3.1 A comprehensive map of chromosomal contacts in chicken liver
cells nuclei
To study the dynamic chromatin interactions in primary chicken liver
cells from WCC and LDC, we carried out Hi-C experiments and sequenced
approximately a total of 295 Gb high quality raw data. Alignment of the
obtained sequences to the chicken reference genome
(ftp://ftp.ensembl.org/pub/release-90/fasta/gallus_gallus/dna/)
resulted in an average of
~263 million paired-end reads mapped for each
individual, among which an average of ~207 million are
intra-chromosomal reads(207,914,357 in LDC and 206,471,795 in WCC)
(Table S1 and S2). Data processing also showed high quality of the Hi-C
data, proving the successful performance of Hi-C experiments.
3.2 Identification and characterization ofcompartments in chicken
liver cells
After data analysis, we acquired chromatin interaction heatmaps at 40-kb
resolution for each sample (Fig. 1 and Fig. S1). The heatmaps
displayed a typical plaid-pattern,
which was demonstrated previously in chicken
erythrocytes and fibroblasts Hi-C
data (Veniamin et al., 2018), as well as in mammalian Hi-C data
(Battulin et al., 2015). The plaid-pattern intimates the existence of
large spatial compartments, such as compartments A/B. We know the genome
consists of actively transcribed compartments A and inactive
compartments B (Lieberman-Aiden et al., 2009), and switching of the
compartments A/B are concerned with comparative changes of gene
expression (Barutcu et al., 2015). We then determined the compartment
types of the genome at 1 Mb resolution in liver cells, and found most
genomic regions reserved the same compartments in LDC liver cells
compared to WCC liver cells (Fig. 2 and Fig. 3). A total of 5% genomic
regions switched between compartment A and
compartment B, and as expected, we
found more genes in the compartment A and they displayed higher
transcriptional levels than those in compartment B (Fig. 4 and Fig. S2).
We next compared TADs in LDC and WCC liver cells.
We called TADs from Hi-C interaction
matrices at 40 kb resolution and identified 396, 386 TADs in
LDC liver cells and WCC liver cells
(Fig. 5 and Table S3), respectively,
and with their median TAD sizes of 2.3 Mb (Fig. S3). Interestingly,
previous studies have found TAD boundaries display an obvious enrichment
of active genes when compared with randomly sampled genomic regions,
which suggested a relationship between TAD formation and gene
transcription (Wang et al., 2018). We thus investigated TAD boundary
distribution, and 280, 261 TAD boundaries were identified in LDC and WCC
genome, respectively (Table S4), with enriched transcription start sites
in TAD boundary (Fig. S4), which further confirmed the reliability of
the sequencing results.