The conserved histone locus body (HLB) assembles prior to zygotic gene activation early during development and concentrates factors into a nuclear domain of coordinated histone gene regulation. Although HLBs form specifically at replication-dependent histone loci, the and factors that target HLB components to histone genes remained unknown. Here we report that conserved GA repeat elements within the bidirectional promoter direct HLB formation in In addition, the CLAMP (chromatin-linked adaptor for male-specific lethal [MSL] proteins) zinc finger protein binds these GA repeat motifs, increases chromatin accessibility, enhances histone gene transcription, and promotes HLB formation. We demonstrated previously that CLAMP also promotes the formation of another domain of coordinated gene regulation: the dosage-compensated male X chromosome. Therefore, CLAMP binding to GA repeat motifs promotes the formation of two distinct domains of coordinated gene activation located at different places in the genome.

In metazoans, histone mRNAs are not polyadenylated but end in a conserved stem-loop. Stem-loop binding protein (SLBP) binds to the stem-loop and is required for all steps in histone mRNA metabolism. The genes for the five histone proteins are linked. A histone locus body (HLB) forms at each histone gene locus. It contains factors essential for transcription and processing of histone mRNAs, and couples transcription and processing. The active form of U7 snRNP contains the HLB component FLASH (FLICE-associated huge protein), the histone cleavage complex (HCC), and a subset of polyadenylation factors including the endonuclease CPSF73. Histone mRNAs are rapidly degraded when DNA replication is inhibited by a 3′ to 5′ pathway that requires extensive uridylation of mRNA decay intermediates.

By using a histone gene replacement platform in Drosophila, we show that interactions among multiple factors contribute to HLB formation, and that the large number of genes at the endogenous histone locus sequesters available factors from attenuated transgenic histone gene arrays, thereby preventing HLB formation and histone gene expression from these arrays.

30The histone locus body (HLB) assembles at replication-dependent (RD) histone loci and 31 concentrates factors required for RD histone mRNA biosynthesis. The D. melanogaster genome 32 has a single locus comprised of ~100 copies of a tandemly arrayed repeat unit containing one 33 copy of each of the 5 RD histone genes. To determine sequence elements required for D. 34 melanogaster HLB formation and histone gene expression, we used transgenic gene arrays 35 containing 12 copies of the histone repeat unit that functionally complement loss of the ~200 36 endogenous RD histone genes. A 12x histone gene array in which all H3-H4 promoters were 37 replaced with H2a-H2b promoters does not form an HLB or express high levels of RD histone 38 mRNA in the presence of the endogenous histone genes. In contrast, this same transgenic array is 39 active in HLB assembly and RD histone gene expression in the absence of the endogenous RD 40 histone genes and rescues the lethality caused by homozygous deletion of the RD histone locus. 41 The HLB formed in the absence of endogenous RD histone genes on the mutant 12x array 42 contains all known factors present in the wild type HLB including CLAMP, which normally 43 binds to GAGA repeats in the H3-H4 promoter. These data suggest that multiple protein-protein 44 and/or protein-DNA interactions contribute to HLB formation, and that the large number of 45 endogenous RD histone gene copies sequester available factor(s) from attenuated transgenic 46 arrays, thereby preventing HLB formation and gene expression. 47 48 3 109In this work, we leveraged transgenic histone gene arrays to test whether the H3-H4 110 promoter region is necessary for in vivo function of the RD histone locus. We found that 111 replacement of H3-H4 promoters with H2a-H2b promoters results in an attenuated transgenic 112 histone gene array that does not function in the presence of the intact endogenous RD histone 113 locus, but surprisingly provides full in vivo function, including normal HLB assembly and 114 histone gene expression, when the endogenous RD histone locus is absent. These results suggest 115 6 that multiple elements in the histone genes and core HLB proteins are involved in HLB 116 assembly. 118 Results 119To study histone gene regulation and the role of histone post-translational modifications 120 in chromatin we previously developed an experimental system in which BAC-based, transgenic 121 histone gene arrays containing 12 copies of the 5kb histone repeat unit assemble HLBs and 122 functionally complement homozygous loss of the ~100 gene copies at the endogenous RD 123 histone locus, HisC (McKay et al., 2015). To study histone gene expression, we created a 124 12x HWT (Histone Wild Type) transgenic construct containing a synonymous polymorphism in the 125 H2a gene (i.e. mutation of a XhoI site) that allows us to distinguish transgenic H2a gene 126 expression from endogenous H2a gene expression (McKay et al., 2015). Here, we extended this 127 design and created a "Designer Wild Type" (DWT) 5kb ...

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