Fig. 4: A catalogue of variants in C-terminal IDRs reveals frameshifts associated with nucleolar mispartitioning and dysfunction.

a, Circos plot of the IDR variant catalogue. The circles indicate the location of genes that contain a truncation (stop gained) or frameshift variant in the dbSNP, 1000 Genomes Project, COSMIC and ClinVar databases. The highlighted genes contain a pathogenic frameshift that creates a sequence of ≥20 amino acids comprising ≥15% arginine residues. b, Summary statistics and features of variant types in C-terminal IDRs. P values are from hypergeometric tests. c, Identification of frameshifts creating a sequence of ≥20 amino acids that consist of ≥15% arginine residues. Plotted is the fraction of arginine residues against the length of the sequence created by the frameshift. The genes containing the variants selected for further validation are highlighted orange. Pathogenic gene variants are in blue. d, Representative images of U2OS cells co-expressing RFP–FIB1 and the indicated eGFP-tagged proteins. Nuclear area revealed by Hoechst staining is shown as dashed white lines. Mutations in the following genes are associated with the indicated conditions: microphthalmia (HMGB3 and RAX); myopathy (MYOD1); congenital central hypoventilation (PHOX2B); myelodysplasia (RUNX1); Axenfeld–Rieger syndrome type 3 (FOXC1); myelofibrosis (CALR); alveolar capillary dysplasia (FOXF1); anophthalmia/microphthalmia-oesophaegalatresia syndrome (SOX2); Paget disease of bone 2, early-onset frontotemporal dementia and amyotrophic lateral sclerosis (SQSTM1); blepharophimosis, ptosis and epicanthus inversus (FOXL2); and hereditary cancer predisposing syndrome (MEN1). Scale bar, 10 µm. e, Nucleolar mispartitioning strongly correlates with the fraction of arginine residues in the frameshift sequence. Plotted are Pearson’s correlation coefficients of the extent of nucleolar mispartitioning of mutant proteins with protein features of their IDRs (left triangle) and features of the sequences created by the frameshifts (right triangle). The colour corresponds to the value of Pearson’s correlation coefficients, and the size of the circles is proportional to the P value of the Pearson’s r. f, RT–qPCR analysis of rRNA species in U2OS cells expressing the indicated WT and mutant proteins. rRNA levels are normalized against an RNAPII transcript (GAPDH), and fold changes are calculated against the rRNA/GAPDH level measured in the cells expressing WT protein. Data are shown as mean ± s.d., P values are from two-tailed Welch’s t-test. AA, amino acid; SNP, single nucleotide polymorphism; nucl. enr., nucleolar enrichment.