Enhanced chromatin accessibility of the dosage compensated Drosophila male X-chromosome requires the CLAMP zinc finger protein.

Jennifer Urban,Erica Larschan,Benjamin Scruggs,Michael Tolstorukov,Guray Kuzu,Telmo Henriques,Sarah Bowman,Karen Adelman,Robert Kingston,Asifa Akhtar

doi:10.1371/journal.pone.0186855

Abstract

The essential process of dosage compensation is required to equalize gene expression of X-chromosome genes between males (XY) and females (XX). In Drosophila, the conserved Male-specific lethal (MSL) histone acetyltransferase complex mediates dosage compensation by increasing transcript levels from genes on the single male X-chromosome approximately two-fold. Consistent with its increased levels of transcription, the male X-chromosome has enhanced chromatin accessibility, distinguishing it from the autosomes. Here, we demonstrate that the non-sex-specific CLAMP (Chromatin-linked adaptor for MSL proteins) zinc finger protein that recognizes GA-rich sequences genome-wide promotes the specialized chromatin environment on the male X-chromosome and can act over long genomic distances (~14 kb). Although MSL complex is required for increasing transcript levels of X-linked genes, it is not required for enhancing global male X-chromosome chromatin accessibility, and instead works cooperatively with CLAMP to facilitate an accessible chromatin configuration at its sites of highest occupancy. Furthermore, CLAMP regulates chromatin structure at strong MSL complex binding sites through promoting recruitment of the Nucleosome Remodeling Factor (NURF) complex. In contrast to the X-chromosome, CLAMP regulates chromatin and gene expression on autosomes through a distinct mechanism that does not involve NURF recruitment. Overall, our results support a model where synergy between a non-sex-specific transcription factor (CLAMP) and a sex-specific cofactor (MSL) creates a specialized chromatin domain on the male X-chromosome.

Highlights

Dosage compensation is an ancient mechanism that functions to regulate transcription of Xchromosome genes to equalize transcript levels between XY males and XX females
To examine whether Chromatin-linked adapter for MSL Proteins (CLAMP) regulates chromatin accessibility, we identified nuclease-accessible regions genome-wide using a recently developed assay that is based on chromatin digestion in a MNase titration series followed by high-throughput sequencing [13] (Fig 1A)
We found that the majority of accessibility changes for both clamp and msl2 RNAi treatments occur within gene bodies (>65% for both treatments), consistent with the most frequent genomic location of CLAMP and Male-specific lethal (MSL) complex binding sites (Fig 1D)

Summary

Introduction

Dosage compensation is an ancient mechanism that functions to regulate transcription of Xchromosome genes to equalize transcript levels between XY males and XX females. In D. melanogaster and across Diptera, dosage compensation occurs by increasing transcript levels of thousands of genes along the length of the single male X-chromosome two-fold to equalize transcript levels with XX females [2,3,4]. This process of increasing X-chromosome transcript levels is mediated by the Male-specific lethal (MSL) histone acetyltransferase complex [3]. These observations led us to hypothesize that a non-sex-specific factor functions upstream of MSL complex to establish the enhanced chromatin accessibility that allows MSL complex to distinguish the male X-chromosome from autosomes

Methods

Results

Conclusion