Spatial arrangement of an RNA zipcode identifies mRNAs under post-transcriptional control.
How RNA-binding proteins recognize specific sets of target mRNAs remains poorly understood because current approaches depend primarily on sequence information. In this study, we demonstrate that specific recognition of messenger RNAs (mRNAs) by RNA-binding proteins requires the correct spatial positioning of these sequences. We characterized both the cis-acting sequence elements and the spatial restraints that define the mode of RNA binding of the zipcode-binding protein 1 (ZBP1/IMP1/IGF2BP1) to the β-actin zipcode. The third and fourth KH (hnRNP K homology) domains of ZBP1 specifically recognize a bipartite RNA element comprised of a 5' element (CGGAC) followed by a variable 3' element (C/A-CA-C/U) that must be appropriately spaced. Remarkably, the orientation of these elements is interchangeable within target transcripts bound by ZBP1. The spatial relationship of this consensus binding site identified conserved transcripts that were verified to associate with ZBP1 in vivo. The dendritic localization of one of these transcripts, spinophilin, was found to be dependent on both ZBP1 and the RNA elements recognized by ZBP1 KH34.
Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
Vivek L
VL
Patel
Somdeb
S
Mitra
Richard
R
Harris
Adina R
AR
Buxbaum
Timothée
T
Lionnet
Michael
M
Brenowitz
Mark
M
Girvin
Matthew
M
Levy
Steven C
SC
Almo
Robert H
RH
Singer
Jeffrey A
JA
Chao
D000199:Actins / Q000378:metabolism; D000818:Animals; D001483:Base Sequence; D002478:Cells, Cultured; D016384:Consensus Sequence; D003712:Dendrites / Q000378:metabolism; D005786:Gene Expression Regulation; D006023:Glycoproteins / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D008024:Ligands; D051379:Mice; D008840:Microfilament Proteins / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009419:Nerve Tissue Proteins / Q000378:metabolism; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism*; D016601:RNA-Binding Proteins; D000099273:Neurabins
D000199:Actins; D006023:Glycoproteins; D008024:Ligands; D008840:Microfilament Proteins; D009419:Nerve Tissue Proteins; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D000099273:Neurabins; C402632:Zbp1 protein, mouse