TY - JOUR

T1 - Degenerate consensus sequences in the 3′-untranslated regions of cellular mRNAs as specific motifs potentially involved in the YB-1-mediated packaging of these mRNAs

AU - Gopanenko, Alexander V.

AU - Malygin, Alexey A.

AU - Kossinova, Olga A.

AU - Tupikin, Alexey E.

AU - Kabilov, Marsel R.

AU - Karpova, Galina G.

N1 - Publisher Copyright: © 2020 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM) Copyright: Copyright 2020 Elsevier B.V., All rights reserved.

PY - 2020/3

Y1 - 2020/3

N2 - The multifunctional protein YB-1 has previously been shown to be the only protein of the cytoplasmic extract of HEK293 cells, which is able to specifically interact with imperfect RNA hairpins containing motifs that are often found in exosomal (e) RNAs. In addition, it has been revealed that similar hairpins formed by degenerate consensus sequences corresponding to three eRNA-specific motifs are responsible for the cooperative binding of YB-1 to RNA in vitro. Here, using the photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation method applied to HEK293 cells producing FLAG-labeled YB-1, we identified mRNAs cross-linked to YB-1 in vivo and then carried out a search for the aforementioned sequences in the regions of the YB-1 cross-linking sites. It turned out that many of the mRNAs found cross-linked to YB-1 encode proteins associated with various regulatory processes, including responses to stress. More than half of all cross-linked mRNAs contained degenerate consensus sequences, which were preferably located in 3′-untranslated regions (UTRs), where most of the YB-1 cross-linking sites appeared, although not close to these sequences. Furthermore, YB-1 was mainly cross-linked to those mRNAs with degenerate consensus sequences, which could be classified as packaged because their translation levels were low compared to cellular levels. This suggests that the cooperative binding of YB-1 to mRNAs through the above sequences probably triggers the well-known multimerization of YB-l, leading to the packaging of these mRNAs. Thus, our findings indicate a previously unknown link between the degenerate consensus sequences present in the 3′-UTRs of many cytoplasmic mRNAs and YB-1-mediated translational silencing.

AB - The multifunctional protein YB-1 has previously been shown to be the only protein of the cytoplasmic extract of HEK293 cells, which is able to specifically interact with imperfect RNA hairpins containing motifs that are often found in exosomal (e) RNAs. In addition, it has been revealed that similar hairpins formed by degenerate consensus sequences corresponding to three eRNA-specific motifs are responsible for the cooperative binding of YB-1 to RNA in vitro. Here, using the photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation method applied to HEK293 cells producing FLAG-labeled YB-1, we identified mRNAs cross-linked to YB-1 in vivo and then carried out a search for the aforementioned sequences in the regions of the YB-1 cross-linking sites. It turned out that many of the mRNAs found cross-linked to YB-1 encode proteins associated with various regulatory processes, including responses to stress. More than half of all cross-linked mRNAs contained degenerate consensus sequences, which were preferably located in 3′-untranslated regions (UTRs), where most of the YB-1 cross-linking sites appeared, although not close to these sequences. Furthermore, YB-1 was mainly cross-linked to those mRNAs with degenerate consensus sequences, which could be classified as packaged because their translation levels were low compared to cellular levels. This suggests that the cooperative binding of YB-1 to mRNAs through the above sequences probably triggers the well-known multimerization of YB-l, leading to the packaging of these mRNAs. Thus, our findings indicate a previously unknown link between the degenerate consensus sequences present in the 3′-UTRs of many cytoplasmic mRNAs and YB-1-mediated translational silencing.

KW - mRNA consensus sequences

KW - mRNA packaging

KW - Photoactivatable-ribonucleoside enhancing cross-linking and immunoprecipitation

KW - Regulation of gene expression

KW - RNA-protein interactions

KW - YB-1

KW - CELLS

KW - COMPLEXES

KW - MECHANISMS

KW - BINDING PROTEIN

KW - TRANSLATION

KW - YB-1 BINDS

KW - GENOME-WIDE ANALYSIS

UR - http://www.scopus.com/inward/record.url?scp=85078089649&partnerID=8YFLogxK

U2 - 10.1016/j.biochi.2020.01.005

DO - 10.1016/j.biochi.2020.01.005

M3 - Article

C2 - 31935443

AN - SCOPUS:85078089649

VL - 170

SP - 152

EP - 162

JO - Biochimie

JF - Biochimie

SN - 0300-9084

ER -