Cell Reports, Volume
41
Supplemental information
Simultaneous mapping of 3D structure and nascent
RNAs argues against nuclear compartments
that preclude transcription
Isabel N. Goronzy, So
fi
a A. Quinodoz, Joanna W. Jachowicz, Noah Ollikainen, Prashant
Bhat, and Mitchell Guttman
1.5
0.0
-1.5
E1
0
50
100
150
183
Position along chr2 (Mb)
10
-2
10
-3
10
-4
10
-5
10
-6
Normalized Contacts (log
10
)
A
B
1.5
0.0
-1.5
10
-2
10
-3
10
-4
10
-5
Normalized Contacts (log
10
)
10
55
Position along chr2 (Mb)
Abi1
Sptan1
Mbd5
22.96
23.02
22.90
23.08
chr2 (Mb)
-1.0
0.0
1.0
Abi1
30.00
30.02
22.98
-1.5
0.0
1.5
chr2 (Mb)
30.05
Sptan1
chr2 (Mb)
-1.0
0.0
1.0
49.20
49.35
49.05
Mbd5
C
(i)
(ii)
(iii)
Supplemental Figure 1. Eigenvector 1 (E1) and A/B compartment assignments calculated from RD-SPRITE
clusters, corresponding to Figure 2 and Figure 3.
E1
E1
E1
E1
10
-1
A
B
A
B
A
B
A
B
A
B
Supplemental Figure 1: Eigenvector 1 (E1) and A/B compartment assignments calculated
from RD
-
SPRITE clusters, corresponding to Figure 2 and Figure 3.
(A)
Weighted DNA
-
DNA contact matrix at 100kb resolution (top) and
eigenvector 1 (
E1
)
at 10kb
resolution (bottom) along chromosome 2.
Both the contact matrix and E1 were calculated from
RD
-
SPRITE clusters containing 2
-
1000 DNA reads (see
Methods
).
(B) Zoom
-
in o
f the 100kb DNA
-
DNA contact matrix and E1 from (A) near the front of
chromosome 2. The positions of one of the A (black) and B (gray) compartment gene triplicates
measured by RNA
-
FISH in Figure 3 (Abi1, Sptan1 and Mbd5) are annotated.
(C) Zoom
-
in of E1 at
10kb resolution near the gene annotations of the three RNA FISH
-
measured
genes in (B). (i) Abi1
-
a B compartment gene, (ii) Sptan1
-
an A compartment gene, and (iii)
Mbd5
–
a B compartment gene. The compartments for each gene were assigned based on the si
gn
of E1 (A compartment > 0; B compartment < 0).
Distance to Nucleolus (log
10
)
(DNA-DNA contact frequency)
10
3
10
3
10
4
10
5
Pearson r=-0.02, Spearman
ρ
=-0.01
A Compartment
B Compartment
pre-mRNA Read Counts (log
10
)
10
3
10
4
10
5
Compartment
A
B
Mann-Whitney p-value = 0.212
A
B
Expression Levels of A vs B Genes
Expression Level vs Distance to Nucleolus
Supplemental Figure 2. Expression level profiles of top 2000 expressed introns, corresponding to
Figure 3 and Figure 4.
pre-mRNA Read Counts (log
10
)
Supplemental Figure
2
: Expression level profiles of top 2000 expressed introns,
corresponding to Figure
3
and Figure 4.
(A)
Violin plot of read counts of selected, top 2000 expressed introns grouped by A/B c
ompartment
assignment
of
the individual
gene
s
. Median and quartiles are shown with dotted lines. The bottom
of each violin was set to the lowest read count. Mann
-
Whitney p
-
value (top) shows no significant
difference in the distributions
of read counts
betw
een
A and B
compartment
genes
.
(B) Scatterplot of read counts versus gen
omic loci
distance to nucleolus for top 2000 expressed
introns. Distance to nucleolus was calculated based on DNA
-
DNA contact frequency of the DNA
region containing the gene locus and
nucleolar hub regions
(see
Methods
)
. Neither Pearson nor
spearman statistics show a correlation between counts and distance.