Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm
- Rangarajan D Nadadur
- Catharina RE Hilvering
- Valerio Bianchi
- Margaret Gadek
- Kaitlyn M Shen
- Joseph Aaron Goldman
- Leonid Tyan
- Jenna Bekeny
- Nutishia Lee
- Carlos Perez-Cervantes
- Ozanna Burnicka-Turek
- Christopher R Weber
- Wouter de Laat
- Alexander J Ruthenburg
- Ivan P Moskowitz
- The University of Chicago, United States
- University Medical Center Utrecht, Netherlands
- Duke University School of Medicine, United States
- Duke University, United States
Figures
Figure 1 with 4 supplements
TF-dependent noncoding transcription defines regulatory elements.
(A) Venn-diagram of peak call overlaps for HL-1 ATAC-sequencing (ATAC.HL1), histone 3 lysine 27 acetylation in mouse heart (H3K27ac.Heart, GSE52123), DNase hypersensitivity in mouse heart …
Figure 1—figure supplement 1
Genomic features of the identified TF-dependent ncRNAs recapitulate known features of annotated lincRNAs.
(A) Pie chart showing the composition for the identified TBX5-dependent ncRNAs using de novo assembly (Cufflinks). The 3067 ncRNAs were categorized into six groups. GENCODE (mm10)-annotated ncRNAs …
Figure 1—figure supplement 2
Genomic view of nine TF-dependent ncRNAs (mm9).
Long noncoding RNAs (lncRNAs) are labeled by nearest TBX5-dependent coding gene. Top track is chromosomal location, followed by the ncRNA read density from R26CreErt2 control and Tbx5fl/fl;R26CreERt2…
Figure 1—figure supplement 3
Identifying TF-dependent ncRNA targets from TF-dependent expressed genes.
(A) TF-dependent genes are coherent with TF-dependent ncRNAs. Volcano-plot of TF-dependent genes (FDR < 0.05, |FC| > 1.5). Genes residing within 2 Mb of coherently TBX5-dependent ncRNAs are colored …
Figure 1—figure supplement 4
Identifying TF-dependent ncRNA targets from open chromatin regions.
161 Tbx5-dependent ncRNAs at open chromatin regions were determined by the overlap between ncRNAs and ATAC peaks (allowing up to 500-bp edge-to-edge distance). The empirical significance of …
Figure 2
TF-dependent ncRNAs predict functional enhancers.
(A) Meta-gene plot showing reads per million (RPM) of Tbx5-dependent ncRNAs, being divided by enhancer makers DNase Hypersensitivity (DHS), ATAC Sequencing in HL-1 cells, TBX5 ChIP-Seq, and H3K27Ac, …
Figure 3 with 1 supplement
Enhancer transcription mediates target gene expression.
(A) Genomic loci showing circularized chromatin conformation capture (4C) from the viewpoint of four identified regulatory elements (near Atp2a2, Wrn, Ryr2, and Ubc). Total reads (top) and …
Figure 3—figure supplement 1
A TBX5-dependent enhancer at Sln that was not identified by TF ChIP-seq.
(A) Genomic view of a Tbx5-activated ncRNA region adjacent to gene Sln. This locus shows significant Tbx5-dependence as determined by transcription expression in mouse atrium, open chromatin …
Figure 4 with 2 supplements
Enhancer-associated ncRNAs at Ryr2 and Atp2a2 are necessary for calcium-handling gene expression and cellular phenotype.
(A) Gene Ontology functional enrichment for gene targets within a 2-Mb window of the TBX5-activated enhancers. Odds Ratio (OR) and P-value of overlap with GO terms ‘Calcium Ion Transport Genes’ and …
Figure 4—figure supplement 1
Knockdown of control Hprt locus does not change Ryr2 or RACER expression.
Gene expression of Ryr2 mRNA and RACER transcript after knockdown of Hprt mRNA. Relative transcript expression (RTE) after mRNA knockdown for RACER 1.23 ± 0.25, p = 0.77; for Ryr2 RTE 0.84 ± 0.09, p …
Figure 4—figure supplement 2
Ryr2 enhancer shows cardiac expression in 3 days post fertilization (dpf) zebrafish.
(A) Representative F0 (left) and F1 (right) 3 dpf zebrafish embryos surviving injection with a reporter construct containing the wildtype Ryr2 enhancer reporter, showing cardiac EGFP expression. …
Figure 5
TF-dependent transcription of regulatory elements.
mRNA and enhancer transcription occur in the presence of transcription factor (TBX5) through the Transcription Preinitiation Complex (PIC) (left). Loss of the TBX5 results in decreased PIC complex, …
Additional files
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Transparent reporting form
- https://doi.org/10.7554/eLife.31683.014
