DOI: 10.5061/dryad.hx3ffbgs1
title: Data for: A systems genetics approach identifies roles for proteasome factors in heart development and congenital heart defects

description: In this study, we sought to take a new approach to identify genetic causes
 of CHDs. By combining analyses of genes that are under strong selective
 constraint along with published embryonic heart transcriptomes, we
 identified over 200 new candidate genes for CHDs. We utilized
 protein-protein interaction (PPI) network analysis to identify a
 functionally-related subnetwork consisting of known CHD genes as well as
 genes encoding proteasome factors, in particular POMP, PSMA6,
 PSMA7, PSMD3, and PSMD6. We used CRISPR targeting in zebrafish embryos to
 preliminarily identify roles for the PPI subnetwork genes in heart
 development. We then used CRISPR to create new mutant zebrafish strains
 for two of the proteasome genes in the subnetwork: pomp and psmd6. We show
 that loss of proteasome gene functions leads to defects in zebrafish heart
 development, including dysmorphic hearts, myocardial cell blebbing, and
 reduced outflow tracts. We also identified deficits in cardiac function in
 pomp and psmd6 mutants. These heart defects resemble those seen in
 zebrafish mutants for known CHD genes and other critical heart development
 genes. Our study provides a novel systems genetics approach to further our
 understanding of the genetic causes of human CHDs.
description: # Data for: A systems genetics approach identifies roles for proteasome
 factors in heart development and congenital heart defects Dataset DOI:
 [10.5061/dryad.hx3ffbgs1](10.5061/dryad.hx3ffbgs1) ## Description of the
 data and file structure The data presented here is an original dataset of
 the raw data underlying the figures in the publication A systems genetics
 approach identifies roles for proteasome factors in heart development and
 congenital heart defects (CHDs). In this publication, we use a
 CRISPR-based approach in zebrafish to specifically eliminate candidate
 heart defect genes and reveal new roles for proteasome genes in heart
 development. We show that loss of functions of two proteasome genes, pomp
 and psmd6, leads to zebrafish heart defects. This study shows that a
 proteasome gene family contributes to heart development, advancing our
 understanding of the causes of CHDs. The data was generated using the
 methods described in the resulting publication. ### Files and variables
 #### This Data file contains the following tables of raw data generated
 for this study. List of Tables provided Fig3G0CRISPRdata.csv This table
 provides the raw data underlying the graphs shown in Fig 3C and Fig 3D.
 Data shown are results of CRISPR guide injections for genes shown, and
 zebrafish embryo heart phenotypes scored. ID, clutch of embryos. hHpf
 hours post fertilization. sev severe. mod moderate. Fig4qPCR.csv This
 table provides the raw data underlying the graphs shown in Fig. 4C and
 Fig. 4D. The data shown are results of qPCR analysis on control versus
 mutant embryos for the genes shown. qPCR, quantitative polymerase chain
 reaction. WT, wild type. Mut, mutant. Cq, cycle threshold. ddCt,
 normalized cycle threshold. Fig4HeartMorphology.csv This table provides
 the raw data underlying the graph shown in Fig. 4T. The graph shows
 frequencies of heart defect categories observed in 4-day-old larvae. WT,
 wild type. DMSO, dimethyl sulfoxide. Fig4pompandpsmd6survival.csv This
 table provides the raw data underlying the graph shown in Fig. 4U, a
 survival plot of two independent clutches each of pomp and psmd6 embryos.
 Hpf, hours post fertilization. Fig5myl7DIGAPinsitus.csv This table
 provides the raw data for the embryo numbers provided in the legend for
 the images shown in Fig. 5A-F. Data shown are heart phenotypes scored for
 myl7 staining using in situ hybridization (DIG AP). WT, wild type. 18s, 18
 somite stage. Hpf, hours post fertilization. Fig5Morphologymyl7GFP48hr.csv
 This table provides the raw data for the embryo numbers provided in the
 legend for the images shown in Fig. 5G-I. Data shown are heart phenotypes
 scored for myl7 staining using GFP (green fluorescent protein) expression.
 WT, wild type. hHr hours of development. hHpf hours post fertilization.
 Mut, mutant. dysm, dysmorphic. n, numbers. Y, N, yes, no.
 Fig5Morphologymyl7GFP72hr.csv This table provides the raw data for the
 embryo numbers provided in the legend for the images shown in Fig. 5G-I.
 Data shown are heart phenotypes scored for myl7 staining using GFP (green
 fluorescent protein) expression. WT, wild type. Hr, hours of development.
 hHpf hours post fertilization. Mut, mutant. dysm, dysmorphic. n, numbers.
 Y, N, yes, no. dDegen degenerating. Fig6Morphologymyl7GFP96hr.csv This
 table provides the raw data for the embryo numbers provided in the graph
 shown in Fig. 6G. Data shown are protruding cardiomyocytes scored for myl7
 staining using GFP (green fluorescent protein) expression in 4 dpf heart.
 IHC, immunohistochemistry. WT, wild type. Hpf, hours post fertilization.
 dpf, days post fertilization. Mut, mutant. dysm, dysmorphic. n, numbers.
 Y, N, yes, no. E, elongated. S, severe. Fig7Heartfunction.csv This table
 provides the raw data for the heart measurements provided in the graphs
 shown in Fig. 7G-L. um, microns. HR, heart rate. bBpm beats per minute.
 MUT, mutant. WT, wild type. Fig8alphaactinin96hr.csv This table provides
 the raw data for embryo numbers describing the images presented in Fig.
 8A-C. The data shown are heart phenotypes scored for alpha-actinin
 staining. WT, wild type. Hr, hours of development. Hpf, hours post
 fertilization. Mut, mutant. dysm, dysmorphic. n, numbers. Y, N, yes, no.
 Fig8Sarcomerelengths.csv This table provides the raw data for the
 measurements provided in the graph shown in Fig. 8F. WT, wild type. Mut,
 mutant.Avgg, average. Um, microns. St dev, standard deviation.
 Fig8Myofiberwidths.csv This table provides the raw data for the
 measurements provided in the graph shown in Fig. 8G. WT, wild type. Mut,
 mutant. Avg, average. um, microns. Fig9elnbmeasurements.csv This table
 provides the raw data for the measurements of the expression domain of the
 gene elnb provided in the graph shown in Fig. 9G-H. WT, wild type. um,
 microns. ID, inner diameter. OD, outer diameter. Hpf, hours post
 fertilization. ## Access information Other publicly accessible locations
 of the data: *
 [https://www.biorxiv.org/content/10.1101/2025.01.16.633339v1](https://www.biorxiv.org/content/10.1101/2025.01.16.633339v1)