Journal article
Context Differences Reveal Insulator and Activator Functions of a Su(Hw) Binding Region
PLoS genetics, Vol.4(8), pp.e1000159-e1000159
08/2008
DOI: 10.1371/journal.pgen.1000159
PMCID: PMC2493044
PMID: 18704163
Abstract
Insulators are DNA elements that divide chromosomes into independent transcriptional domains. The Drosophila genome contains hundreds of binding sites for the Suppressor of Hairy-wing [Su(Hw)] insulator protein, corresponding to locations of the retroviral
gypsy
insulator and non-
gypsy
binding regions (BRs). The first non-
gypsy
BR identified, 1A-2, resides in cytological region
1A
. Using a quantitative transgene system, we show that 1A-2 is a composite insulator containing enhancer blocking and facilitator elements. We discovered that 1A-2 separates the
yellow
(
y
) gene from a previously unannotated, non-coding RNA gene, named
yar
for
y
-
a
chaete
(
ac
) intergenic
R
NA. The role of 1A-2 was elucidated using homologous recombination to excise these sequences from the natural location, representing the first deletion of any Su(Hw) BR in the genome. Loss of 1A-2 reduced
yar
RNA accumulation, without affecting mRNA levels from the neighboring
y
and
ac
genes. These data indicate that within the
1A
region, 1A-2 acts an activator of
yar
transcription. Taken together, these studies reveal that the properties of 1A-2 are context-dependent, as this element has both insulator and enhancer activities. These findings imply that the function of non-
gypsy
Su(Hw) BRs depends on the genomic environment, predicting that Su(Hw) BRs represent a diverse collection of genomic regulatory elements.
Insulators are conserved genomic elements that define domains of independent transcription. One class of insulators in the Drosophila genome are defined by the binding of the Su(Hw) protein, with the
gypsy
insulator representing the classic Su(Hw)-dependent insulator. Su(Hw) associates with hundreds of non-
gypsy
regions distributed throughout the genome that differ in sequence and organization from the
gypsy
insulator. To gain insights into the role of Su(Hw) in genome organization, we defined the properties of the first non-
gypsy
Su(Hw) binding region identified, 1A-2. Our studies reveal differences in 1A-2 activity, depending on the context tested. We show that 1A-2 is an insulator in enhancer blocking studies but functions as a transcriptional activator within the natural genomic location. Our findings are reminiscent of properties of binding regions that associate with the vertebrate CTCF protein, which have defined insulator, activator, and repressor functions. Finally, our studies indicate that a noncoding RNA gene may contribute to independent transcriptional regulation in the genome.
Details
- Title: Subtitle
- Context Differences Reveal Insulator and Activator Functions of a Su(Hw) Binding Region
- Creators
- Alexey A SoshnevXingguo LiMisty D WehlingPamela K Geyer
- Resource Type
- Journal article
- Publication Details
- PLoS genetics, Vol.4(8), pp.e1000159-e1000159
- DOI
- 10.1371/journal.pgen.1000159
- PMID
- 18704163
- PMCID
- PMC2493044
- NLM abbreviation
- PLoS Genet
- ISSN
- 1553-7390
- eISSN
- 1553-7404
- Publisher
- Public Library of Science; San Francisco, USA
- Alternative title
- Transcriptional Effects of the 1A-2 Insulator
- Language
- English
- Date published
- 08/2008
- Academic Unit
- Obstetrics and Gynecology; Biochemistry and Molecular Biology
- Record Identifier
- 9984024553502771
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