CENP-B cooperates with Set1 in bidirectional transcriptional silencing and genome organization of retrotransposons

Expression profiling of mutant cells compared to wild-type cells. Expression profiling of S. pombe CENP-B homolog cbp1∆ (abp1/SPBC1105.04c) and histone deacetylase double mutant clr3∆ clr6-1 (SPBC800.03 SPBC36.05c) cells. Wildtype and mutant cDNA was reverse transcribed from total RNA using the Invitrogen SuperscriptIII Indirect labeling kit and the supplied anchored oligo-dT according to the manufacturer's instructions. cDNA from mutant and wildtype samples were labeled with Alexa Fluor 555 and 647 dyes, respectively. Biological duplicates were performed for each mutant and wildtype sample. An Agilent 44K in situ 60mer DNA microarray that tiles the entire Schizosaccharomyces pombe genome every 300 bp alternately on both strands was used to probe expression of transcripts in CENP-B homolog cbp1∆ (abp1/SPBC1105.04c) and histone deacetylase double mutants clr3∆ clr6-1 (SPBC800.03 SPBC36.05c) cells versus wildtype.