Histone locus regulation by the <i>Drosophila</i> dosage compensation adaptor protein CLAMP

Rieder, Leila E.; Koreski, Kaitlin P.; Boltz, Kara A.; Kuzu, Guray; Urban, Jennifer A.; Bowman, Sarah K.; Zeidman, Anna; Jordan, William T.; Tolstorukov, Michael Y.; Marzluff, William F.; Duronio, Robert J.; Larschan, Erica

doi:10.1101/gad.300855.117

Cited by 49 publications

(250 citation statements)

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“…S1B). One difference between the two promoters is that the H2a-H2b region lacks the CLAMP-binding GAGA repeats present in the H3-H4 promoter (Rieder et al ., 2017). Otherwise it is an intact, native bidirectional histone gene promoter.…”

Section: Resultsmentioning

confidence: 99%

“…Using transgenes containing a wild type or mutant derivative of a single histone repeat, we previously demonstrated that the bidirectional H3-H4 promoter stimulated HLB assembly and transcription of the single histone repeat in salivary glands (Salzler et al ., 2013). We subsequently showed that the conserved GAGA repeat elements present in the H3-H4 promoter region are targeted by the zinc-finger transcription factor CLAMP (Chromatin-Linked Adaptor for MSL Proteins), and that this interaction promotes HLB assembly (Rieder et al ., 2017). Thus, the H3-H4 promoter region might act to seed HLB assembly.…”

Section: Introductionmentioning

confidence: 99%

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DrosophilaHistone Locus Body assembly and function involves multiple interactions

Koreski¹,

Rieder

McLain³

et al. 2020

Preprint

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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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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

DrosophilaHistone Locus Body assembly and function involves multiple interactions

Koreski¹,

Rieder

McLain³

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

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“…We therefore hypothesized that CLAMP identifies its binding sites prior to MSLc. To test this hypothesis, we performed ChIPseq on maleenriched embryo pools for CLAMP, MSL3 (a component of MSLc), and the H4K16ac mark, and on femaleenriched embryo pools for CLAMP (Rieder et al, 2017) and H4K16ac. MSLc does not assemble in female embryos due to posttranscriptional repression of the structural MSL2 component by the master sex regulator Sex lethal .…”

Section: Mslc Identifies the Male Xchromosome In A Multistage Processmentioning

confidence: 99%

“…Female embryo CLAMP ChIPseq data are deposited in NCBI GEO under accession number GSE119448 (Rieder et al 2017) . Cell culture CLAMP ChIPseq data are deposited in NCBI GEO under accession number GSE39271 (Soruco et al 2013) .…”

Section: Datasetsmentioning

confidence: 99%

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Targeting of the dosage-compensated male X-chromosome during earlyDrosophiladevelopment

Rieder

Jordan

Larschan

2019

Preprint

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The essential process of dosage compensation, which corrects for the imbalance in Xlinked gene expression between XX females and XY males, represents a key model for how genes are targeted for coordinated regulation. However, the mechanism by which dosage compensation complexes identify the Xchromosome during early development remained unknown because of the difficulty of sexing embryos prior to zygotic transcription. We used meiotic drive to sex Drosophila embryos prior to zygotic transcription and ChIPseq to measure dynamics of dosage compensation factor targeting. The Drosophila MaleSpecific Lethal dosage compensation complex (MSLc) requires the ubiquitous zincfinger protein ChromatinLinked Adaptor for MSL Proteins (CLAMP) to identify the Xchromosome. We observe a multistage process in which MSLc first identifies CLAMP binding sites throughout the genome followed by concentration at the strongest Xlinked MSLc sites. We provide insight into the dynamic mechanism by which a large transcription complex identifies its binding sites during early development.

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Regulatory Architecture of the Neuronal Cacng2/Tarpγ2 Gene Promoter: Multiple Repressive Domains, a Polymorphic Regulatory Short Tandem Repeat, and Bidirectional Organization with Co-regulated lncRNAs

et al. 2018

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CACNG2 (TARPγ2, Stargazin) is a multi-functional regulator of excitatory neurotransmission and has been implicated in the pathological processes of several brain diseases. Cacng2 function is dependent upon expression level, but currently, little is known about the molecular mechanisms that control expression of this gene. To address this deficit and investigate disease-related gene variants, we have cloned and characterized the rat Cacng2 promoter and have defined three major features: (i) multiple repressive domains that include an array of RE-1 silencing transcription factor (REST) elements, and a calcium regulatory element-binding factor (CaRF) element, (ii) a (poly-GA) short tandem repeat (STR), and (iii) bidirectional organization with expressed lncRNAs. Functional activity of the promoter was demonstrated in transfected neuronal cell lines (HT22 and PC12), but although selective removal of REST and CaRF domains was shown to enhance promoter-driven transcription, the enhanced Cacng2 promoter constructs were still about fivefold weaker than a comparable rat Synapsin-1 promoter sequence. Direct evidence of REST activity at the Cacng2 promoter was obtained through co-transfection with an established dominant-negative REST (DNR) construct. Investigation of the GA-repeat STR revealed polymorphism across both animal strains and species, and size variation was also observed in absence epilepsy disease model cohorts (Genetic Absence Epilepsy Rats, Strasbourg [GAERS] and non-epileptic control [NEC] rats). These data provide evidence of a genotype (STR)-phenotype correlation that may be unique with respect to proximal gene regulatory sequence in the demonstrated absence of other promoter, or 3′ UTR variants in GAERS rats. However, although transcriptional regulatory activity of the STR was demonstrated in further transfection studies, we did not find a GAERS vs. NEC difference, indicating that this specific STR length variation may only be relevant in the context of other ( Cacna1h and Kcnk9 ) gene variants in this disease model. Additional studies revealed further (bidirectional) complexity at the Cacng2 promoter, and we identified novel, co-regulated, antisense rat lncRNAs that are paired with Cacng2 mRNA. These studies have provided novel insights into the organization of a synaptic protein gene promoter, describing multiple repressive and modulatory domains that can mediate diverse regulatory inputs. Electronic supplementary material The online version of this article (10.1007/s12031-018-1208-x) contains supplementary material, which is available to authorized users.

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Histone locus regulation by the Drosophila dosage compensation adaptor protein CLAMP

Cited by 49 publications

References 76 publications

DrosophilaHistone Locus Body assembly and function involves multiple interactions

DrosophilaHistone Locus Body assembly and function involves multiple interactions

Targeting of the dosage-compensated male X-chromosome during earlyDrosophiladevelopment

Regulatory Architecture of the Neuronal Cacng2/Tarpγ2 Gene Promoter: Multiple Repressive Domains, a Polymorphic Regulatory Short Tandem Repeat, and Bidirectional Organization with Co-regulated lncRNAs

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