science.sciencemag.org/content/366/6462/eaav2642/suppl/DC1

Supplementary Materials for

The forebrain synaptic transcriptome is organized by clocks

but its proteome is driven by sleep Sara B. Noya, David Colameo, Franziska Brüning, Andrea Spinnler, Dennis Mircsof,

Lennart Opitz, Matthias Mann, Shiva Tyagarajan*, Maria S. Robles*, Steven A. Brown*

*Corresponding author. Email: steven.brown@pharma.uzh.ch (S.A.B.); charo.robles@med.uni-muenchen.de (M.S.R.); tyagarajan@pharma.uzh.ch (S.T.)

Published 11 October 2019, Science 366, eaav2642 (2019)

DOI: 10.1126/science.aav2642

This PDF file includes:

Figs. S1 to S12 Captions for Excel Tables S1 to S9 References

Other Supplementary Material for this manuscript includes the following: (available at science.sciencemag.org/content/366/6462/eaav2642/suppl/DC1)

Excel Tables S1 to S9

1

Fig. S1. (A) Overlap of the Enriched synaptic transcriptome with that from the synaptoneurosomal

fraction from the mouse cortex identified in a recent study (32). (B) Quantification by real-time

PCR of Neat1, an intronic region of Meg3, Arc and CamKII in whole-forebrain homogenate, pellet

(containing nuclei) and gradient-purified synaptoneurosomes. (Two-way ANOVA, ***p

2

Fig. S2. (A) Overlap of cycling transcripts from synaptic enriched mRNAs using Perseus (Perseus

Time Series Periodic analysis, period=24h, q-value

3

Fig. S3. (A) Representative images (top) of time course for single-molecule in situ hybridization

of Cry1 in the stratum pyramidale of the CA1 of the hippocampus. For better visualization, a red

line surrounds nuclei and size of single mRNA (black dots) is increased to 0.5 μm. (Bottom) Plot

showing the quantification of the in situ hybridization (n=13-18, from 3 biological replicates, Mean

± SD). (B) Same as in A, from the axodendritic compartment of cortex.

4

Fig. S4. (A) Confirmation of rhythmicity by single-molecule in situ hybridization of Lingo1 in the

stratum radiatum of the CA1 of the hippocampus (top panels) and in the axodendritic compartment

of cortex (lower panels, top). For better visualization, a red line segments nuclei and size of single

5

mRNA is increased to 0.5 μm. (Bottom) mRNA in the somas of the cortex. (B) Plot showing the

quantification of the in situ hybridization of A (n=13-18, from 3 biological replicates, Mean ± SD).

6

Fig. S5. Overlap of the GO Biological Processes enriched in the synaptic transcriptome compared

to the forebrain transcriptome (grey), for transcripts peaking in the light phase, anticipating dusk

(yellow), and for transcripts peaking in the dark phase, anticipating dawn (blue). Complete

functional segregation is observed between light and dark phase terms (http://www.funrich.org,

BH adjusted p-value

7

A

B

C

D

ZT4 ZT12 ZT20ZT8 ZT0ZT16

ZT4 ZT12 ZT20ZT8 ZT0ZT16

Time (h)

RE

MS

(h/4

h)

NR

EM

S(h

/4h

)

0 12 24 36 48 60 720.0

0.2

0.4

0.6

0

1

2

3ZT4 ZT12 ZT120

Time (h)

RE

MS

(h/4

h)

0 12 24 36 48 60 720.0

0.2

0.4

0.6

ZT8 ZT16 ZT0

NR

EM

S(h

/4h

)

0

1

2

3

8

Fig. S6. (A) and (B ) Time spent in NREM (up) and REM bottom during the time course. This

data supplements Fig. 5A and B. (C) Sleep onset latency, calculated from the end of the sleep

deprivation to the first consolidated NREM sleep bout (1-way ANOVA, ***P

9

Fig. S7. (A) Heatmap of expression of transcripts for which cycling is not affected by SD (Perseus

Time Series Periodic analysis, period=24h, q-value 0.05). Note that the oscillations of most transcripts

are blunted after SD, but time-dependent variations remain clearly visible.

10

Fig. S8. (A) Overlap of the synaptic cycling transcriptome with synaptic locally translated RNAs

identified by SynapTRAP in a recent study looking at synaptic mRNAs from the mouse cortex

(24).

11

Fig. S9. (A) Overlap of common proteins quantified in the synaptic and corresponding forebrain

proteomes. (B) Fraction of cycling (Perseus Time Series Periodic analysis, period=24h, q-value

12

Fig. S10. (A) Pie chart showing the fraction of cycling proteins (Perseus Time Series Periodic

analysis, period=24h, q-value

13

Overlap of the rhythmic proteome (Perseus Time Series Periodic analysis, period=24h, q-value

14

Fig. S11. (A) Heatmap of the intensities of cycling proteins in forebrain (Perseus Time Series

Periodic analysis, period=24h, q-value

15

free z-scored normalized intensity values and proteins are ordered by peak of abundance. (B)

Heatmap of the intensities of cycling proteins in synapses (Perseus Time Series Periodic analysis,

period=24h, q-value

16

Fig. S12. (A) Overlap of the synaptic proteome and synaptic enriched transcriptome. (B) Pie chart

depicting the fraction of the synaptic cycling proteome (Perseus Time Series Periodic analysis,

period=24h, q-value

17

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aav2642-Noya-SM-FRONTaav2642-Noya-BODY-CORRECTEDaav2642-Noya-SM-REFSReferences and NotesReferences and Notes