Chromosome-wide gene-specific targeting of theDrosophiladosage compensation complex

Abstract

The dosage compensation complex (DCC) of Drosophila melanogaster is capable of distinguishing the single male X from the other chromosomes in the nucleus. It selectively interacts in a discontinuous pattern with much of the X chromosome. How the DCC identifies and binds the X, including binding to the many genes that require dosage compensation, is currently unknown. To identify bound genes and attempt to isolate the targeting cues, we visualized male-specific lethal 1 (MSL1) protein binding along the X chromosome by combining chromatin immunoprecipitation with high-resolution microarrays. More than 700 binding regions for the DCC were observed, encompassing more than half the genes found on the X chromosome. In addition, several rare autosomal binding sites were identified. Essential genes are preferred targets, and genes binding high levels of DCC appear to experience the most compensation (i.e., greatest increase in expression). DCC binding clearly favors genes over intergenic regions, and binds most strongly to the 3 end of transcription units. Within the targeted genes, the DCC exhibits a strong preference for exons and coding sequences. Our results demonstrate gene-specific binding of the DCC, and identify several sequence elements that may partly direct its targeting.[Keywords: Transcription; histone modification; chromatin remodeling; MSL complex; microarray; gene expression] Supplemental material is available at http://www.genesdev.org.

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

“…In flies, dosage compensation is accomplished by the male-specific lethal (MSL) complex, composed of proteins and RNA. The MSL complex binds within the body of X-linked genes and alters chromatin to enhance transcription (Alekseyenko et al 2006;Gilfillan et al 2006;Legube et al 2006). The protein-coding components of the MSL complex were identified by the male-specific lethality of mutations in these genes.…”

Structural and Biochemical Studies on the Chromo-barrel Domain of Male Specific Lethal 3 (MSL3) Reveal a Binding Preference for Mono- or Dimethyllysine 20 on Histone H4

“…Supporting a role for H4K20Me 1 in the recruitment of the MSL complex, H4K20Me 1 is an abundant modification on histone tails in Drosophila and humans, and its presence correlates positively with the level of transcriptional activity along human genes, at least as well as for H3K36Me 3 (59,(62)(63)(64)(65)(66)(67). Furthermore, other studies have shown that H4K20Me 1 is found to be preferentially deposited on nucleosomes residing within exons (68,69), a pattern mirrored in the X-chromosome binding of the Drosophila MSL complex (30). However, there is no published polytene chromosome immunofluorescence evidence for H4K20Me 1 being enriched at the sites of Drosophila MSL complex binding (70,71).…”

“…The absence of any of the MSL components results in male lethality (14,15,(23)(24)(25)(26)). The precise specificity of MOF for H4K16 and the targeting to specific domains of the male X-chromosome is determined by other components of the complex, in particular 23,26,[28][29][30]32).…”

“…Male flies homozygous for the Y31A mutant did not survive as well as females (30.9% male survival; Table 3), suggesting that Tyr 31 does play a role in dosage compensation, consistent with its contribution to H4K20Me 1 binding in vitro. In a previously published study of msl3 chromo-barrel domain mutants, the Tyr 31 residue was mutated to alanine along with two adjacent residues (Leu 30 and Thr 32 ) (20). However, the triple amino acid mutant had a 0% rescue frequency and was unstable.…”

“…The most well studied MOF-containing complex is the Drosophila melanogaster male specific lethal or MSL complex that binds selectively to large regions of the X-chromosome in male flies (14,15,(21)(22)(23)(24)(25)(26) where it is enriched at the 3Ј ends of actively transcribed genes (27)(28)(29)(30) and acetylates lysine 16 on histone H4 (H4K16Ac) (22,31), thereby balancing male Xchromosomal gene expression. The Drosophila MSL complex contains the dMSL1, dMSL2, and dMSL3 proteins, the RNA/ DNA helicase MLE, the HAT enzyme MOF, and one of two apparently functionally redundant non-coding RNAs (roX1 and roX2) (reviewed in Refs.…”