Science - USA (2021-10-29)

SCIENCEscience.org 29 OCTOBER 2021¥VOL 374 ISSUE 6567 589

A

B

Imaging loci in Chr10 (1-Mb resolution)

# of genes

Fraction of loci

SF3a66-DNA loci in spatial proximity

Gene density per 1 Mb

GC content per 1 Mb

%

DAPI-DNA loci profile

H3K27me3-DNA loci profile

C

D

Exc (Cell 1689) Astro (Cell 2463)

Chr15 Chr19 Other chromosomes ITS1 DAPI

5 μm

H

G rDNA ITS1 rDNA ITS1 DAPI Slc17a7 Mfge8 DAPI

Exc

Astro

E

5 μm

OffOn

Fraction of rDNA focioverlapped by ITS1 foci Fraction of rDNA focioverlapped by DAPI foci

Cell type, cell line Cell type, cell line

F

E

ITS1-DNA loci profile

Imaging loci in Chr19 (1-Mb resolution)

# of genesITS1-DNA loci in spatial proximity

Fraction of loci

%

Gene density per 1 Mb

GC content per 1 Mb

Imaging loci in Chr5 (1-Mb resolution)

# of genesH3K27me3-DNA loci in spatial proximity

Fraction of loci

%

Gene density per 1 Mb

GC content per 1 Mb

Imaging loci in Chr9 (1-Mb resolution)

# of genesDAPI-DNA loci in spatial proximity

Fraction of loci

%

Gene density per 1 Mb

GC content per 1 Mb

Pvalb

Astro

Exc

-1

1

0

Pearson’s

r

SF3a66-DNA loci profile Away from

Away from nucleolus nucleolus

Closer

in Exc

Closer

in Astro

SF3a66

Fraction of loci (Exc)

H3K27me3

DAPI

Fraction of loci (Astro)

Log

fold change (Exc/Astro) 2

Closer

in Exc

Closer

in Astro

Closer

in Astro

Closer

in Exc

p = 1.4e-03

p = 2.6e-08

p = 1.6e-01

p = 1.7e-02

p = 7.4e-10

p = 5.1e-05p = 1.4e-04

p = 2.8e-02p = 5.2e-01

Fig. 3. Chromatin profiles and proximal points across cell types.(Ato
D) GC content, gene density, and cell type–specific chromatin profiles defined by
the fraction of loci found within 300 nm of DAPI, H3K27me3, SF3a66, and ITS1
exteriors (left panels). Pearson correlation between those (n= 2340 autosomal
loci; right panels). (E) Comparison of fraction of loci for each marker between
excitatory neurons and astrocytes (n= 2340 autosomal loci) (left panels)
and fold change of differentially expressed genes between cell types at top 5%
differentially associated loci to each mark colored in left panels (n= 117 loci
for each cell type) or other loci as control (n= 2106 loci) (right panels).Pvalues
by two-sided Wilcoxon’s signed rank-sum test.n= 1895, 155, and 152 cells
for excitatory neurons, Pvalb inhibitory neurons, and astrocytes, respectively,

from three biological replicates in (A) to (E). (F) Representative 3D images of

nucleoli by ITS1 RNA FISH, heterochromatic bodies stained by DAPI, and

chromosomes 15 and 19 by DNA seqFISH+ in the excitatory neuron (left) and

astrocyte (right). (G) rDNA staining confirms that some of the ribosomal repeat

regions appear outside of the nucleolus and are located at DAPI-enriched

heterochromatin in postmitotic cells in the brain. The images are from a single

z-section. (H) The fraction of rDNA loci present in the nucleolus or close to

heterochromatic regions.n= 365, 18, and 32 for excitatory neurons, Pvalb

inhibitory neurons, and astrocytes, respectively, from five fields of view in

one mouse brain section, andn= 305 and 334 cells for E14 mouse ES cells and

NIH3T3 cells from seven and eight fields of view in each sample.

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