A Sequence Motif within Chromatin Entry Sites Directs MSL Establishment on the Drosophila X Chromosome

Abstract

Summary The Drosophila MSL complex associates with active genes specifically on the male X chromosome to acetylate histone H4 at lysine 16, and increase expression approximately two-fold. To date, no DNA sequence has been discovered to explain the specificity of MSL binding. We hypothesized that sequence-specific targeting occurs at “chromatin entry sites”, but the majority of sites are sequence-independent. Here we characterize 150 potential entry sites by ChIP-chip and ChIP-seq and discover a GA-rich MSL recognition element (MRE). The motif is only slightly enriched on the X chromosome (~2 fold), but this is doubled when considering its preferential location within or 3’ to active genes (>4 fold enrichment). When inserted on an autosome, a newly identified site can direct local MSL spreading to flanking active genes. These results provide strong evidence for both sequence-dependent and -independent steps in MSL targeting of dosage compensation to the male X chromosome.

Imprinting of the Y Chromosome Influences Dosage Compensation inroX1 roX2 Drosophila melanogaster

“…This is particularly interesting as the roX RNAs are central to recognition and modification of the X chromosome, but the molecular basis of roX activity is poorly understood. Short identity elements that are enriched on the X chromosome are proposed to underlie recognition (Alekseyenko et al 2008). It is possible that integration of roX RNA into the MSL complex promotes cooperative binding, favoring the modest enrichment of identity elements on the X chromosome.…”

Dosage Compensation inDrosophila

“…Again, a genomic approach has provided key insights into how targeting might occur. Results from ChIP of MSL2 in msl3 mutant embryos, or MSL1 or MSL2 in suboptimal crosslinking conditions, identified a set of 130-150 candidate entry sites by their high affinity (Alekseyenko et al 2008;Straub et al 2008). These sites included the previously characterized entry sites in the roX1 and roX2 genes .…”

Epigenetics meets next-generation sequencing

“…This enabled the investigator to determine specific regions of interest to be interrogated with an array. In addition to whole-genome arrays, we, for instance, have used custom arrays to study the Drosophila X-chromosome 5,6 (tiled along with an autosome as a control) as well as the human HOX regions. 7 For the former, 100 bp resolution was chosen so that all the probes can be contained in a single array; for the latter, 5 bp resolution was specified in order to locate nucleosomes in the small region.…”