Science - USA (2021-10-29)

as chromatin immunoprecipitation sequenc-
ing (ChIP-seq) and split-pool recognition of
interactions by tag extension (SPRITE) at 1-Mb
resolution in mouse ES cells ( 17 ).
Some chromatin profiles showed specific
patterns that varied between cell types at 1-Mb
resolution (Fig. 3, A to D, and figs. S9 to S12).

The chromatin profiles for constitutive het-

erochromatin stained by DAPI were distinct

between neurons and astrocytes (Fig. 3A and

fig. S10, A and B), even though the associations

were typically enriched in the centromere-

proximal genomic loci ( 9 , 17 ) and adenine-

thymine (AT)–rich regions ( 24 ) in all cell types

(Fig. 3A and fig. S10C). Furthermore, the chro-

matin profiles for H3K27me3 were distinct

acrosscelltypesinthebrainandmouseES

cells (Fig. 3B and fig. S11).

DNA loci associated with nuclear speckle

markers (SF3a66 and Malat1) were highly cor-

related among different cell types and with

588 29 OCTOBER 2021•VOL 374 ISSUE 6567 science.orgSCIENCE

CD Z-score

DAPI meta features

UMAP 1

UMAP 2

E

B

n = 701 cells

UMAP 1

UMAP 2

Immunofluorescence intensities

n = 2,762 cells

A

1 (Pvalb)

5 (Astro)

9 (Exc)

2 (Vip)

3 (Ndnf)

4 (Sst)

6 (Micro)

7 (Endo)

8 (OPC/Oligo)

DAPI 120 3000 H3K27me3 350 2400 mH2A1 380 6500

1

1

3

2

58

(^68)
5
7
7
(^99)
9
9
9
9
9
9
(^999)
(^999)
9
9
9
9
9
(^99)
9
9
mRNA clusters (cell types)
10 μm
Pvalb: Chr5 3.6-151.7 Mb Astro: Chr5 3.6-151.7 Mb Exc: Chr5 3.6-151.7 Mb
Chr5 imaging loci (1-Mb resolution)
F
Spatial
distance (μm)
0.2
1.7
3.2
Pvalb: Chr7 44.6 46.1 Mb Astro: Chr7 44.6 46.1 Mb Exc: Chr7 44.6 46.1 Mb
Chr7 imaging loci (25-kb resolution)
Spatial
distance (μm)
0.1
0.5
0.9
Chr5 physical scaling (1-Mb res.)
Chr7 physical scaling (25-kb res.)
Fig. 2. Nuclear morphology, global chromatin states, and chromosome
scaling are cell type dependent.(A) DAPI, H3K27me3, and mH2A1 staining from
a single z-section superimposed on the transcriptionally defined cell clusters.
Color bars represent fluorescence intensity (a.u., arbitrary units). (B) UMAP
representation shows separation of excitatory, inhibitory, and glial cells on the
basis of overall intensities for eight IF markers in single cells. A total of 2762 cells
from three biological replicates were used. (C) UMAP representation of cells based
on DAPI meta features used in (D). Cells are colored by their transcriptional
cell types in (B) and (C). (D) Hierarchical clustering of the DAPI meta features
compared with the RNA seqFISH clusters shown on top. A total of 701 cells in the
center z-sections from three biological replicates were used in (C) and (D).
(E) Physical distance as a function of genomic distance across transcriptional
defined cell types. (F) Spatial distance between pairs of intrachromosomal loci
within cells by DNA seqFISH+ in different cell types at 1-Mb resolution (top row;
quartile spatial distance within cells) and at 25-kb resolution (bottom row;
median spatial distance within alleles). A total of 2762 cells were used for (E)
and 155 cells for Pvalb, 152 cells for astrocytes, and 1895 cells for excitatory
neurons were used in (F) from three biological replicates.
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