A comparative genomic analysis of targets of Hox protein Ultrabithorax amongst distant insect species

Prasad, Naveen; Tarikere, Shreeharsha; Khanale, Dhanashree; Habib, Farhat; Shashidhara, L. S.

doi:10.1038/srep27885

Cited by 32 publications

(43 citation statements)

References 39 publications

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“…Here we used the phycitine Indian Mealmoth (P. interpunctella) as a model system to investigate additional aspects of lepidopteran wing specialization. First, we confirmed that the UbdA antigen (anti-Ubx/abd-A FP6.87 monoclonal antibody) is absent from the forewing imaginal disks, and expressed throughout the hindwing, thus corroborating the hindwing-specific expression of Ubx described in other lepidopterans (Weatherbee et al, 1998;Tong et al, 2014;Prasad et al, 2016). Then, we generated Ubx mosaic knock-outs and observed homeotic clones on the hindwing that were most conspicuous as transpositions toward black-andbrown pigmented states on the dorsal side ( Figures 6A,B and Supplementary Figure 6).…”

Section: Ubx Permits the Morphological Specialization Of Pyralid Hindsupporting

confidence: 80%

Ultrabithorax Is a Micromanager of Hindwing Identity in Butterflies and Moths

et al. 2021

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The forewings and hindwings of butterflies and moths (Lepidoptera) are differentiated from each other, with segment-specific morphologies and color patterns that mediate a wide range of functions in flight, signaling, and protection. The Hox gene Ultrabithorax (Ubx) is a master selector gene that differentiates metathoracic from mesothoracic identities across winged insects, and previous work has shown this role extends to at least some of the color patterns from the butterfly hindwing. Here we used CRISPR targeted mutagenesis to generate Ubx loss-of-function somatic mutations in two nymphalid butterflies (Junonia coenia, Vanessa cardui) and a pyralid moth (Plodia interpunctella). The resulting mosaic clones yielded hindwing-to-forewing transformations, showing Ubx is necessary for specifying many aspects of hindwing-specific identities, including scale morphologies, color patterns, and wing venation and structure. These homeotic phenotypes showed cell-autonomous, sharp transitions between mutant and non-mutant scales, except for clones that encroached into the border ocelli (eyespots) and resulted in composite and non-autonomous effects on eyespot ring determination. In the pyralid moth, homeotic clones converted the folding and depigmented hindwing into rigid and pigmented composites, affected the wing-coupling frenulum, and induced ectopic scent-scales in male androconia. These data confirm Ubx is a master selector of lepidopteran hindwing identity and suggest it acts on many gene regulatory networks involved in wing development and patterning.

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Section: Ubx Permits the Morphological Specialization Of Pyralid Hindsupporting

confidence: 80%

Ultrabithorax Is a Micromanager of Hindwing Identity in Butterflies and Moths

et al. 2021

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“…( e ) Browser representation of the slit locus. Silk gland FAIRE, from top to bottom: silk gland FAIRE peaks, BmE FAIRE peaks, and Ubx chip peaks 47 . …”

Section: Resultsmentioning

confidence: 99%

Genome-wide open chromatin regions and their effects on the regulation of silk protein genes in Bombyx mori

Zhang

Cheng

Jin

et al. 2017

Sci Rep

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Nucleosome-depleted open chromatin regions (OCRs) often harbor transcription factor (TF) binding sites that are associated with active DNA regulatory elements. To investigate the regulation of silk-protein genes, DNA molecules isolated from the silk glands of third-day fifth-instar silkworm larvae and embryo-derived (BmE) cells were subjected to formal dehyde-assisted isolation of regulatory elements (FAIRE) and high-throughput sequencing. In total, 68,000 OCRs were identified, and a number of TF-binding motifs were predicted. In particular, OCRs located near silk-protein genes contained potential binding sites for functional TFs. Moreover, many TFs were found to bind to clusters of OCRs upstream of silk-protein genes, and to regulate the expression of these genes. The expression of silk protein genes may be related not only to regulating TFs (such as fkh, Bmdimm, and Bmsage), but also to developmental and hormone-induced TFs (such as zen, eve, Br, and eip74ef). Elucidation of genome-wide OCRs and their regulatory motifs in silk protein genes will provide valuable data and clues for characterizing the mechanisms of transcriptional control of silk protein genes.

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“…For example, enhancers of some developmental genes in beetles, honeybees and even spiders were demonstrated to be active in their expected contexts in Drosophila (e.g. Ayyar et al, 2010;Cande et al, 2009a,b;Kazemian et al, 2014;Lai et al, 2018;Prasad et al, 2016;Wolff et al, 1998;Zinzen et al, 2006). These studies show the power of the cross-species reporter assay using Drosophila as an in vivo test tube, but with one unavoidable concern: are these non-Drosophila enhancers really showing biologically relevant activities in Drosophila?…”

Section: Testing Activity Of Non-drosophila Enhancers In Drosophilamentioning

confidence: 99%

How to study enhancers in non-traditional insect models

Tomoyasu

Halfon

2020

Journal of Experimental Biology

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Transcriptional enhancers are central to the function and evolution of genes and gene regulation. At the organismal level, enhancers play a crucial role in coordinating tissue-and context-dependent gene expression. At the population level, changes in enhancers are thought to be a major driving force that facilitates evolution of diverse traits. An amazing array of diverse traits seen in insect morphology, physiology and behavior has been the subject of research for centuries. Although enhancer studies in insects outside of Drosophila have been limited, recent advances in functional genomic approaches have begun to make such studies possible in an increasing selection of insect species. Here, instead of comprehensively reviewing currently available technologies for enhancer studies in established model organisms such as Drosophila, we focus on a subset of computational and experimental approaches that are likely applicable to non-Drosophila insects, and discuss the pros and cons of each approach. We discuss the importance of validating enhancer function and evaluate several possible validation methods, such as reporter assays and genome editing. Key points and potential pitfalls when establishing a reporter assay system in non-traditional insect models are also discussed. We close with a discussion of how to advance enhancer studies in insects, both by improving computational approaches and by expanding the genetic toolbox in various insects. Through these discussions, this Review provides a conceptual framework for studying the function and evolution of enhancers in non-traditional insect models.

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A comparative genomic analysis of targets of Hox protein Ultrabithorax amongst distant insect species

Cited by 32 publications

References 39 publications

Ultrabithorax Is a Micromanager of Hindwing Identity in Butterflies and Moths

Ultrabithorax Is a Micromanager of Hindwing Identity in Butterflies and Moths

Genome-wide open chromatin regions and their effects on the regulation of silk protein genes in Bombyx mori

How to study enhancers in non-traditional insect models

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