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Fig. 1 | BMC Biology

Fig. 1

From: Human Satellite 1A analysis provides evidence of pericentromeric transcription

Fig. 1

HSat1A sequence analysis and copy number/expression evaluation. A Obtained HSat1A clones (GenBank accession numbers: OP172545–OP172627) were analyzed in Tandem Repeats Finder and proved to be systematically composed of 42-bp repeats. HSat1A clone was BLAST searched against CHM13-T2T v2.0 (GenBank assembly accession GCA_009914755.4) and filtrated hits were mapped into chromosomes. HSat1A BLAST hits are represented (in blue) in CHM13-T2T chromosome 13 (CP068265.2), reported to have a large HSat1A array [14]. The ideogram was adapted from the Ensembl genome browser. In silico mapping of HSat1A hits was performed in Geneious. Concatenated hits are observable in a 5-Mb extent. HSat1A clones, HSA13 T2T HSat1A array [13, 64], and pTRI-6 (L01057.1) sequence stretches were aligned (Additional file 1: Supplementary Table S3). B HSat1A periodicity spectrum and heatmap in GM12878 sequencing data. NTRprism reveals two predominant peaks: one corresponding to HSat1A monomer and the second to a 9-mer higher repeat. C HSat1A monomer copy number quantification in several human cell lines. Values are mean ± SD (n = 3) (Additional file 4). Statistical analysis is detailed in Additional file 1: Supplementary Fig. S2. HSat1A estimation in percentage of the haploid human reference genome (bp/total bp). D HSat1A ncRNA relative quantification by RT-qPCR in fold change (MCF10A set as reference). Values are mean ± SD (n = 3) (Additional file 4). *p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001, ****p ≤ 0.0001, ns, not statistically significant (one-way ANOVA with Tukey’s multiple comparisons test)

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