TALE factors use two distinct functional modes to control an essential zebrafish gene expression program
- University of Massachusetts Medical School, United States
- University of Manchester, United Kingdom
Abstract
TALE factors are broadly expressed embryonically and known to function in complexes with transcription factors (TFs) like Hox proteins at gastrula/segmentation stages, but it is unclear if such generally expressed factors act by the same mechanism throughout embryogenesis. We identify a TALE-dependent gene regulatory network (GRN) required for anterior development and detect TALE occupancy associated with this GRN throughout embryogenesis. At blastula stages, we uncover a novel functional mode for TALE factors, where they occupy genomic DECA motifs with nearby NF-Y sites. We demonstrate that TALE and NF-Y form complexes and regulate chromatin state at genes of this GRN. At segmentation stages, GRN-associated TALE occupancy expands to include HEXA motifs near PBX:HOX sites. Hence, TALE factors control a key GRN, but utilize distinct DNA motifs and protein partners at different stages - a strategy that may also explain their oncogenic potential and may be employed by other broadly expressed TFs.
Data availability
RNA-seq data has been deposited in GEO under accession code GSE102662ChIP-seq data has been deposited in ArrayExpress under accession code E-MTAB-5967
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Zebrafish TALE KD RNA-seqPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE102662).
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Prep1 (ChIP-Seq)Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM1545025).
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H3K4me1_dome, danRer7Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM915193).
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H3K4me3_dome, danRer7Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM915189).
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H3K27ac_dome, danRer7Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM915197.
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H3K27ac_80%epi, danRer7Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM915198).
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H3K27ac_24hpf, danRer7Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM915199).
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H3K27me3 ChIP-seq domePublicly available at the NCBI Gene Expression Omnibus (accession no: GSM1081557).
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nucleosome dome rep 1Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM1081554).
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Pol II ChIP-seq dome 8WG16Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM1081560).
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MeDIP_4.5hpfPublicly available at the NCBI Gene Expression Omnibus (accession no: GSM1274386).
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ChIP-Seq NF-YAPublicly available at the NCBI Gene Expression Omnibus (accession no: GSM1370111).
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LICR_ChipSeq_ES-E14_H3K4me1_E0Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM1000121).
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LICR_ChipSeq_ES-E14_H3K4me3_E0Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM1000124).
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LICR_ChipSeq_ES-E14_H3K27ac_E0Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM1000126).
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LICR_ChipSeq_ES-Bruce4_H3K27me3_EPublicly available at the NCBI Gene Expression Omnibus (accession no: GSM1000089).
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UW_DnaseSeq_ES-E14_E0_129/OlaPublicly available at the NCBI Gene Expression Omnibus (accession no: GSM1014154).
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E14 MeDIP-seqPublicly available at the NCBI Gene Expression Omnibus (accession no: GSM859494).
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Input_DNA (ChIP-Seq control)Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM1545026).
Article and author information
Author details
Charles G Sagerström
Funding
National Institute of Neurological Disorders and Stroke (NS38183)
- Charles G Sagerström
Biotechnology and Biological Sciences Research Council (BB/N00907X/1)
- Nicoletta Bobola
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: This study was submitted to and approved by the University of Massachusetts Medical School Institutional Animal Care and Use Committee (protocol A-1565) and the University of Massachusetts Medical School Institutional Review Board (protocol I-149).
Copyright
© 2018, Ladam et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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TALE factors use two distinct functional modes to control an essential zebrafish gene expression program
eLife 7:e36144.
https://doi.org/10.7554/eLife.36144
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