Science - USA (2021-10-29)

Because proximal points have cell type–
specific patterns for different chromatin marks
across the genome, they can scaffold and con-
strain the nuclear organization of chromosomes
by their association to the nuclear bodies or
chromatin marks in individual nuclei (Fig. 4
and fig. S16). For example, chromosomes 7 and
17 have proximal points for nuclear speckles
(SF3a66) and heterochromatic bodies (DAPI)
in excitatory neurons, inhibitory neurons, and
astrocytes, and both chromosomes straddled

these nuclear bodies in single cells of all three

cell types (Fig. 4B). Similarly, chromosome 8

has nuclear speckles and H3K27me3 proximal

points in all three cell types and spans those

nuclear globules in single cells (Fig. 4B). To-

gether, these findings in the mouse brain show

that chromatin proximal points serve as or-

ganizational invariants in the nuclei of single

cells across cell types, despite the highly vari-

able appearance of individual chromosomes

and nuclear bodies in individual cells.

Cell typeÐspecific nuclear bodies determine

interchromosomal proximity and

radial positioning

We examined whether the proximal point

association to nuclear bodies in different cell

typesaccountsforthecelltype–specific inter-

chromosomal interaction and radial chromo-

somal positioning (Fig. 5, A to D, and fig. S17).

For example, chromosome 17 contains many

heterochromatin proximal points in neu-

rons (Fig. 4B). At the same time, a few large

SCIENCEscience.org 29 OCTOBER 2021•VOL 374 ISSUE 6567 591

Top 15% variable loci for radial positioning

A

D

Average gene density in chromosome (per 1 Mb) 7 16 B

Astro (Cell 2327)

Normalized inter-

chromosomal distance (μm)

DAPI-enriched

locus pairs

SF3a66-enriched

locus pairs

H3K27me3-enriched

locus pairs

E

Imaging loci on Chr1-19, X (1-Mb resolution)

Median radial position from center

Exc

Pvalb

Astro

Chr 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X

r = 0.93 r = 0.81 r = 0.91

Radial score for pairs of chromosomes from nuclear center

Inter-chromosomal

distance (μm)

Sum of radial position of pairs of chromosomes from nuclear center

Inter-chromosomal distance

Chr7,17

Chr11,19

Chr1-19, X

Chr1-19, X

Chr1-19, X

Chr1-19, X

Chr7,17 Chr7,17

Chr7,17

Chr11,19 Chr11,19

Chr11,19

Spatial distance (μm)

0.4 1.4

1.5 4.5

Radial score from nuclear center

C

Exc Pvalb Astro

Exc Pvalb Astro

Exc Pvalb Astro

Exc (Cell 2170) Pvalb (Cell 720)

Whole genome Cross section Whole genome Cross section Whole genome Cross section

Chr11

Chr19

Chr7

Chr17

Other chromosomes SF3a66

Chr7 SF3a66 proximal points

Chr17 SF3a66 proximal points

Chr7

Chr17

DAPI

Chr7 DAPI proximal points

Chr17 DAPI proximal points

Chr7

Chr17

H3K27me3

Chr11 H3K27me3 proximal points

Chr19 H3K27me3 proximal points

Chr11

Chr19

2 μm 2 μm 2 μm 2 μm 2 μm 2 μm

Fig. 5. Proximal points and nuclear bodies organize nuclear architecture.
(A) Median radial positioning from the nuclear center for all 2460 loci imaged at
1-Mb resolution for three major cell types. Gene density (top panel) and the top 15%
variable loci in terms of radial positioning among the three cell types (middle panel)
are shown. (B) Comparison of mean pairwise distance between chromosomes
(top panels) and the radial position scores for pairs of chromosomes (bottom
panels) for the three major cell types. (C) Scatter plot of mean pairwise distance
between chromosomes and the sum of radial position scores for pairs of
chromosomes shown in (B). (D) Normalized interchromosomal distance between
pairs of proximal points enriched in association with specific nuclear bodies
and chromatin marks. The distances are normalized by subtracting an averaged

interchromosomal spatial distance from all interchromosomal pairs of loci in each

cell type. The boxplots represent the median, interquartile ranges, whiskers within

1.5 times the interquartile range, and outliers. (E) Chromosomes 7 and 17 are

closer to the nuclear interior in neurons, shown with the proximal points on nuclear

speckles (excitatory neuron, left) and heterochromatin (Pvalb inhibitory neuron,

middle). Chromosomes 11 and 19 are closer to the nuclear interior in the astrocyte

with the proximal points on H3K27me3 globules (right). The cells are shown

with 2-mm cross sections for the excitatory and Pvalb inhibitory neuron and with

1-mm cross section for the astrocyte for visual clarity.n= 1895, 155, and 152 cells for

excitatory neurons, Pvalb inhibitory neurons, and astrocytes, respectively, from

three biological replicates.

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