gene densities and guanine-cytosine (GC)
content, at 1-Mb resolution (Fig. 3C and figs.
S9A and S12). However, some DNA loci are
differentially associated with nuclear speckles
at 1-Mb resolution between cell types. These
small fraction changes toward nuclear speckles
are often associated with transcriptional up-
regulation of genes in those regions (Fig. 3E
and fig. S13). Conversely, transcriptionally up-
regulated loci between cell types increased
association toward nuclear speckles (fig. S14).
In comparison, we only observed transcription-
al decrease at loci with increased H3K27me3
association or DAPI association in specific cell
type comparisons (Fig. 3E and fig. S13), sug-
gesting a more subtle contribution at this
resolution. Our observation extends to tissues
the findings by tyramide signal amplification
sequencing (TSA-seq) in cell lines ( 25 ) and
includes multiple chromatin markers.
We observed a similar cell type–dependent
association of chromosomes with the nucleolus
stained by internal transcribed spacer 1 (ITS1)
noncoding RNA in the mouse brain cortex (Fig.
3D). We observed that the 45Sribosomal DNA
(rDNA)–containing chromosomes 15 and 19
were not in physical proximity to the nucleoli
but were close to DAPI-rich heterochromatin
regions in some cells (Fig. 3F and fig. S15, A
to C), possibly owing to rDNA silencing ( 26 ).
To confirm this, we performed imaging of
rDNA loci by DNA FISH and found that dif-
ferent fractions of rDNA loci were associated
with the nucleolus and DAPI-rich hetero-
chromatin regions among neurons, astro-
cytes, mouse ES cells, and cultured fibroblasts
(Fig. 3, G and H, and fig. S15D), lending sup-
port to the notion that nucleolar organizer
regions can be stably silenced ( 26 ) in a tissue-
specific fashion.Cell typeÐspecific proximal points anchor
chromosomes to nuclear bodies in single cells
We defined DNA loci that were consistently as-
sociated, at least 2 standard deviations above
the mean association frequency, with a partic-
ular chromatin mark or nuclear body in each
cell type as“proximal points”(methods) (fig.
S16). For example, SF3a66 proximal points,
such asNxph4andMalat1loci, are within
300 nm of nuclear speckles at nearly 80% of
the instances in single excitatory neurons ( 23 ).
We previously observed that certain DNA loci
for each IF marker consistently appear on the
exterior of the respective marker in single
mouse ES cells ( 17 ). This phenomenon extends
to the mouse brain and appears to be consistent
in different cell types, despite the differences in
the morphological features and arrangement
of nuclear bodies in individual neuronal and
glial cells (fig. S16).590 29 OCTOBER 2021•VOL 374 ISSUE 6567 science.orgSCIENCE
Chr7Chr7Chr17Chr17Chr8Chr8Chr7Chr7Chr8Chr8Chr17Chr17Chr7Chr7Chr8Chr8Chr17Chr17B Exc: Chr7 (DAPI +SF3a66)Pvalb: Chr7 (DAPI +SF3a66)Astro: Chr7 (DAPI +SF3a66)Exc: Chr17 (DAPI +SF3a66)Pvalb: Chr17 (DAPI +SF3a66)Astro: Chr17 (DAPI +SF3a66)ACell 347Cell 2153ExcPvalbAstroSF3a66 proximal points
DAPI proximal points
H3K27me3 proximal pointsNon-proximal pointsTwo associationsHeterochromatin (DAPI)Heterochromatin (DAPI)Nuclear
speckle (SF3a66)Nuclear
speckle (SF3a66)H3K27me3H3K27me3Exc: Chr8 (SF3a66+ H3K27me3)Astro: Chr8 (SF3a66+ H3K27me3)()Cell 178566) 66Cell 1661Cell 1262 Cell 2638 Cell 830Cell 1440 Cell 2687Pvalb: Chr8 (SF3a66 + H3K27me3)1 142 1 83 1 1131 1421 1421 831 831 1131 1132 μm2 μm2 μmFig. 4. Proximal points straddle across nuclear bodies.(A) Illustration showing chromosomes 7 and 17 with proximal points for SF3a66 and DAPI and
chromosome 8 with proximal points for SF3a66 and H3K27me3 across cell types (Exc, excitatory neurons; Pvalb, Pvalb inhibitory neurons; Astro, astrocytes).
(B) Representative 3D images of individual chromosomes and markers showing that each chromosome has cell typeÐspecific proximal points and spans the
corresponding nuclear bodies in single cells. The same coloring as (A).
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