Integrative Omics Indicate FMRP Sequesters MRNA from Translation and Deadenylation in Human Neuronal Cells

Overview

Journal Mol Cell

Publisher Cell Press

Specialty Cell Biology

Date 2022 Nov 10

PMID 36356584

Authors

Tatsuaki Kurosaki

Shuhei Mitsutomi

Alexander Hewko

Nobuyoshi Akimitsu

Lynne E Maquat

Affiliations

Soon will be listed here.

Abstract

How fragile X syndrome protein (FMRP) binds mRNAs and regulates mRNA metabolism remains unclear. Our previous work using human neuronal cells focused on mRNAs targeted for nonsense-mediated mRNA decay (NMD), which we showed are generally bound by FMRP and destabilized upon FMRP loss. Here, we identify >400 high-confidence FMRP-bound mRNAs, only ∼35% of which are NMD targets. Integrative transcriptomics together with SILAC-LC-MS/MS reveal that FMRP loss generally results in mRNA destabilization and more protein produced per FMRP target. We use our established RIP-seq technology to show that FMRP footprints are independent of protein-coding potential, target GC-rich and structured sequences, and are densest in 5' UTRs. Regardless of where within an mRNA FMRP binds, we find that FMRP protects mRNAs from deadenylation and directly binds the cytoplasmic poly(A)-binding protein. Our results reveal how FMRP sequesters polyadenylated mRNAs into stabilized and translationally repressed complexes, whose regulation is critical for neurogenesis and synaptic plasticity.

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References

Tang B, Wang T, Wan H, Han L, Qin X, Zhang Y . Fmr1 deficiency promotes age-dependent alterations in the cortical synaptic proteome. Proc Natl Acad Sci U S A. 2015; 112(34):E4697-706. PMC: 4553823. DOI: 10.1073/pnas.1502258112. View

Caku A, Seidah N, Lortie A, Gagne N, Perron P, Dube J . New insights of altered lipid profile in Fragile X Syndrome. PLoS One. 2017; 12(3):e0174301. PMC: 5363930. DOI: 10.1371/journal.pone.0174301. View

Mi H, Muruganujan A, Thomas P . PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res. 2012; 41(Database issue):D377-86. PMC: 3531194. DOI: 10.1093/nar/gks1118. View

Subramanian M, Rage F, Tabet R, Flatter E, Mandel J, Moine H . G-quadruplex RNA structure as a signal for neurite mRNA targeting. EMBO Rep. 2011; 12(7):697-704. PMC: 3128965. DOI: 10.1038/embor.2011.76. View

Liu B, Li Y, Stackpole E, Novak A, Gao Y, Zhao Y . Regulatory discrimination of mRNAs by FMRP controls mouse adult neural stem cell differentiation. Proc Natl Acad Sci U S A. 2018; 115(48):E11397-E11405. PMC: 6275535. DOI: 10.1073/pnas.1809588115. View

Ramos A, Hollingworth D, Pastore A . G-quartet-dependent recognition between the FMRP RGG box and RNA. RNA. 2003; 9(10):1198-207. PMC: 1370484. DOI: 10.1261/rna.5960503. View

Park E, Gleghorn M, Maquat L . Staufen2 functions in Staufen1-mediated mRNA decay by binding to itself and its paralog and promoting UPF1 helicase but not ATPase activity. Proc Natl Acad Sci U S A. 2012; 110(2):405-12. PMC: 3545820. DOI: 10.1073/pnas.1213508110. View

Goering R, Hudish L, Guzman B, Raj N, Bassell G, Russ H . FMRP promotes RNA localization to neuronal projections through interactions between its RGG domain and G-quadruplex RNA sequences. Elife. 2020; 9. PMC: 7279889. DOI: 10.7554/eLife.52621. View

Wheeler E, Van Nostrand E, Yeo G . Advances and challenges in the detection of transcriptome-wide protein-RNA interactions. Wiley Interdiscip Rev RNA. 2017; 9(1). PMC: 5739989. DOI: 10.1002/wrna.1436. View

10.

Maquat L, Li X . Mammalian heat shock p70 and histone H4 transcripts, which derive from naturally intronless genes, are immune to nonsense-mediated decay. RNA. 2001; 7(3):445-56. PMC: 1370100. DOI: 10.1017/s1355838201002229. View

11.

Vasilyev N, Polonskaia A, Darnell J, Darnell R, Patel D, Serganov A . Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP. Proc Natl Acad Sci U S A. 2015; 112(39):E5391-400. PMC: 4593078. DOI: 10.1073/pnas.1515737112. View

12.

Nalavadi V, Muddashetty R, Gross C, Bassell G . Dephosphorylation-induced ubiquitination and degradation of FMRP in dendrites: a role in immediate early mGluR-stimulated translation. J Neurosci. 2012; 32(8):2582-7. PMC: 3427762. DOI: 10.1523/JNEUROSCI.5057-11.2012. View

13.

Liao Y, Smyth G, Shi W . featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2013; 30(7):923-30. DOI: 10.1093/bioinformatics/btt656. View

14.

Corbin F, Bouillon M, Fortin A, Morin S, Rousseau F, Khandjian E . The fragile X mental retardation protein is associated with poly(A)+ mRNA in actively translating polyribosomes. Hum Mol Genet. 1997; 6(9):1465-72. DOI: 10.1093/hmg/6.9.1465. View

15.

Hu Y, Chen Z, Fu Y, He Q, Jiang L, Zheng J . The amino-terminal structure of human fragile X mental retardation protein obtained using precipitant-immobilized imprinted polymers. Nat Commun. 2015; 6:6634. DOI: 10.1038/ncomms7634. View

16.

Lorenz R, Bernhart S, Honer Zu Siederdissen C, Tafer H, Flamm C, Stadler P . ViennaRNA Package 2.0. Algorithms Mol Biol. 2011; 6:26. PMC: 3319429. DOI: 10.1186/1748-7188-6-26. View

17.

Feng Y, Absher D, Eberhart D, Brown V, Malter H, Warren S . FMRP associates with polyribosomes as an mRNP, and the I304N mutation of severe fragile X syndrome abolishes this association. Mol Cell. 1998; 1(1):109-18. DOI: 10.1016/s1097-2765(00)80012-x. View

18.

Lumaban J, Nelson D . The Fragile X proteins Fmrp and Fxr2p cooperate to regulate glucose metabolism in mice. Hum Mol Genet. 2015; 24(8):2175-84. PMC: 4380067. DOI: 10.1093/hmg/ddu737. View

19.

Ceman S, ODonnell W, Reed M, Patton S, Pohl J, Warren S . Phosphorylation influences the translation state of FMRP-associated polyribosomes. Hum Mol Genet. 2003; 12(24):3295-305. DOI: 10.1093/hmg/ddg350. View

20.

Ishizuka A, Siomi M, Siomi H . A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins. Genes Dev. 2002; 16(19):2497-508. PMC: 187455. DOI: 10.1101/gad.1022002. View