A library-based method to rapidly analyse chromatin accessibility at multiple genomic regions.
Traditional chromatin analysis methods only test one locus at the time or use different templates for each locus, making a standardized analysis of large genomic regions or many co-regulated genes at different loci a difficult task. On the other hand, genome-wide high-resolution mapping of chromatin accessibility employing massive parallel sequencing platforms generates an extensive data set laborious to analyse and is a cost-intensive method, only applicable to the analysis of a limited set of biological samples. To close this gap between the traditional and the high-throughput procedures we have developed a method in which a condition-specific, genome-wide chromatin fragment library is produced and then used for locus-specific DNA fragment analysis. To validate the method, we used, as a test locus, the well-studied promoter of the divergently transcribed niiA and niaD genes coding for nitrate assimilation enzymes in Aspergillus. Additionally, we have used the condition-specific libraries to study nucleosomal positioning at two different loci, the promoters of the general nitrogen regulator areA and the regulator of secondary metabolism, aflR.
Basheer
Asjad
A
Austrian Research Centers, Department of Applied Genetics and Cell Biology, BOKU University Vienna, Vienna, Austria.
Berger
Harald
H
Reyes-Dominguez
Yazmid
Y
Gorfer
Markus
M
Strauss
Joseph
J
D001233:Aspergillus nidulans / Q000235:genetics; D002843:Chromatin / Q000737:chemistry*; D017931:DNA Primers; D004262:DNA Restriction Enzymes; D005456:Fluorescent Dyes; D005656:Fungal Proteins / Q000235:genetics; D015723:Gene Library; D023281:Genomics / Q000379:methods*; D008836:Micrococcal Nuclease; D009707:Nucleosomes / Q000737:chemistry; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000235:genetics
C079728:AreA protein, Aspergillus nidulans; D002843:Chromatin; D017931:DNA Primers; D005456:Fluorescent Dyes; D005656:Fungal Proteins; D009707:Nucleosomes; D014157:Transcription Factors; D004262:DNA Restriction Enzymes; D008836:Micrococcal Nuclease