The specific contributions of cohesin-SA1 to cohesion and gene expression

Figures & data

Figure 1. Cohesin composition and mechanism of action. (A) Cohesin (blue circle) can entrap DNA segments in trans to mediate sister chromatid cohesion (left) and in cis to form chromatin loops (right). (B) Subunit composition of cohesin and schematic representation of SA1 and SA2 showing their sequence homology.

Figure 2. Division of labor between the two cohesin complexes that mediate cohesion along the chromosome. Left: Schematic representation of the distribution of cohesin complexes containing either SA1 and SA2 along the mouse chromosome. Right: Representative images of metaphase chromosomes from MEFs wild type, SA1-null, and wild type treated with SA2 siRNA stained with DAPI (top) or both with DAPI (blue) and a telomeric repeat FISH probe (red). Centromeric cohesion defects are apparent only in the absence of SA2. Aberrant telomere structures (also known as fragile telomeres) reflect defective replication and are visualized as irregularly shaped telomere signals (white arrowhead).

Figure 3. Transcriptional dysregulation in Nipbl +/− and SA1 −/− embryos and CdLS. (A) Percentage of genes with peaks of SA1 or SMC1 located 1kb upstream Transcription Start Site (TSS) for genes genome-wide or genes dysregulated in Nipbl +/− brains. GraphPad Prism 5 software was used to calculate two-tailed χ² test (with Yates’ correction, ***p < 0.0001). (B) Circos diagram representing chromosomal location of Differentially Expressed Genes (FDR < 0.15) in SA1-null MEFs (black) and genes dysregulated in brains from Nipbl +/− embryos (blue). Regions shorter than 1 Mb containing two or more regulated genes are indicated by purple lines and the genes are shadowed in the same color. Binding sites at gene promoters (up to 1kb upstream the TSS) are depicted for SA1 (red) and SMC1 (green). (C) SA1 and SMC1 peaks at Zfp608 gene, a proposed biomarker of CdLS. This is one of the regions in the mouse genome with highest cohesin peak density. (D) Frequency distribution for pairs of proximal genes (< 1 Mb) in 10,000 random data sets of sample size equivalent to our experimental data set (as defined in B, n = 185). Red line highlights the frequency of pairs of proximal genes observed in the experimental data set.

Table 1. List of gene promoters with highest density of SA1 binding sites (≥ 4 SA1 peaks in the 5 kb region upstream the TSS).

Gene Symbol	Chromosome	Start	End	SA1 binding sites
Zfp608	chr18	55149834	55154834	4
Zfp949	chr9	88437857	88442857	4
Pcdh7	chr5	58104259	58109259	4
Bdnf	chr2	109528719	109533719	4

Table 2. Top five widest SA1 binding regions. All the regions correspond to gene promoters (5 kb upstream the TSS).

Gene Symbol	Chromosome	Start	End	Length (bp)
Myc	chr15	61814652	61820007	5356
Trib2	chr12	15820962	15824328	3367
Hjurp	chr1	90172374	90174983	2610
Sox4	chr13	29043476	29046028	2553
Tsc22d1	chr14	76902752	76905136	2385