses of intronic mutations can help in elucidating the intronic determinants of the splicing code. The deletion of 4 bp within the ATM intron 20 has previously been reported to affect the process of splicing, leading to the ATM cryptic exon activation and eventually generating an aberrantly spliced mature mRNA. This deep intronic GTAA deletion in the ATM gene differs from the majority of described intronic variants as it is not directly related to the changes at splice sites but instead affects an Intronic Splicing Processing LY294002 Abmole DGAEE, a newly synthesized derivative of glycyrrhetinic acid, potently attenuates mouse septic shock via its main metabolite DGA in an IL-10-dependent manner element whose disruption then abolishes a non-canonical interaction with U1 snRNP and consequently leads to the activation of two nearby cryptic splice sites. However, this mutation per se does not give rise to the aberrant mature RNA transcript as its production depends on the downstream Alu-derived ISE. To test the hypothesis that ISEdependent cryptic exon activation requires interaction of the ISE with trans-acting factors, the binding capacity of the ISE sequence was evaluated and four proteins with binding affinity towards ISE element were detected: RNA helicase DHX36, DAZAP1, hnRNPA1 and HuR. HuR is an RNA-binding protein that shuttles between the cytoplasm and the nucleus and binds with high affinity to AU-rich elements . HuR was originally reported to be implicated in stabilization of AREcontaining mRNAs but it has been recently shown that is also involved in splicing regulation where it promotes Fas exon 6 skipping by binding to an exonic splicing silencer. Recent work also reports an extensive association of HuR with hnRNP proteins within the mRNP complex in the nucleus and cytoplasm suggesting a very important role of HuR in mRNA processing. A few data are available for RNA helicase DHX36 that has been found to be involved in degradation and deadenylation of mRNAs containing ARE sequence element in their 39-UTR. This substrate ����specificity���� is mediated indirectly by its RNAdependent interaction with the ARE-binding proteins HuR and NFAR1 and it is believed that RNA helicase DHX36 might actually serve as a ����molecular motor���� to drive the mechanics of complex RNA remodeling/decay reactions through interactions with HuR and NFAR proteins. Interestingly, there exist two different isoforms of RNA helicase DHX36, which are generated through alternative splicing and that differ in an 8-amino acids long sequence that encodes for a nuclear localization signal. The RNA helicase DHX36 isoform that we detected in pull down experiments contains the NLS thus suggesting possible role of this protein in nuclear mRNA processing. DAZAP1 is involved in mRNA transport, stability and translational regulation. This protein was shown to interact with many members of hnRNP family of proteins including the hnRNPA1 protein.