CLAMP and Zelda function together to promoteDrosophilazygotic genome activation

Abstract

Because zygotic genome activation (ZGA) is an essential process across metazoans, it is key to evolve multiple pioneer transcription factors (TFs) to protect organisms from loss of a single factor. Pioneer TF Zelda (ZLD) is the only known factor which increases accessibility of chromatin to promote ZGA in the early Drosophila embryo. However, many genomic loci remain accessible without ZLD and have GA-rich motifs. Therefore, we hypothesized that other pioneer TFs that function with ZLD have not yet been identified in early embryos, especially those that bind to GA-rich motifs, such as CLAMP (Chromatin-linked adaptor for Male-specific lethal MSL proteins). Here, we determine that CLAMP is a novel pioneer TF which interacts directly with nucleosomes, regulates zygotic genome transcription, promotes chromatin accessibility, and facilitates the binding of ZLD to promoters. Thus, the maternal factor CLAMP functions with ZLD as a pioneer TF to open chromatin and drive zygotic genome activation.

Sex-specific transcript diversity is regulated by a maternal transcription factor in earlyDrosophilaembryos

“…We found very low levels of overlap with maternally deposited transcripts (Fig 2E). Therefore, most of the sex-specifically spliced genes we observed are likely to be zygotic transcripts, consistent with the function of CLAMP as a pioneer TF in the early embryo (Duan et al 2020).…”

“…Once formed in males, the MSL complex targets the male X-chromosome at high-affinity binding sequences called C hromatin E ntry S ites ( CES ) rich in multiple GA-repeats (Alekseyenko et al 2008; Straub et al 2013). The maternally deposited Chromatin linked adapter for MSL complex (CLAMP) protein opens chromatin (Urban et al 2017a; Duan et al 2020) and directly contacts MSL-2 (Albig et al 2019) to promote MSL complex recruitment. Subsequently, the MSL complex increases transcript levels on the male X-chromosome by promoting transcription elongation (Larschan et al 2011).…”

“…CLAMP is an essential pioneer T ranscription F actor ( TF ) that opens chromatin (Urban et al 2017a; Duan et al 2020). Loss of CLAMP results in complete loss of MSL complex from the male X-chromosome causing male lethality (Soruco et al 2013).…”

“…Unlike MSL complex component mutants, which cause only male-specific lethality, clamp mutants show lethality in both males and females. All embryos die early in embryogenesis after losing maternal CLAMP (Duan et al 2020). Furthermore, CLAMP is bound to both intronic and promoter regions on chromatin (Kaye et al 2018).…”

Sex-specific splicing occurs genome-wide during early Drosophila embryogenesis

“…Several lines of evidence led us to hypothesize that the maternally deposited TF CLAMP (chromatin-linked adapter for MSL proteins) is a good candidate to study how the loss of maternally deposited TFs modulates sex-specific AS: (1) mass spectrometry identified association with 33 RBPs on chromatin, 6 of which regulate AS Urban et al, 2017c ; (2) CLAMP is bound to approximately equal numbers of intronic regions as promoter regions Kaye et al, 2018 ; (3) many CLAMP binding sites evolved from intronic polypyrimidine tracts Quinn et al, 2016 ; (4) maternal CLAMP is essential for viability in both males and females suggesting a role beyond male-specific dosage compensation ( Duan, 2020 ).…”