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Series GSE43478 Query DataSets for GSE43478
Status Public on Apr 05, 2013
Title HP1a, Su(var)3-9, SETDB1 and POF stimulate or repress gene expression depending on genomic position, gene length and expression pattern in Drosophila melanogaster
Organism Drosophila melanogaster
Experiment type Expression profiling by array
Summary Heterochromatin protein 1a (HP1a) is a chromatin associated protein that has been well studied in many model organisms, such as Drosophila, where it is a determining factor for classical heterochromatin. HP1a is associated with the two histone methyltransferases SETDB1 and Su(var)3-9, which mediate H3K9 methylation marks and participate in the establishment and spreading of HP1a enriched chromatin. While HP1a is generally regarded as a factor that represses gene transcription, several reports have linked HP1a binding to active genes, and in some cases, it has been shown to stimulate transcriptional activity. To clarify the function of HP1a in transcription regulation and its association with Su(var)3-9, SETDB1 and the chromosome 4 specific protein POF, we conducted genome-wide expression studies and combined the results with available binding data in Drosophila melanogaster. The results suggested that HP1a has a repressing function on chromosome 4, where it preferentially targets non-ubiquitously expressed genes (NUEGs), and a stimulating function in pericentromeric regions. Further, we showed that the effects of SETDB1 and Su(var)3-9 are similar to HP1a, and on chromosome 4, Su(var)3-9, SETDB1 and HP1a target the same genes. In contrast, transposons are repressed by HP1a and Su(var)3-9 but are un-affected by SETDB1 and POF. In addition, we found that the binding level and expression effects of HP1a are affected by gene length. Our results indicate that genes have adapted to be properly expressed in their local chromatin environment.
 
Overall design We prepared total RNA from 1st instar larvae trans-heterozygous for HP1a04/HP1a05, trans-heterozygous Su(var)3-9evo/Su(var)3-906, homozygous Setdb110.1/ Setdb110.1 mutants and trans-heterozygous HP1a04 PofD119/HP1a05 PofD119 double mutants three biological replicates, as well as from six biological replicates of wildtype control 1st instar larvae.
 
Contributor(s) Lundberg LE, Stenberg P, Larsson J
Citation(s) 23476027
Submission date Jan 14, 2013
Last update date May 04, 2018
Contact name Jan Larsson
E-mail(s) jan.larsson@molbiol.umu.se
Organization name Umea University
Department Molecular Biology
Lab Jan Larsson
Street address Umea University
City Umea
ZIP/Postal code SE-90187
Country Sweden
 
Platforms (1)
GPL1322 [Drosophila_2] Affymetrix Drosophila Genome 2.0 Array
Samples (18)
GSM1063506 1st instar larvae_HP1a04/HP1a05_replicate_A
GSM1063507 1st instar larvae_HP1a04/HP1a05_replicate_B
GSM1063508 1st instar larvae_HP1a04/HP1a05_replicate_C
Relations
BioProject PRJNA186531

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE43478_RAW.tar 36.0 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table
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