A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease

Hieu T. Nim; Louis Dang; Harshini Thiyagarajah; Daniel Bakopoulos; Michael See; Natalie Charitakis; Tennille Sibbritt; Michael P. Eichenlaub; Stuart K. Archer; Nicolas Fossat; Richard E. Burke; Patrick P.L. Tam; Coral G. Warr; Travis K. Johnson; Mirana Ramialison

doi:10.1186/s13059-021-02539-0

A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease

Hieu T. Nim, Louis Dang, Harshini Thiyagarajah, Daniel Bakopoulos, Michael See, Natalie Charitakis, Tennille Sibbritt, Michael P. Eichenlaub, Stuart K. Archer, Nicolas Fossat, Richard E. Burke, Patrick P.L. Tam, Coral G. Warr, Travis K. Johnson, Mirana Ramialison

Research output: Contribution to journal › Article › Research › peer-review

3 Citations (Scopus)

Abstract

Background: Congenital heart diseases are the major cause of death in newborns, but the genetic etiology of this developmental disorder is not fully known. The conventional approach to identify the disease-causing genes focuses on screening genes that display heart-specific expression during development. However, this approach would have discounted genes that are expressed widely in other tissues but may play critical roles in heart development.

Results: We report an efficient pipeline of genome-wide gene discovery based on the identification of a cardiac-specific cis-regulatory element signature that points to candidate genes involved in heart development and congenital heart disease. With this pipeline, we retrieve 76% of the known cardiac developmental genes and predict 35 novel genes that previously had no known connectivity to heart development. Functional validation of these novel cardiac genes by RNAi-mediated knockdown of the conserved orthologs in Drosophila cardiac tissue reveals that disrupting the activity of 71% of these genes leads to adult mortality. Among these genes, RpL14, RpS24, and Rpn8 are associated with heart phenotypes.

Conclusions: Our pipeline has enabled the discovery of novel genes with roles in heart development. This workflow, which relies on screening for non-coding cis-regulatory signatures, is amenable for identifying developmental and disease genes for an organ without constraining to genes that are expressed exclusively in the organ of interest.

Original language	English
Article number	335
Number of pages	21
Journal	Genome Biology
Volume	22
Issue number	1
DOIs	https://doi.org/10.1186/s13059-021-02539-0
Publication status	Published - 15 Dec 2021

Keywords

Computational genomics
Congenital heart disease
Drosophila
Heart development
Regulatory elements
RNAi
Tissue-specific expression

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10.1186/s13059-021-02539-0Licence: CC BY

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Nim, H. T., Dang, L., Thiyagarajah, H., Bakopoulos, D., See, M., Charitakis, N., Sibbritt, T., Eichenlaub, M. P., Archer, S. K., Fossat, N., Burke, R. E., Tam, P. P. L., Warr, C. G., Johnson, T. K., & Ramialison, M. (2021). A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease. Genome Biology, 22(1), Article 335. https://doi.org/10.1186/s13059-021-02539-0

@article{a87f8376477c41c2b0dd308cec8ea01a,

title = "A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease",

abstract = "Background: Congenital heart diseases are the major cause of death in newborns, but the genetic etiology of this developmental disorder is not fully known. The conventional approach to identify the disease-causing genes focuses on screening genes that display heart-specific expression during development. However, this approach would have discounted genes that are expressed widely in other tissues but may play critical roles in heart development. Results: We report an efficient pipeline of genome-wide gene discovery based on the identification of a cardiac-specific cis-regulatory element signature that points to candidate genes involved in heart development and congenital heart disease. With this pipeline, we retrieve 76% of the known cardiac developmental genes and predict 35 novel genes that previously had no known connectivity to heart development. Functional validation of these novel cardiac genes by RNAi-mediated knockdown of the conserved orthologs in Drosophila cardiac tissue reveals that disrupting the activity of 71% of these genes leads to adult mortality. Among these genes, RpL14, RpS24, and Rpn8 are associated with heart phenotypes. Conclusions: Our pipeline has enabled the discovery of novel genes with roles in heart development. This workflow, which relies on screening for non-coding cis-regulatory signatures, is amenable for identifying developmental and disease genes for an organ without constraining to genes that are expressed exclusively in the organ of interest.",

keywords = "Computational genomics, Congenital heart disease, Drosophila, Heart development, Regulatory elements, RNAi, Tissue-specific expression",

author = "Nim, {Hieu T.} and Louis Dang and Harshini Thiyagarajah and Daniel Bakopoulos and Michael See and Natalie Charitakis and Tennille Sibbritt and Eichenlaub, {Michael P.} and Archer, {Stuart K.} and Nicolas Fossat and Burke, {Richard E.} and Tam, {Patrick P.L.} and Warr, {Coral G.} and Johnson, {Travis K.} and Mirana Ramialison",

note = "Funding Information: We thank Jeannette Hallab, Markus Tondl, Mark Drvodelic, Henry Chiu, Julian Stolper, Denis Bienroth, and all the members of the Ramialison laboratory for their support and feedback. We thank the Monash eResearch platform for their support with the server, the Australian Drosophila Biomedical Research Facility (OzDros) for fly stock importation, and the Vienna Drosophila Resource Center, Darshana Vadgama for technical assistance, and Zhe Han for fly stocks. We thank Robert Bryson-Richardson, Peter Currie, Kelly Smith, Guillaume Junion, Mauro Costa, Milena Furtado, and Nadia Rosenthal for their critical input. The review history is available as Additional file 3. Tim Sands was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team. Funding Information: This work was supported by the Australian Research Council Discovery Project grants DP140101067; a National Health and Medical Research Council (NHMRC)/Heart Foundation Career Development Fellowship (1049980), NHMRC Ideas Grant (APP1180905) and Sun foundation to M.R.; NHMRC Ideas grant (1182330) to T.K.J and Australian Research Council Discovery Project grant (DP160100933) to P.P.L.T. The Australian Regenerative Medicine Institute is supported by grants from the State Government of Victoria and the Australian Government. This work was further supported by the Monash University Science-Medicine, Nursing, and Health Science Faculties Interdisciplinary Research Scheme. Publisher Copyright: {\textcopyright} 2021, The Author(s).",

year = "2021",

month = dec,

day = "15",

doi = "10.1186/s13059-021-02539-0",

language = "English",

volume = "22",

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Nim, HT, Dang, L, Thiyagarajah, H, Bakopoulos, D, See, M, Charitakis, N, Sibbritt, T, Eichenlaub, MP, Archer, SK, Fossat, N, Burke, RE, Tam, PPL, Warr, CG, Johnson, TK & Ramialison, M 2021, 'A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease', Genome Biology, vol. 22, no. 1, 335. https://doi.org/10.1186/s13059-021-02539-0

TY - JOUR

T1 - A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease

AU - Nim, Hieu T.

AU - Dang, Louis

AU - Thiyagarajah, Harshini

AU - Bakopoulos, Daniel

AU - See, Michael

AU - Charitakis, Natalie

AU - Sibbritt, Tennille

AU - Eichenlaub, Michael P.

AU - Archer, Stuart K.

AU - Fossat, Nicolas

AU - Burke, Richard E.

AU - Tam, Patrick P.L.

AU - Warr, Coral G.

AU - Johnson, Travis K.

AU - Ramialison, Mirana

N1 - Funding Information: We thank Jeannette Hallab, Markus Tondl, Mark Drvodelic, Henry Chiu, Julian Stolper, Denis Bienroth, and all the members of the Ramialison laboratory for their support and feedback. We thank the Monash eResearch platform for their support with the server, the Australian Drosophila Biomedical Research Facility (OzDros) for fly stock importation, and the Vienna Drosophila Resource Center, Darshana Vadgama for technical assistance, and Zhe Han for fly stocks. We thank Robert Bryson-Richardson, Peter Currie, Kelly Smith, Guillaume Junion, Mauro Costa, Milena Furtado, and Nadia Rosenthal for their critical input. The review history is available as Additional file 3. Tim Sands was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team. Funding Information: This work was supported by the Australian Research Council Discovery Project grants DP140101067; a National Health and Medical Research Council (NHMRC)/Heart Foundation Career Development Fellowship (1049980), NHMRC Ideas Grant (APP1180905) and Sun foundation to M.R.; NHMRC Ideas grant (1182330) to T.K.J and Australian Research Council Discovery Project grant (DP160100933) to P.P.L.T. The Australian Regenerative Medicine Institute is supported by grants from the State Government of Victoria and the Australian Government. This work was further supported by the Monash University Science-Medicine, Nursing, and Health Science Faculties Interdisciplinary Research Scheme. Publisher Copyright: © 2021, The Author(s).

PY - 2021/12/15

Y1 - 2021/12/15

N2 - Background: Congenital heart diseases are the major cause of death in newborns, but the genetic etiology of this developmental disorder is not fully known. The conventional approach to identify the disease-causing genes focuses on screening genes that display heart-specific expression during development. However, this approach would have discounted genes that are expressed widely in other tissues but may play critical roles in heart development. Results: We report an efficient pipeline of genome-wide gene discovery based on the identification of a cardiac-specific cis-regulatory element signature that points to candidate genes involved in heart development and congenital heart disease. With this pipeline, we retrieve 76% of the known cardiac developmental genes and predict 35 novel genes that previously had no known connectivity to heart development. Functional validation of these novel cardiac genes by RNAi-mediated knockdown of the conserved orthologs in Drosophila cardiac tissue reveals that disrupting the activity of 71% of these genes leads to adult mortality. Among these genes, RpL14, RpS24, and Rpn8 are associated with heart phenotypes. Conclusions: Our pipeline has enabled the discovery of novel genes with roles in heart development. This workflow, which relies on screening for non-coding cis-regulatory signatures, is amenable for identifying developmental and disease genes for an organ without constraining to genes that are expressed exclusively in the organ of interest.

AB - Background: Congenital heart diseases are the major cause of death in newborns, but the genetic etiology of this developmental disorder is not fully known. The conventional approach to identify the disease-causing genes focuses on screening genes that display heart-specific expression during development. However, this approach would have discounted genes that are expressed widely in other tissues but may play critical roles in heart development. Results: We report an efficient pipeline of genome-wide gene discovery based on the identification of a cardiac-specific cis-regulatory element signature that points to candidate genes involved in heart development and congenital heart disease. With this pipeline, we retrieve 76% of the known cardiac developmental genes and predict 35 novel genes that previously had no known connectivity to heart development. Functional validation of these novel cardiac genes by RNAi-mediated knockdown of the conserved orthologs in Drosophila cardiac tissue reveals that disrupting the activity of 71% of these genes leads to adult mortality. Among these genes, RpL14, RpS24, and Rpn8 are associated with heart phenotypes. Conclusions: Our pipeline has enabled the discovery of novel genes with roles in heart development. This workflow, which relies on screening for non-coding cis-regulatory signatures, is amenable for identifying developmental and disease genes for an organ without constraining to genes that are expressed exclusively in the organ of interest.

KW - Computational genomics

KW - Congenital heart disease

KW - Drosophila

KW - Heart development

KW - Regulatory elements

KW - RNAi

KW - Tissue-specific expression

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U2 - 10.1186/s13059-021-02539-0

DO - 10.1186/s13059-021-02539-0

M3 - Article

AN - SCOPUS:85121312445

SN - 1474-760X

VL - 22

JO - Genome Biology

JF - Genome Biology

IS - 1

M1 - 335

ER -

A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease

Abstract

Keywords

Access to Document

Other files and links

Role of human non-coding DNA regulatory elements (REs) in heart development and disease

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Cite this

A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease

Abstract

Keywords

Access to Document

Other files and links

Projects

Role of human non-coding DNA regulatory elements (REs) in heart development and disease

Defining diets to treat inborn errors of amino acid metabolism

How to build the head: A molecular mechanistic insight

Cite this