Paralogs hnRNP L and hnRNP LL exhibit overlapping but distinct RNA binding constraints.
HnRNP (heterogeneous nuclear ribonucleoprotein) proteins are a large family of RNA-binding proteins that regulate numerous aspects of RNA processing. Interestingly, several paralogous pairs of hnRNPs exist that exhibit similar RNA-binding specificity to one another, yet have non-redundant functional targets in vivo. In this study we systematically investigate the possibility that the paralogs hnRNP L and hnRNP LL have distinct RNA binding determinants that may underlie their lack of functional redundancy. Using a combination of RNAcompete and native gel analysis we find that while both hnRNP L and hnRNP LL preferentially bind sequences that contain repeated CA dinucleotides, these proteins differ in their requirement for the spacing of the CAs. Specifically, hnRNP LL has a more stringent requirement for a two nucleotide space between CA repeats than does hnRNP L, resulting in hnRNP L binding more promiscuously than does hnRNP LL. Importantly, this differential requirement for the spacing of CA dinucleotides explains the previously observed differences in the sensitivity of hnRNP L and LL to mutations within the CD45 gene. We suggest that overlapping but divergent RNA-binding preferences, as we show here for hnRNP L and hnRNP LL, may be commonplace among other hnRNP paralogs.
Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
Sarah A
SA
Smith
Debashish
D
Ray
Kate B
KB
Cook
Michael J
MJ
Mallory
Timothy R
TR
Hughes
Kristen W
KW
Lynch
D000818:Animals; D001665:Binding Sites; D024202:Electrophoretic Mobility Shift Assay; D034664:Heterogeneous-Nuclear Ribonucleoprotein L / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D034441:Heterogeneous-Nuclear Ribonucleoproteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D012326:RNA Splicing
D034664:Heterogeneous-Nuclear Ribonucleoprotein L; D034441:Heterogeneous-Nuclear Ribonucleoproteins