The in-silico zebrafish matrisome: A new tool to study extracellular matrix gene and protein functions

Highlights

• The first draft of the zebrafish matrisome has been characterized using an in-silico gene-orthology-based approach.

• The zebrafish matrisome encodes 1002 genes, a third of which belongs to the core matrisome.

• The different categories of matrisome genes are differentially subjected to evolutionary pressure.

• The robustness of the orthology-based approach was demonstrated using cross-validation strategies.

• The zebrafish matrisome is a new tool to comprehensively annotate experimental “omics” data.

Abstract

Extracellular matrix (ECM) proteins are major components of most tissues and organs. In addition to their crucial role in tissue cohesion and biomechanics, they chiefly regulate various important biological processes during embryonic development, tissue homeostasis and repair. In essence, ECM proteins were defined as secreted proteins that localized in the extracellular space. The characterization of the human and mouse matrisomes provided the first definition of ECM actors by comprehensively listing ECM proteins and classified them into categories. Because zebrafish is becoming a popular model to study ECM biology, we sought to characterize the zebrafish matrisome using an in-silico gene-orthology-based approach. We report the identification of 1002 genes encoding the in-silico zebrafish matrisome. Using independent validations, we provide evidence for the robustness of the orthology-based approach. Moreover, we evaluated the orthology relationships between human and zebrafish genes at the whole-genome and matrisome levels and showed that the different categories of ECM genes are differentially subjected to evolutionary pressure. Last, we illustrate how the zebrafish matrisome list can be employed to annotate big data using the example of a previously published proteomic study of the skeletal ECM. The establishment of the zebrafish matrisome will undoubtedly facilitate the analysis of ECM components in “-omic” data sets.

Introduction

Extracellular matrix (ECM) proteins are major components of multicellular organisms that influence tissue biomechanics and a large number of biological processes. ECM proteins localized outside the cell or at the cell membrane where they adopt diverse conformations. Their specific structural features allowed their classification into different families, such as the laminins, the proteoglycans and the collagens [1], [2], [3].

To clarify the definition of an ECM protein and to identify all the corresponding protein-coding genes, the human and mouse matrisomes have been characterized. They were respectively established as composed of 1027 and 1110 genes, which represent about 4 to 5% of the gene content of their genomes [4], [5], [6]. Based on structural and functional features, matrisome genes were divided in two main divisions: the core matrisome and the matrisome-associated genes. The core matrisome group was further divided in three categories: collagens, proteoglycans and glycoproteins; matrisome-associated genes were further classified as encoding ECM-affiliated proteins, ECM regulators or secreted factors [4]. The different gene sets are available on the Matrisome Project website (http://matrisome.org/) and are now widely used to comprehensively annotate “-omic” data [6].

The zebrafish model rapidly gained popularity in developmental biology and health research because it presents several attractive features such as the small size of the larvae and adults, the large numbers of offspring, the external development of embryos, and genetic similarities with humans, to name but a few [7]. Morpholino-based gene knockdown and, later on, the CRISPR/Cas9 genome editing methodology, have truly revolutionized zebrafish genetics and rose it up to the rank of «top model» to study development, human diseases, and conduct drug screening [8], [9], [10], [11], [12]. Several studies have convincingly demonstrated the usefulness of zebrafish to study the contribution of ECM to a range of biological processes [13], [14], [15], [16], [17], [18], [19]. It has also emerged as a powerful model to understand human connective tissue diseases and other ECM-associated diseases such as cancers [17], [18], [19], [20].

Although ECM genes are often enriched in “-omic” datasets, no list is available to comprehensively annotate ECM genes and proteins in large-scale datasets obtain in zebrafish. We decided to fill this gap by defining the first draft of the zebrafish matrisome. To do so, we took advantage of the work previously done to establish the human and murine matrisome and devised an orthology-based approach to build the in-silico zebrafish matrisome. This novel tool should greatly facilitate the study of ECM proteins in zebrafish.