protein production for long ORFs ( 58 – 60 ).
In part, this observation can be explained by
reduced initiation rates of longer transcripts
[correlation coefficientr=−0.29;Pvalue <
2.2 × 10−^16 ; see also ( 61 )]. Contrasting obser-
vations, however, have been made in yeast,
where monosomes preferentially occupy short
ORFs ( 27 ). This discrepancy might be ex-
plained by differences in the translational
regulatory mode between organisms, such as
an expansion in the UTR length and/or com-
plexity during evolution from lower to higher
eukaryotes ( 2 , 62 , 63 ).
We also observed that monosome-preferring
transcripts were often subject to a negative
translational regulation, with moderate initiation
and elongation kinetics.Notably, proteins pre-
dominantly encoded by monosome-preferring
transcripts were not only longer but also
structurally more complex. A“quality mode”
slow translation of themonosome-preferring
transcripts might allow the fine-tuning of
cotranslational folding events, ensuring the
functionality and preventing the aggregation
of the encoded proteins. On the other hand,
we found that polysome-preferring transcripts
displayed increased initiation and elonga-
tion rates, allowing a more efficient transla-
tion. Polysome-preferring transcripts may
thus encode proteins of lower structural com-
plexity, which require less de novo protein fold-
ing fidelity, potentially allowing their translation
in a fast“productivity mode”( 28 , 29 ).
Some transcripts exhibited a differential
M/P preference between the somata and neu-
ropil. Neurons differentially localize 5′and/or
3 ′UTR isoforms between subcellular com-
partments ( 64 ). Because these cis-regulatory
mRNA elements regulate initiation efficiency
( 62 , 63 ), neurons may fine-tune their M/P pref-
erence through selective targeting of com-
petitive UTR isoforms between compartments.
Notably,Arc, a previously reported natural
NMD target that contains 3′UTR introns ( 65 ),
was monosome-preferring in the somata but
polysome-preferring in the neuropil. Accord-
ing to the model proposed by Giorgiet al.
( 65 ),ArcmaybesilencedbyNMDintheso-
mata, whereas in the neuropil, synaptic activity
could trigger its release from NMD, resulting
in a translational up-regulation (i.e., polysome
translation).
Alternatively, differences in the monosome
preference between somata and neuropil could
also arise from differential localization or ac-
tivity of specific translational regulators, in-
cluding RNA-binding proteins (RBPs) ( 66 , 67 ),
microRNAs( 68 , 69 ), initiation and elongationfactors ( 57 ), or the ribosome itself ( 70 ). For
instance, the RBP FMRP is thought to in-
hibit the translation of selective transcripts
in neuronal processes by pausing the trans-
location of polysomes or by directly interacting
with the RNA-induced silencing complex
( 71 , 72 ). Synaptic activity has also been re-
ported to regulate the local translational
machinery through changes in the phospho-
rylation status of initiation and elongation
factors ( 57 ). Thus, local activity-induced sig-
naling events may also control the flow of
ribosomes on an mRNA and dictate its M/P
preference.
A rapid up-regulation in the number of poly-
somes has been observed in electron micro-
graphs of dendritic shafts and spines after
synaptic plasticity induction ( 7 ). Our data
show that, for many transcripts, monosome
translation is the preferred mode of protein
synthesis in neuronal processes and presum-
ably satisfies the local demands under basal
conditions. The formation of polysomes, how-
ever, could be required to supply synapses
with de novo plasticity-related proteins in
response to stimulation. We identified tran-
scripts that prefer the predominant ribosome
population present in either somata (poly-
somes) or neuropil (monosomes) and thusBieveret al.,Science 367 , eaay4991 (2020) 31 January 2020 7of14
EF
neuropil proteome vs. transcriptome neuropil proteome vs. translatomeB
post-synapseR^2 : 0.068A
pre-synapseR^2 : 0.018D
163 177(^1079) R (^2) : 0.021 149
15
20
25
30
35
-2 0 2
monosome vs polysome (log 2 FC)
neuropil protein (log
iBAQ) 2
0 2 4 6 8 10 12 14
neuropil RNA (log 2 TPM)
10
15
20
25
30
35
neuropil protein (log
iBAQ) 2
R^2 : 0.26
0 2 4 6 8 10 12 14
neuropil translation rate
10
15
20
25
30
35
R^2 : 0.33
C
10
15
20
25
30
35
poly mono
neuropil protein (log
iBAQ) 2
p = 2.735e-06
Ap2a1
Atp6v0c
Sept8
Ap2b1
Sept9
Arhgdia
Rph3a
Sept11
Ap1b1
Ap3m2
Exoc2
Cdh2
Camk2a
Camk2d
Flot1
Ncs1
Cacna2d1
Pclo
Slc6a1
Atp6v1e1
Nrxn1
Rab10 Nrcam
Nrxn3
Sgta
Rab11b
Rab21
Atp6v1c1Bsn
Rims1
Sept2
L1cam
-1 (^01)
monosome vs polysome (log 2 FC)
10000
10
100
1000
protein copy number 10
100
1000
Cacng8 Prkcg
Shank1
Cacng3 Dlg2
Shank2
Ppp1ca
Grin2a
Gria1
Dlg4
Cacng4
Baiap2
Dlg1
Camk2b
Camk2g
Dlgap2
Camk2a
Cyld
Homer1 Gria2
Camk2d
Lrrc7
Grin1
Dlgap4 Ctnna2 Grin2b
Dlgap3
Anks1b
Shank3 Cacng2
Fam81a
Dlgap1 Dlg3
Nlgn3
Gria3
-0.5 (^0) 0.5
monosome vs polysome (log 2 FC)
Fig. 6. Monosome translation can contribute to the maintenance of
the local proteome.(AandB) M/P fold changes in the neuropil were not
correlated with the copy numbers of some key presynaptic ( 43 ) (A) and
postsynaptic proteins ( 42 ) (B). Regression lines and corresponding adjusted
R^2 values are represented (presynapseP= 0.1488, postsynapseP=
0.07145). (C) Box plots of protein (log 2 iBAQ) measurements in the neuropil
for monosome-enriched (mono, cyan) or polysome-enriched (poly,
orange) genes.P= 2.735 × 10−^6 , Wilcoxon rank-sum test. Of 463 and
372 monosome- and polysome-preferring transcripts in the neuropil,
326 and 242, respectively, passed the stringent proteomics filtering criteria
(see Materials and methods). (D) Scatter plot of the protein abundance
(log 2 iBAQ) versus M/P fold changes for monosome-enriched (cyan),
polysome-enriched (orange), and nonenriched (gray) genes (R^2 = 0.021,
P= 2.944 × 10−^11 ). The dashed line indicates the mean log 2 iBAQ value.
Monosome-preferring transcripts encoding proteins with abundances
greater than average are highlighted by dark cyan dots (mono-high). (EandF) The local proteome correlates with the local transcriptome and translatome. Scatter
plots of the protein abundance (log 2 iBAQ) versus RNA (log 2 TPM) (R^2 = 0.26,P< 2.2 × 10−^16 ) (E) and translation rate (obtained from total footprints, without
biochemical fractionation) (R^2 = 0.33,P< 2.2 × 10−^16 ) (F) measurements for all neuronal genes are shown. Monosome-preferring genes encoding high-abundance
proteins are highlighted by dark cyan dots.
RESEARCH | RESEARCH ARTICLE