Research News
Structure solved by Dr. Keqiong Ye's lab elucidates molecular mechanism of X chromosome dosage compensation in Drosophila
On Dec. 1, 2014, Dr. Keqiong Ye's lab published a research article entitled "Structural basis of X chromosome DNA recognition by the MSL2 CXC domain during Drosophila dosage compensation".
Most animals contain different numbers of X chromosome in male (XY) and female (XX) and are hence faced with the problem of unbalanced expression levels for X-linked genes in two sexes. The widespread dosage compensation process equalizes the gene expression level from the X chromosome between two sexes, but its mechanism varies greatly among different organisms. For example, one of two X chromosomes is silenced in human females, whereas the single X chromosome is transcriptionally upregulated by twofolds in fly males.
In Drosophila male, the MSL (male-specific lethal) dosage compensation complex is specifically localized at the X chromosome and acetylates histone H4 K14 to activate transcription. The mechanism by which the MSL complex distinguishes the X chromosome from other autosomes remains poorly understood. According to the prevalent model, the MSL complex initially binds at about 150 high affinity sites in the X chromosome and then spreads to flanking active genes. The GA-rich MSL recognition element (MRE) sequence motif has been shown to nucleate MSL assembly, but how it is recognized has not yet understood.
MSL2, a protein in the MSL complex, is required for binding high affinity sites. MSL2 contains a cysteine-rich DNA-binding CXC domain. The Ye laboratory has previously solved the solution structure of CXC domain by NMR spectroscopy and found that it contains an unusual Zn3Cys9 cluster and bears a remarkable structural similarity with the pre-SET domain of histone methyltransferases.
In the latest study, the Ye laboratory found that the CXC domain specifically recognizes the MRE motif and determined its crystal structures bound with specific and non-specific DNAs. The CXC domain spans about a region of 6 base pairs, but binds primarily with only one strand of DNA. In the specific binding mode, an arginine at position 543 inserts deeply into the minor groove of DNA and interacts with two adjacent bases, which constitutes the only interaction in the structure that directly recognizes DNA sequence. Such a DNA-binding mode is unusual given that other DNA-binding domains commonly recognize DNA sequence from the major groove. In addition, the central region of the MRE motif is bound cooperatively by two CXC domains, which likely constitutes the key feature of the high affinity MRE motif. Interestingly, the CXC domain adopts a different conformation when binding non-specific DNA: the arginine 543 becomes flexible and no longer recognizes the DNA sequence and there is no binding cooperativity. It is likely that the CXC domain employs such a non-specific, non-cooperative mode to search for the MRE motif. In vivo study shows that specific DNA-binding mutants of MSL2 are impaired in MRE binding and X chromosome localization. In sum, this study reveals multiple DNA-binding modes of the CXC domain that target the MSL complex to the X chromosome.
Sanduo Zheng, a NIBS graduate student, is the first author of this paper. The in vivo mutagenesis experiment was conducted by Raffaella Villa at the laboratory of Dr. Peter Becker, Ludwig-Maximilians-University,Germany. Other authors include Jia Wang from NIBS, Dr. Yingang Feng from Qingdao Institute of BioEnergy and Bioprocess Technology, and Dr. Jinfeng Wang from Institute of Biophysics. Dr. Keqiong Ye is the corresponding author.
