Large-scale analysis of the integration of enhancer-enhancer signals by promoters
- Division of Gene Regulation, Netherlands Cancer Institute, Netherlands
- Oncode Institute, Netherlands
- Division of Molecular Genetics, Netherlands Cancer Institute, Netherlands
Figures
Figure 1 with 1 supplement
Schematic of three-way combinatorial approach.
(A) Three-way combinatorial massively parallel reporter assay (MPRA) design to test enhancer-enhancer-promoter combinations. Eight barcoded reporter assay libraries, one per promoter, were …
Figure 1—figure supplement 1
Schematic of cloning strategy to generate enhancer-enhancer-promoter libraries.
First the eight different promoters were cloned into a reporter vector. Each of the eight vectors was barcoded and linearised, random enhancer-enhancer, enhancer-control, and control-control …
Figure 2 with 3 supplements
Effects of single enhancers across promoters.
(A) Enhancer-promoter median boost index matrix of single enhancers. For each single enhancer a median boost index (see figure and Methods, log2(Activity_Combination/Activity_control-control_baseline…
Figure 2—figure supplement 1
Reproducibility of experimental data matrix of replicate correlations for all eight enhancer-enhancer-promoter (EEP) libraries.
Lower left panels represent the two-dimensional density plots of replicate-replicate activity correlations. Middle panels represent the one-dimensional density plot of each replicate. Upper right …
Figure 2—figure supplement 2
Position and orientation bias.
(A) Relationship between single enhancer boost indices across all enhancer-control (EC) combinations in position 1 versus in position 2 (see Figure 1). (B) Relationship between single enhancer boost …
Figure 2—figure supplement 3
Selectivity of single enhancers.
(A) Relationship between average boost index of each single enhancer across all promoters and the F-statistic of a Welch F-test for that enhancer across all promoters. Colours indicate significance …
Figure 3 with 1 supplement
Effects of enhancer-enhancer (EE) combinations.
(A) Fragment-fragment combinatorial boost index matrix for the Lefty1 promoter. Each square represents one control-control (CC), enhancer-control (EC or CE), or EE combination. Colour coding …
Figure 3—figure supplement 1
Additivity versus multiplicativity for all promoters.
Relationship between observed and expected activities (additive in A, multiplicative in B) for all enhancer-enhancer combinations for the all promoters. The blue lines represent the linear fit of …
Figure 4
Supra- and sub-additive behaviours of enhancer combinations.
(A) Distributions of log2 observed activities over expected additive activities ratios of enhancer-enhancer combinations across promoters. Coloured in turquoise are supra- and sub-additive …
Figure 5 with 2 supplements
Non-linear responses of promoters to enhancer-enhancer combinations.
(A) Relationship between observed boost indices and average boost index across promoters for all shared enhancer-enhancer combinations. Blue lines represent the linear fit of the data. (B) …
Figure 5—figure supplement 1
Promoter-promoter boost index correlations for all shared enhancer-enhancer combinations.
Lower left panels represent the two-dimensional density plots of promoter-promoter boost index correlations. Middle panels represent the one-dimensional density plot of each promoter. Upper right …
Figure 5—figure supplement 2
Non-linear responses of promoters to enhancer-control (single enhancers) combinations.
(A) Relationship between observed boost indices of single enhancers and average boost index across promoters for all shared single enhancer-control combinations. Blue lines represent the linear fit …
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Cell line (Mus musculus) | E14tg2a mouse embryonic stem cell (mESC) | ATCC | CRL-1821 | |
| Gene (M. musculus) | Klf2 | GenBank | 16598 | Promoters and enhancers; coordinates in Supplementary file 1 |
| Gene (M. musculus) | Sox2 | GenBank | 20674 | Promoters and enhancers; coordinates in Supplementary file 1 |
| Gene (M. musculus) | Otx2 | GenBank | 18424 | Promoters and enhancers; coordinates in Supplementary file 1 |
| Gene (M. musculus) | Lefty1 | GenBank | 13590 | Promoters and enhancers; coordinates in Supplementary file 1 |
| Gene (M. musculus) | Fgf5 | GenBank | 14176 | Promoters and enhancers; coordinates in Supplementary file 1 |
| Gene (M. musculus) | Tbx3 | GenBank | 21386 | Promoters and enhancers; coordinates in Supplementary file 1 |
| Gene (M. musculus) | Nanog | GenBank | 71950 | Promoters and enhancers |
| Gene (M. musculus) | Ap1m1 | GenBank | 11767 | Promoters and enhancers |
| Recombinant DNA reagent | Downstream Assay vector (JvAp102) | Martinez-Ara et al., 2022 | JvAp102 | Downstream reporter assay plasmid; ‘see Methods |
| Sequence-based reagent | Enhancer and promoter oligos | This paper | Primers | Supplementary file 4 |
| Sequence-based reagent | Barcoding primers and sequencing primers | Martinez-Ara et al., 2022 | Barcoding reagents | Supplementary file 4 |
| Sequence-based reagent | Synthetic DNA negative controls | This paper | Negative controls | Supplementary file 2 |
| Peptide, recombinant protein | Gibson Assembly Master Mix | NEB | Cat# E2611S | |
| Peptide, recombinant protein | I-CeuI | NEB | #R0699S | |
| Peptide, recombinant protein | I-SceI | NEB | #R0694S | |
| Commercial assay or kit | Mouse Embryonic Stem Cell Nucleofector Kit | Lonza | #VPH-1001 | |
| Chemical compound, drug | TRIsure | Bioline | (#BIO-38032) | |
| Commercial assay or kit | GeneJET RNA extraction kit | Thermo Fisher | #K0732 | |
| Peptide, recombinant protein | DNase I | Roche | #04716728001 | |
| Peptide, recombinant protein | Maxima Reverse transcriptase | Thermo Fisher | #EP0743 | |
| Peptide, recombinant protein | MyTaq Red mix | Bioline | #BIO-25043 | |
| Strain, strain background (Escherichia coli) | e. cloni 10G supreme | Lucigen | #60081-1 | Electrocompetent cells |
| Peptide, recombinant protein | Takara ligation kit version 2.1 | Takara | #6022 | |
| Peptide, recombinant protein | Klenow HC 3′ ->5′ exo | NEB | #M0212L | |
| Commercial assay or kit | ISOLATE II PCR and Gel Kit | Bioline | BIO-52059 | |
| Peptide, recombinant protein | Fast-link ligase | Lucigen | LK0750H | |
| Peptide, recombinant protein | End-It DNA End-Repair Kit | Epicentre | #ER0720 | |
| Commercial assay or kit | dsDNA High sensitivity Qubit kit | Invitrogen | #Q33231 | |
| Commercial assay or kit | CleanPCR magnetic beads | CleanNA | #CPCR-0050 | |
| Peptide, recombinant protein | XcmI | NEB | #R0533S | |
| Peptide, recombinant protein | T4 DNA ligase | Roche | #10799009001 | |
| Peptide, recombinant protein | AvrII | Thermo Fisher | #ER1561 | |
| Peptide, recombinant protein | NheI | NEB | #R0131S | |
| Strain, strain background (Escherichia coli) | 5-alpha Competent E. coli | NEB | #C2987 | Competent cells |
| Peptide, recombinant protein | LIF | Sigma-Aldrich | #ESG1107 | 2i+LIF media |
| Chemical compound, drug | Monothioglycerol | Sigma-Aldrich | #M6145-25ML | 2i+LIF media |
| Chemical compound, drug | CHIR-99021 | MedChemExpress | #HY-10182 | 2i+LIF media |
| Chemical compound, drug | PD0325901 | MedChemExpress | #HY-10254 | 2i+LIF media |
| Other | BSA | Gibco | #15260-037 | 2i+LIF media |
| Other | DMEM-F12medium | Gibco | #11320-033 | 2i+LIF media |
| Other | Neurobasal medium | Gibco | #21103-049 | 2i+LIF media |
| Chemical compound, drug | N27 | Gibco | #17504-044 | 2i+LIF media |
| Chemical compound, drug | B2 | Gibco | #17502-048 | 2i+LIF media |
| Commercial assay or kit | MycoAlert Mycoplasma Detection Kit | Lonza | #LT07-318 | |
| Software, algorithm | BatchPrimer3 version 1.0 | You et al., 2008 | version 1.0 | https://wheat.pw.usda.gov/demos/BatchPrimer3/ |
| Software , algorithm | Starcode | Zorita et al., 2015 | version 1.1 | https://github.com/gui11aume/starcode |
| Software, algorithm | Python | Rossum and Drake, 2009 | version 3.6 | https://www.python.org/downloads/release/python-362/ |
| Software, algorithm | Bowtie2 | Langmead and Salzberg, 2012 | version 2.3.4 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Software, algorithm | R | R Development Core Team, 2021 | version 4.0.5 | https://www.r-project.org/ |
| Software, algorithm | ggplot2 | Wickham, 2016 | ggplot2 | https://ggplot2.tidyverse.org/ |
| Software, algorithm | Snakemake | Köster and Rahmann, 2012 | version 4.4.0 | https://anaconda.org/bioconda/snakemake/files?version=4.4.0 |
Additional files
-
Supplementary file 1
mm10 genomic coordinates of the regulatory elements tested in this study.
- https://cdn.elifesciences.org/articles/91994/elife-91994-supp1-v1.zip
-
Supplementary file 2
Sequences of the synthetic controls used in this study.
- https://cdn.elifesciences.org/articles/91994/elife-91994-supp2-v1.zip
-
Supplementary file 3
Processed and normalised data for all the enhancer-enhancer-promoter (EEP) combinations tested in this study.
- https://cdn.elifesciences.org/articles/91994/elife-91994-supp3-v1.zip
-
Supplementary file 4
Sequences of the primers used in this study.
- https://cdn.elifesciences.org/articles/91994/elife-91994-supp4-v1.zip
-
MDAR checklist
- https://cdn.elifesciences.org/articles/91994/elife-91994-mdarchecklist1-v1.docx
