(A) Schematic of genome integrity screens showing the cellular phenotype measured (top box – i.e. pigmentation for CTF, capacity to mate for ALF, acquired 5′FOA and canavanine resistance for GCR), the chromosomal context of the CIN marker (lower box; blue line indicates chromosome, black oval indicates the centromere, other features are described below) and the type of alleles screened by each assay (bottom). For CTF (left), red pigment accumulates due to a block in adenine production (ade2-101) that is relieved in the presence of SUP11 (black rectangle) carried on a non-essential fragment of chromosome III or VII (CF) (Blue line). Strains carrying the CF will be unpigmented while those that lose the CF will be red. Colonies of mutants with whole chromosome instability will grow with red sectors in an unpigmented colony. For ALF (center), loss of the MATα locus leads to dedifferentiation to an a-mating phenotype. α-mating type mutant strains are mated to a MATα test strain and growth of diploid mated progeny is assessed on selective media, where the ability to mate and form diploids reflects loss, deletion or inactivation of the MATα locus. For GCR (right), URA3 is integrated near the CAN1 gene on the left arm of chromosome V where the distal portion of the chromosome arm is non-essential. GCR assay strains are patched onto double counter-selection media where only ura3, can1 strains can survive thus revealing increased rates of terminal chromosome arm deletion and non-reciprocal rearrangements. (B) Overview of CIN gene list. (i) CIN mutations in essential, non-essential and overexpressed genes. (ii) Overlap among five high-throughput CIN phenotypes links 683 of the CIN genes (overlap of 36 LOH mutants (dotted lines) is not shown for clarity). (iii) CIN phenotypic strength in nuclear localized versus other genes. Bars colored according to 1C. (C) Cellular schematic of 692 CIN genes grouped according to function (Table S1). The large dotted circle represents the nucleus. Colors indicate a strong phenotype (red) or a weak phenotype (blue) where darker represents CIN in multiple assays and lighter represents CIN in a single assay. Yellow boxes and bold labels indicate groups, and dotted circles and italic labels indicate subgroups or protein complexes. Subgroup abbreviations; IMP – inosine monophosphate synthesis; SRP – signal recognition particle; GPI – glycophosphatidylinositol synthesis; NUP – nucleoporins; PFD – prefoldin complex; FeS – Iron Sulfur cluster synthesis; m-ribosome – mitochondrial ribosomal subunit.