Science - USA (2021-10-29)

592 29 OCTOBER 2021¥VOL 374 ISSUE 6567 science.orgSCIENCE

Boundary scorein each subcluster

CTCF

RAD21

Chr3

subcluster 7

Chr3

subcluster 1

Chr3

subcluster 8

Boundary

score

1 60

0.2

0.7

Chr3 imaging loci (25-kb resolution)

0

0.4

0.8

Spatial distance (μm)

Cell 2507

allele 2

Cell 2731

allele 1

Cell 2090

allele 1

Cell 822

allele 2

Cell 886

allele 1

Cell 1611

allele 1

500 nm

Chr3: 7.7 Mb 9.3 Mb

1 60 1 60 1 60

AB

1 60

Boundary score

in each Xa/Xi subcluster

Subclusters

% of Xa or Xi alleles

ChrX imaging loci (25-kb resolution)

E

C D

0.1

0.9

Cell 968 Xi Cell 2412 Xi Cell 818 Xi Cell 2070 Xi Cell 2303 Xi Cell 2192 Xi

Cell 992 Xa Cell 2321 Xa Cell 1871 Xa Cell 1875 Xa Cell 928 Xa Cell 2707 Xa

500 nm ChrX: 75.3 Mb 77.0 Mb

1 60 1 60 1 60

Xa

Xi

Dxz4

1 60

Boundary

score

Xa

Xi

0

0.3

0.6

Spatial distance (μm)

Chr3 (25-kb res.)

in Exc

ChrX (25-kb res.)

in Exc

ChrX

subcluster 5

ChrX

subcluster 2

ChrX

subcluster 9

500 nm

Xist = -0.1

Z-scoreH3K27me3 = 0.3

= -0.2

= 0.4

= -0.2

= 0.0

= 0.7

= 1.0

= -0.1

= 0.2

= -0.2

= 0.5

= 11.4

= 7.1

= 14.0

= 7.6

= 4.1

= 4.4

= 8.5

= 3.6

= 11.1

= 7.4

Xist = 9.6

Z-scoreH3K27me3 = 5.9

0

0.4

0.8

Spatial distance (μm)

0

0.3

0.6

Spatial distance (μm)

1 60

Fig. 6. Heterogeneous domain structures in single chromosomes.(A) Bulk
averaged pairwise distance map from excitatory neurons (top) shows distinct domains in
the chromosome 3 region, with boundaries and high median boundary score regions
matching CTCF and cohesin binding sites. Single chromosomes were clustered into
different domain structures with distinct median boundary score profiles (methods).
(B) Examples for three of the structural subclusters are shown with different pairwise
distance map structures. Single chromosome distance maps and chromosome
structures from individual cells are shown below for each subcluster. Chromosomes with

20% loci detected inn= 1895 excitatory neurons from three biological replicates
were used in (A) and (B). (C) Pairwise median distance maps for Xa (top, upper triangle)
and Xi (top, lower triangle) in excitatory neurons from the 25-kb DNA seqFISH+ data at

Dxz4locus ( 33 ). Clustering of the domain structures for individual Xa and Xi shown with

the median boundary scores for Xa and Xi (middle) and for each subcluster containing

Xa and Xi (bottom) in excitatory neurons. The subclusters highlighted with blue stars

in (A) and (C) are shown in (B) and (D), respectively, as spatial distance maps.

(D) Examples for subclusters with corresponding single-cell pairwise distance maps and

single-cell 3D chromosome structures for Xa and Xi in excitatory neurons. Individual

Xa and Xi with different underlying epigenetic states, shown with z-scored fluorescence

intensity for Xist and H3K27me3 on the imaged chromosomal regions, can have

similar domain structures. (E) The frequency of each subcluster occurring in single cells

for Xa and Xi from 805 excitatory neurons.n= 805 cells with >20% loci detected for

both Xa and Xi regions from three biological replicates in (C) to (E).

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