# The ER/Golgi Protein FNDC3B Facilitates Climbing Fibre to Purkinje Cell Synapse Elimination in the Developing Mouse Cerebellum

**Authors:** Céline Louise Mercier, Takaki Watanabe, Yuto Okuno, Kyoko Matsuyama, Kyoko Kushibe, Henry Denny, Taisuke Miyazaki, Miwako Yamasaki, Meiko Kawamura, Manabu Abe, Kenji Sakimura, Masahiko Watanabe, Naofumi Uesaka, Masanobu Kano

PMC · DOI: 10.1111/ejn.70411 · 2026-01-23

## TL;DR

This study shows that the protein FNDC3B helps eliminate extra synapses on Purkinje cells in the developing mouse cerebellum.

## Contribution

FNDC3B is newly identified as a facilitator of climbing fiber synapse elimination in the developing cerebellum.

## Key findings

- FNDC3B is involved in synapse elimination from postnatal day 9 in mice.
- FNDC3B deletion impairs synapse elimination and CF extension at P10 and P21, but effects are recovered by P40.
- FNDC3B does not affect parallel fiber or inhibitory synaptic inputs to Purkinje cells.

## Abstract

Synapse elimination during development is crucial for refining neural circuits by removing excess synapses formed around birth. In the neonatal cerebellum, Purkinje cells (PCs) are initially innervated by multiple climbing fibers (CFs) with similar synaptic strengths. During subsequent postnatal development, a single CF is strengthened and retained, while the other CFs are eliminated. Here, our PC‐specific RNAi knockdown (KD) screening revealed that fibronectin type III domain containing 3B (FNDC3B), an endoplasmic reticulum protein, was involved in CF synapse elimination from around postnatal day 9 (P9) in mice. We showed that FNDC3B mRNA was expressed in PCs during CF synapse elimination. In PC‐selective FNDC3B conditional knockout (FNDC3B‐cKO) mice, CF synapse elimination from P10 was impaired, and the extension of CFs along PC dendrites was reduced at P21. However, these phenotypes were recovered by P40. In contrast, parallel fiber‐mediated excitatory synaptic inputs and inhibitory synaptic inputs to PCs were not affected in FNDC3B‐cKO mice. These results suggest that FNDC3B facilitates CF synapse elimination during postnatal development, highlighting a new role of FNDC3B in the developing brain.

We investigated the role of fibronectin type III domain containing 3B (FNDC3B) in climbing fiber (CF) to Purkinje cell (PC) synapse elimination during postnatal development of the mouse cerebellum. We performed PC‐specific deletion of FNDC3B by RNAi‐mediated knockdown or PC‐specific conditional knockout in mice and examined CF to PC synapse development both electrophysiologically and morphologically. Our results show that FNDC3B in PCs facilitates CF synapse elimination from around postnatal day 10 and the extension of CFs along PC dendrites, but the effects of FNDC3B deletion in PCs are recovered in the adult cerebellum.

## Linked entities

- **Genes:** FNDC3B (fibronectin type III domain containing 3B) [NCBI Gene 64778]
- **Proteins:** FNDC3B (fibronectin type III domain containing 3B)
- **Species:** Mus musculus (taxon 10090)

## Full-text entities

- **Genes:** Slc17a7 (solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 7) [NCBI Gene 72961] {aka 2900052E22Rik, Vglut1}, Fndc3a (fibronectin type III domain containing 3A) [NCBI Gene 319448] {aka 1700094E19Rik, D14Ertd453e, F730017H24Rik, Fndc3, sys}, Adgrb3 (adhesion G protein-coupled receptor B3) [NCBI Gene 210933] {aka A830096D10Rik, Bai3}, C1ql1 (complement component 1, q subcomponent-like 1) [NCBI Gene 23829] {aka Adil, C1qrf, CRF, CTRP14, gliacolin}, Glud-ps (glutamate dehydrogenase, pseudogene) [NCBI Gene 104277] {aka EG545999, Glud-2, Glud2, Gm5902}, Prkcg (protein kinase C, gamma) [NCBI Gene 18752] {aka PKCgamma, Pkcc, Prkcc}, Arc (activity regulated cytoskeletal-associated protein) [NCBI Gene 11838] {aka Arc3.1, arg3.1, mArc}, Calb1 (calbindin 1) [NCBI Gene 12307] {aka Brain-2, CB, Calb, Calb-1}, Htr3a (5-hydroxytryptamine (serotonin) receptor 3A) [NCBI Gene 15561] {aka 5-HT3, 5-HT3A, 5-HT3R}, Actb (actin, beta) [NCBI Gene 11461] {aka Actx, E430023M04Rik, beta-actin}, Plcb3 (phospholipase C, beta 3) [NCBI Gene 18797] {aka mKIAA4098}, Sema7a (sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A) [NCBI Gene 20361] {aka 2900057C09Rik, CDw108, H-Sema K1, H-Sema-L, M-Sema-L, Semal}, Plxna4 (plexin A4) [NCBI Gene 243743] {aka 9330117B14, Plxa4, mKIAA1550}, Slc32a1 (solute carrier family 32 (GABA vesicular transporter), member 1) [NCBI Gene 22348] {aka VGAT, Viaat}, Igl (immunoglobulin lambda chain complex) [NCBI Gene 111519] {aka Igl-x}, Fndc3b (fibronectin type III domain containing 3B) [NCBI Gene 72007] {aka 1600019O04Rik, Fad104, mKIAA4164}, Stat3 (signal transducer and activator of transcription 3) [NCBI Gene 20848] {aka 1110034C02Rik, Aprf}, Nlgn2 (neuroligin 2) [NCBI Gene 216856] {aka NL2, NLG2}, Nlgn3 (neuroligin 3) [NCBI Gene 245537] {aka A230085M13Rik, HNL3, NL3, NLG3}, Car8 (carbonic anhydrase 8) [NCBI Gene 12319] {aka Ca8, Cals, Cals1, Carp, wdl}, Gnaq (guanine nucleotide binding protein, alpha q polypeptide) [NCBI Gene 14682] {aka 1110005L02Rik, 6230401I02Rik, Dsk1, Dsk10, Galphaq, Gq}, Slc17a6 (solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6) [NCBI Gene 140919] {aka 2900073D12Rik, DNPI, VGLUT2}, Myo5a (myosin VA) [NCBI Gene 17918] {aka 9630007J19Rik, Dbv, MVa, Myo5, MyoVA, Sev-1}, Zfp64 (zinc finger protein 64) [NCBI Gene 22722] {aka Gm38422}, Grm1 (glutamate receptor, metabotropic 1) [NCBI Gene 14816] {aka 4930455H15Rik, Gm10828, Gprc1a, mGluR1, nmf373, rcw}, FNDC3B (fibronectin type III domain containing 3B) [NCBI Gene 64778] {aka FAD104, PRO4979, YVTM2421}, Gpr3 (G-protein coupled receptor 3) [NCBI Gene 14748] {aka Gpcr20, Gpcr21, Gpcr3}, Bdnf (brain derived neurotrophic factor) [NCBI Gene 12064], Pcx (pyruvate carboxylase) [NCBI Gene 18563] {aka Pc, Pcb}, Sema3a (sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A) [NCBI Gene 20346] {aka Hsema-I, SEMA1, SemD, Semad, coll-1}
- **Diseases:** PC (MESH:D015324), PC (MESH:D002292), neonatal death (MESH:D066087), PPR (MESH:C537238), virus infection (MESH:D014777), CF (MESH:D003550), CF (MESH:D000071075), ACSF (MESH:D002559), melanoma (MESH:D008545), cancer (MESH:D009369), epilepsy (MESH:D004827), PCL (MESH:D008209), brain tumors (MESH:D001932)
- **Chemicals:** polyacrylamide (MESH:C016679), pentobarbital (MESH:D010424), picrotoxin (MESH:D010852), CsCl (MESH:C028019), CO2 (MESH:D002245), NaCl (MESH:D012965), isoflurane (MESH:D007530), KCl (MESH:D011189), HEPES (MESH:D006531), NBQX (MESH:C062865), streptomycin (MESH:D013307), NaHCO3 (MESH:D017693), CaCl2 (MESH:D002122), PFA (MESH:C003043), Triton X-100 (MESH:D017830), phosphate (MESH:D010710), FITC (MESH:D016650), tetrodotoxin (MESH:D013779), PVDF (MESH:C024865), ATP (MESH:D000255), fluorescein (MESH:D019793), O2 (MESH:D010100), MgSO4 (MESH:D008278), TSA (MESH:C481298), DIG (MESH:D004076), MgCl2 (MESH:D015636), BLOCKING ONE (-), penicillin G (MESH:D010400), Alexa Fluor 647 (MESH:C569686), BAPTA (MESH:C025603), nitrogen (MESH:D009584), SDS (MESH:D012967), lipid (MESH:D008055), GTP (MESH:D006160), Calcium (MESH:D002118), Alexa Fluor 488 (MESH:C000711379), glucose (MESH:D005947)
- **Species:** Homo sapiens (human, species) [taxon 9606], Drosophila melanogaster (fruit fly, species) [taxon 7227], Rattus norvegicus (brown rat, species) [taxon 10116], Mus musculus (house mouse, species) [taxon 10090], Lentivirus (genus) [taxon 11646]
- **Mutations:** arginine to cysteine substitution of amino acid residue 451, C in 0, F to I, C-4 C, R451C
- **Cell lines:** HEK — Homo sapiens (Human), Human papillomavirus-related endocervical adenocarcinoma, Cancer cell line (CVCL_M624), C57BL/6N — Mus musculus (Mouse), Embryonic stem cell (CVCL_2H81), /6N — Mus musculus (Mouse), Transformed cell line (CVCL_D461), 293T — Homo sapiens (Human), Transformed cell line (CVCL_0063)

## Figures

7 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12828876/full.md

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Source: https://tomesphere.com/paper/PMC12828876