Key resources table.
| Reagent type or resources |
Designation | Source or reference | Identifier | Additional information |
|---|---|---|---|---|
| Antibody | Rabbit polyclonal anti-Prep |
(Choe et al., 2014) | N/A | |
| Antibody | Rabbit polyclonal anti-Pbx4 |
(Choe et al., 2014) | N/A | |
| Antibody | Rabbit polyclonal anti-NF-YB |
Santa-Cruz | sc13045 | RRID:AB_2152107 |
| Antibody | Rabbit polyclonal anti-H3K27ac |
Abcam | ab4729 | RRID:AB_2118291 |
| Antibody | Rabbit polyclonal anti-Histone H3 |
Abcam | ab1791 | RRID:AB_302613 |
| Antibody | Mouse monoclonal anti-Myc |
Roche | 11667149001 | RRID:AB_390912 |
| Antibody | Mouse monoclonal anti-Flag |
Sigma-Aldrich | F3165 | RRID:AB_259529 |
| Antibody | Rabbit polyclonal anti-HA |
Abcam | ab9110 | RRID:AB_307019 |
| Antibody | Rabbit polyclonal anti-IgG control |
Abcam | ab46540 | RRID:AB_2614925 |
| Antibody | Mouse polyclonal anti-IgG control |
Millipore | 12-371b | RRID:AB_2617156 |
| Antibody | Anti-mouse IgG, HRP-linked secondary antibody |
GE healthcare | LNA91V/AG | |
| Antibody | Anti-mouse IgG, Alexa Fluor 488 conjugated secondary antibody |
Molecular Probes | A11001 | RRID:AB_2534069 |
| Antibody | Mouse monoclonal 3A10 |
Developmental Studies Hybridoma bank |
531874 | RRID:AB_531874 |
| Antibody | Anti-rabbit IgG, HRP-linked secondary antibody |
Jackson Laboratories | 211-032-171 | RRID:AB_2339149 |
| Antibody | Lipofectamine 2000 | Invitrogen | 52887 | |
| Strain, strain background (E. coli) |
Subcloning Efficiency DH5α Competent Cells |
ThermoFisher Scientific | 18265017 | |
| Chemical compound, drug |
4-Thiouridine | Santa-Cruz | sc204628 | |
| Chemical compound, drug |
EZ-Link HPDP-Biotin | Pierce | 21341 | |
| peptide, recombinant protein |
Dynabeads MyOne Streptavidin C1 |
ThermoFisher Scientific | 65001 | |
| peptide, recombinant protein |
Protein-A Dynabeads | ThermoFisher Scientific | 10001D | |
| Commercial assay or kit |
TruSeq ChIP Library Preparation Kit |
Illumina | IP-202–1012 | |
| Commercial assay or kit |
TruSeq Stranded mRNA LT sample prep Kit |
Illumina | RS-122–2101 | |
| Commercial assay or kit |
mMESSAGE mMACHINE SP6 Transcription Kit |
ThermoFisher Scientific | AM1340 | |
| Commercial assay or kit |
Q5 Site-Directed Mutagenesis Kit |
New England Biolabs | E0554S | |
| Other | Prep ChIP-seq and Inputs in 3.5hpf zebrafish embryos |
This paper | GEO | Deposited data |
| Other | Prep ChIP-seq and Inputs in 12hpf zebrafish embryos |
This paper | GEO | Deposited data |
| Other | TALE knock-down and control RNA-seq in 6hpf zebrafish embryos |
This paper | GSE102662 | Deposited data |
| Other | TALE knock-down and control RNA-seq in 12hpf zebrafish embryos |
This paper | GSE102662 | Deposited data |
| Other | Prep1 ChIP-seq and Inputs in mESCs, WIG files |
(Laurent et al., 2015) | GSM1545025 and GSM1545026 | Deposited data |
| Other | ATAC-seq in 4hpf zebrafish embryos, fastq files |
(Kaaij et al., 2016) | SRR2747531 | Deposited data |
| Other | H3K4me1 ChIP-seq in 4.5hpf zebrafish embryos, WIG files |
(Bogdanovic et al., 2012) | GSM915193 | Deposited data |
| Other | H3K4me3 ChIP-seq in 4.5hpf zebrafish embryos, WIG files |
(Bogdanovic et al., 2012) | GSM915189 | Deposited data |
| Other | H3K27ac ChIP-seq in 4.5hpf zebrafish embryos, WIG files |
(Bogdanovic et al., 2012) | GSM915197 | Deposited data |
| Other | H3K27ac ChIP-seq in 9hpf zebrafish embryos, WIG files |
(Bogdanovic et al., 2012) | GSM915198 | Deposited data |
| Other | H3K27ac ChIP-seq in 24hpf zebrafish embryos, WIG files |
(Bogdanovic et al., 2012) | GSM915199 | Deposited data |
| Other | H3K27me3 ChIP-seq in 4.5hpf zebrafish embryos, WIG files |
(Zhang et al., 2014) | GSM1081557 | Deposited data |
| Other | MNase-seq in 4.5hpf zebrafish embryos, WIG files |
(Zhang et al., 2014) | GSM1081554 | Deposited data |
| Other | RNA-Pol2 ChIP-seq in 4.5hpf zebrafish embryos, WIG files |
(Zhang et al., 2014) | GSM1081560 | Deposited data |
| Other | MeDIP-seq (Methyl CpG) in 4.5hpf zebrafish embryos, BedGraph files |
(Lee et al., 2015) | GSM1274386 | Deposited data |
| Other | NF-YA ChIP-seq in mESCs | (Oldfield et al., 2014) | GSM1370111 | Deposited data |
| Other | H3K4me1 in mESCs, BigWig files |
ENCODE www.encodeproject.org |
GSM1000121 | Deposited data |
| Other | H3K4me3 in mESCs, BigWig files |
ENCODE www.encodeproject.org |
GSM1000124 | Deposited data |
| Other | H3K27ac in mESCs, BigWig files |
ENCODE www.encodeproject.org |
GSM1000126 | Deposited data |
| Other | H3K27me3 in mESCs, BigWig files |
ENCODE www.encodeproject.org |
GSM1000089 | Deposited data |
| Other | DNase-seq in mESCs, BigWig files |
ENCODE www.encodeproject.org |
GSM1014154 | Deposited data |
| Other | MeDIP-seq (Methyl CpG) in mESCs |
(C.-C. Chen et al., 2013) | GSM859494 | Deposited data |
| Cell line (Human) | HEK-293T cells | ATCC | ATCC CRL-3216 | RRID:CVCL_0063 |
| Strain, strain background (Zebrafish) |
strain EKW | Ekkwill breeders | http://www.ekkwill.com/ | |
| Other | Oligonucleotides | See Supplementary file 5 | ||
| Recombinant DNA |
6xMyc-Prep1.1 in PCS2 + MT |
(Choe et al., 2002) | N/A | |
| Recombinant DNA |
HA-Pbx4 in PCS2+ | (Choe et al., 2009) | N/A | |
| Recombinant DNA |
Flag-NF-YA in PCS2+ | This Paper | N/A | |
| Recombinant DNA |
Flag-NF-YB in PCS2+ | This Paper | N/A | |
| Recombinant DNA |
NF-YDN in PCS2+ | This paper | N/A | |
| Recombinant DNA |
pGL3-Promoter vector | Promega | E1761 | |
| Recombinant DNA |
Tle3 element in pGL3 Promoter vector |
This paper | N/A | |
| Recombinant DNA |
Pax5 element in pGL3 Promoter vector |
This paper | N/A | |
| Recombinant DNA |
Prdm14 element in pGL3 Promoter vector |
This paper | N/A | |
| Recombinant DNA |
Tcf3a element in pGL3 Promoter vector |
This paper | N/A | |
| Recombinant DNA |
Her6 element in pGL3 Promoter vector |
This paper | N/A | |
| Recombinant DNA |
Dachb element in pGL3 Promoter vector |
This paper | N/A | |
| Recombinant DNA |
Fgf8 element in pGL3 Promoter vector |
This paper | N/A | |
| Recombinant DNA |
pGL3-Control vector | Promega | E1741 | |
| Software, algorithm | FastQC | Babraham Institute | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | RRID:SCR_014583 |
| Software, algorithm | FastQ Screen | Babraham Institute | https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/ | RRID:SCR_000141 |
| Software, algorithm | Trimmomatic 0.32 | (Bolger et al., 2014) | https://github.com/timflutre/trimmomatic | RRID:SCR_011848 |
| Software, algorithm | Bowtie 2.2.3 | (Langmead and Salzberg, 2012) | https://github.com/BenLangmead/bowtie2 | RRID:SCR_005476 |
| Software, algorithm | SAMtools 0.1.19 | (Li et al., 2009) | https://github.com/samtools/samtools | RRID:SCR_002105 |
| Software, algorithm | MACS 2.1.0.20140616 | (Zhang et al., 2008) | https://github.com/taoliu/MACS | |
| Software, algorithm | RSEM 1.2.28 in the Dolphin interface of University of Massachuetts Worcester Biocore |
(Li and Dewey, 2011) | http://www.umassmed.edu/biocore/introducing-dolphin/ | RRID:SCR_013027 |
| Software, algorithm | DESeq2 in the Dolphin interface of University of Massachuetts Worcester Biocore |
(Anders and Huber, 2010) | http://www.umassmed.edu/biocore/introducing-dolphin/ | RRID:SCR_015687 |
| Software, algorithm | Galaxy web interface | (Goecks et al., 2010) | https://usegalaxy.org | RRID:SCR_006281 |
| Software, algorithm | BedTools in galaxy | (Quinlan and Hall, 2010) | https://usegalaxy.org | RRID:SCR_006646 |
| Software, algorithm | DeepTools in galaxy | (Ramírez et al., 2014) | https://usegalaxy.org | |
| Software, algorithm | MEME-ChIP | (Machanick and Bailey, 2011; Bailey et al., 2009) |
http://meme-suite.org/tools/meme-chip | RRID:SCR_001783 |
| Software, algorithm | DAVID 6.8 | (Huang et al., 2009b, 2009a) | https://david.ncifcrf.gov/ | RRID:SCR_001881 |
| Software, algorithm | GREAT 3.0.0 | (McLean et al., 2010; Hiller et al., 2013) |
http://bejerano.stanford.edu/great/public/html | RRID:SCR_005807 |
| Other | anti-Prep1.1 morpholino oligonucleotide |
Gene Tools, LLC | N/A | |
| Other | 5'-TGGACACAGACTGGGCAG CCATCAT-3'Fluorescein |
(Deflorian et al., 2004) | ||
| Other | anti-Pbx2 morpholino oligonucleotide |
Gene Tools, LLC | N/A | |
| Other | 5'-CCGTTGCCTGTGATG GGCTGCTGCG-3' |
(Erickson et al., 2007) | ||
| Other | anti-Pbx4 morpholino oligonucleotide |
Gene Tools, LLC | N/A | |
| Other | 5'-AATACTTTTGAGCCGA ATCTCTCCG-3' |
(Erickson et al., 2007) |