Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos

Abstract

Pioneer factors such as Zelda (Zld) help initiate zygotic transcription in Drosophila early embryos, but whether other factors support this dynamic process is unclear. Odd-paired (Opa), a zinc-finger transcription factor expressed at cellularization, controls the transition of genes from pair-rule to segmental patterns along the anterior-posterior axis. Finding that Opa also regulates expression through enhancer sog_Distal along the dorso-ventral axis, we hypothesized Opa’s role is more general. Chromatin-immunoprecipitation (ChIP-seq) confirmed its in vivo binding to sog_Distal but also identified widespread binding throughout the genome, comparable to Zld. Furthermore, chromatin assays (ATAC-seq) demonstrate that Opa, like Zld, influences chromatin accessibility genome-wide at cellularization, suggesting both are pioneer factors with common as well as distinct targets. Lastly, embryos lacking opa exhibit widespread, late patterning defects spanning both axes. Collectively, these data suggest Opa is a general timing factor and likely late-acting pioneer factor that drives a secondary wave of zygotic gene expression.

Decoding gene regulation in the fly brain

“…There are hundreds of cell types in the fly brain, impeding the use of bulk datasets for accurately deciphering diversity. Even more, compared to the embryo 58,[83][84][85][86][87] or imaginal discs 59,[88][89][90][91][92][93][94] , the number of ChIP-seq or other epigenomic datasets is very limited in the brain 24,[95][96][97] . In contrast, in this study we constructed 40 eGRNs at once, covering 88 transcription factors with 7833 enhancers that are linked to 3776 target genes.…”

A comprehensive temporal patterning gene network in Drosophila medulla neuroblasts revealed by single-cell RNA sequencing

“…Opa is a zinc finger transcription factor homologous to mammalian Zic proteins, and has been shown to function in the embryonic patterning process as a pioneer factor 61,62 , as well as in adult head development 63,64 . In the type II neuroblast lineage, Opa is expressed in early-born INPs and required for the temporal progression of the INP temporal cascade 23 .…”

“…These antibodies are generous gifts from the fly community: Rabbit anti-SoxN (1:100) from Steven Russell55 ; Rabbit anti-Hth (1:500) from Richard Mann; Guinea-pig anti-Run, Rabbit anti-Bsh, Rabbit anti-Slp1, Guinea-pig anti-Slp2, Rabbit anti-D, Guinea-pig anti-Tll and Rabbit anti-Sox102F (all used at 1:500) from Claude Desplan; Rabbit anti-D (1:1000) from John R. Nambu96 ;Rat anti-Dfr (1:200) from Makoto Sato57 , Guinea-pig anti-Kn (1:500) from Adrian Moore 97 , Guinea-pig anti-Dpn (1:500) from Chris Doe; Rabbit anti Opa (1:100) from J. Peter Gergen61 ; Rat anti-BarH1 (1: 200) from Tiffany Cook98 .Commercially available antibodies include: sheep anti-GFP (1:500, AbD Serotec, 4745-1051), Goat anti-beta-gal (1:1000, Abcam, ab12081), rabbit anti-RFP (1:1000, Abcam, ab62341), Mouse anti V5-Tag:DyLight®550 (1:200, Bio-Rad, MCA1360D550GA), Rat anti-Deadpan[11D1BC7] …”

Patterning with clocks and genetic cascades: Segmentation and regionalization of vertebrate versus insect body plans

“…Each of these late-acting enhancers drives the full pair-rule pattern (7 stripes in Drosophila ) in enhancer reporter assays, and, hence, are sometimes called “7-stripe” or “zebra” elements [ 141 ] ( Fig 4B ). This rewiring of the pair-rule network (and possibly other genes involved in AP and dorsoventral patterning in the early Drosophila embryo) seems to be mediated by timing factors encoded by 2 pioneer factors: Zelda and Opa, where Zelda is responsible for activating the early network and Opa for the late network [ 142 – 144 ]. Indeed, in opa mutants, the frequency doubling of pair-rule genes is lost in Drosophila [ 142 ].…”

“…This is in line with the observation that the gap gene Kr in Drosophila is regulated by 2 enhancers, one initiates its expression and the other maintains it [ 52 ]. Interestingly, open chromatin at early acting enhancers in the Drosophila embryo has been shown to be mediated by the pioneer factor Zelda and at late-acting enhancers by the pioneer factor Opa [ 143 , 144 ]. One could imagine then a scenario in which a gradual switch between early and late-acting enhancers in Tribolium to be mediate by opposing gradients of opa [ 13 ] and zelda [ 145 ], where the expressions of opa and/or zelda are regulated by (or interact with) the Wnt/Cad gradient.…”