Gene expression changes due to genome region inversions was studied. Four strains of Saccharomyces cerevisiae strains with inversions engineered between TY1 elements were compared to matching controls.

Transcription profiling by array of four strains of budding yeast with inversions engineered between TY1 elements against matching controls

Affymetrix GeneChip Yeast Genome 2.0 Array [Yeast_2]

Widespread Impact of Chromosomal Inversions on Gene Expression Uncovers Robustness via Phenotypic Buffering.

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Gene expression changes due to genome region inversions was studied. Four strains of Saccharomyces cerevisiae strains with inversions engineered between TY1 elements were compared to matching controls.


The inverted and non-inverted strains were grown in SD medium (Synthetic Dextrose Medium containing: Bacto-yeast nitrogen base without amino acids (0.67%), glucose (2%), amino acids specific for each strain and distilled water.) to mid-log phase (OD595nm = 0.5) in triplicate and total RNA was extracted.

Inversions were made between yeast transposable elements ôTY1ö on different chromosomes in S. cerevisiae strain BY4741. In stage one of construction a Ty universal insertion cassette having a single loxP with a resistant antibiotic marker (loxP-kanMX) and containing DNA homologous to all Ty1 was inserted inside of every TY1 element without deleting the whole TY1 sequence. Since the sequences of all 31 TY1 elements are highly similar, this characteristic was used in our favour. Out of the planned 31 strains, 25 strains inserted with loxP-kanMX were successfully produced and confirmed by colony PCR. These ôStage 1ö strains were used to generate the loxP-kanMX+loxP-hphNT1 strains which were further used to generate inversions. In nature chromosomal inversions will occur among the TY elements which are present in head to head or tail to tail orientation. Therefore, strains possessing loxP-kanMX at TY1 orientated in opposite direction on the chromosome were chosen to create the inversion. Four inversion strains were selected for gene expression studies. The names and inversion locations are: IV-D (chrIV:884220-1206704), VII-B (chrVII:535760-823306), XIV (chrXIV:96610-525062) and XVI-B (chrXVI:56452-810562). The controls for each inversion strain contain the loxP-kanMX insertion in the same region prior to inversion.

Total RNA was extracted using Trizol reagent following the manufacturerÆs instructions (Invitrogen, catalogue # 155-96-018). RNA was quantified using the nanodrop ultra-low-volume spectrophotometer (Nanodrop Technologies) and the quality of total RNA was determined using Agilent Bioanalyzer 2100 (Agilent Technologies Ltd, UK). Whenever required RNA was treated with DNaseI (Fermentas catalogue no. EN0521).

Hybridization to Affymetrix Yeast Genome 2.0 Array

Scanned with Affymetrix GeneChip Scanner 3000 and quality control checks for control hybridizations were performed, again using Affymetrix GCOS (V1.4) software.

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Transcription profiling by array of four strains of budding yeast with inversions engineered between TY1 elements against matching controls

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