Jordi GarciaFernandez

University of Barcelona | UB · Department of Genetics

Around 50 years ago, molecular biology opened the path to understand changes in forms, adaptations, complexity, or the basis of human diseases through myriads of reports on gene birth, gene duplication, gene expression regulation, and splicing regulation, among other relevant mechanisms behind gene function. Here, with the advent of big data and ar...

Charles Darwin changed the world more than two centuries ago. And around 50 years from now, molecular biology opened the path to understand changes in forms, adaptations, complexity or the basis of human diseases, trough myriads of reports on gene birth, gene duplication, gene expression regulation and splicing regulation, among other relevant mech...

The retina is particularly vulnerable to genetic and environmental alterations that generate oxidative stress and cause cellular damage in photoreceptors and other retinal neurons, eventually leading to cell death. CERKL (CERamide Kinase-Like) mutations cause Retinitis Pigmentosa and Cone-Rod Dystrophy in humans, two disorders characterized by phot...

Genetic variants in YWHAZ contribute to psychiatric disorders such as autism spectrum disorder and schizophrenia, and have been related to an impaired neurodevelopment in humans and mice. Here, we have used zebrafish to investigate the mechanisms by which YWHAZ contributes to neurodevelopmental disorders. We observed that ywhaz expression was pan-n...

A central question in chordate evolution is the origin of sessility in adult ascidians, and whether the appendicularian complete free-living style represents a primitive or derived condition among tunicates1. According to the ‘a new heart for a new head’ hypothesis, the evolution of the cardiopharyngeal gene regulatory network appears as a pivotal...

c-Jun N-terminal kinase (JNK) is a multi-functional protein involved in a diverse array of context-dependent processes, including apoptosis, cell cycle regulation, adhesion, and differentiation. It is integral to several signalling cascades, notably downstream of non-canonical Wnt and mitogen activated protein kinase (MAPK) signalling pathways. As...

Which is the origin of genes is a fundamental question in Biology, indeed a question older than the discovery of genes itself. For more than a century, it was uneven to think in origins other than duplication and divergence from a previous gene. In recent years, however, the intersection of genetics, embryonic development, and bioinformatics, has b...

The retina is a highly active metabolic organ that displays a particular vulnerability to genetic and environmental factors causing stress and homeostatic imbalance. Mitochondria constitute a bioenergetic hub that coordinates stress response and cellular homeostasis, therefore structural and functional regulation of the mitochondrial dynamic networ...

A key problem in understanding chordate evolution has been the origin of sessility of ascidians, and whether the appendicularian free-living style represents a primitive or derived condition of tunicates. To address this problem, we performed comprehensive developmental and genomic comparative analyses of the cardiopharyngeal gene regulatory networ...

The forkhead box (Fox) genes encode transcription factors that control several key aspects of development. Present in the ancestor of all eukaryotes, Fox genes underwent several duplications followed by loss and diversification events that gave rise to the current 25 families. However, few Fox members have been identified from the Lophotrochozoa cl...

RNA editing is a relatively unexplored process in which transcribed RNA is modified at specific nucleotides before translation, adding another level of regulation of gene expression. Cephalopods use it extensively to increase the regulatory complexity of their nervous systems, and mammals use it too, but less prominently. Nevertheless, little is kn...

The forkhead box (Fox) genes encode transcription factors that control several key aspects of development. Present in the ancestor of all eukaryotes, Fox genes underwent several duplications followed by loss and diversification events that gave rise to the current 25 families. However, few Fox members have been identified from the Lophotrochozoa cl...

Background: The homeobox genes Pdx and Cdx are widespread across the animal kingdom and part of the small ParaHox gene cluster. Gene expression patterns suggest ancient roles for Pdx and Cdx in patterning the through-gut of bilaterian animals although functional data are available for few lineages. To examine evolutionary conservation of Pdx and C...

Control of cell number is crucial to define body size during animal development and to restrict tumoral transformation. The cell number is determined by the balance between cell proliferation and cell death. Although many genes are known to regulate those processes, the molecular mechanisms underlying the relationship between cell number and body s...

The cerebrospinal fluid (CSF) is a waterly, colorless fluid contained within the brain ventricles and the cranial and spinal subarachnoid spaces. CSF physiological functions range from hydromechanical protection of the central nervous system (CNS) to CNS modulation of developmental processes and regulation of interstitial fluid homeostasis. Optic n...

Homologous long non-coding RNAs (lncRNAs) are elusive to identify by sequence similarity due to their fast-evolutionary rate. Here we develop LincOFinder, a pipeline that finds conserved intergenic lncRNAs (lincRNAs) between distant related species by means of microsynteny analyses. Using this tool, we have identified 16 bona fide homologous lincRN...

Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterize DNA methylation, chromatin accessibility, histone modifications and transcriptomes a...

Glutamate receptors are divided in two unrelated families: ionotropic (iGluR), driving synaptic transmission, and metabotropic (mGluR), which modulate synaptic strength. The present classification of GluRs is based on vertebrate proteins and has remained unchanged for over two decades. Here we report an exhaustive phylogenetic study of GluRs in met...

Toll-like receptors (TLRs) are important for raising innate immune responses in both invertebrates and vertebrates. Amphioxus belongs to an ancient chordate lineage which shares key features with vertebrates. The genomic research on TLR genes in Branchiostoma floridae and Branchiostoma belcheri reveals the expansion of TLRs in amphioxus. However, t...

Phylogenetic analysis of B. floridae, B. belcheri and B. lanceolatum TLRs. The phylogenetic tree was constructed by maximum-likelihood method (IQ-TREE) using TIR domain sequences of B. floridae, B. belcheri, B. lanceolatum, S. kowalevskii and representative vertebrate TLRs. D. melanogaster Toll sequence was used as an outgroup to root the tree. Seq...

Phylogenetic analysis of BlTLR. The phylogenetic tree was constructed by maximum-likelihood method (IQ-TREE) using full-length protein sequences. BlTLR, BbtTLR1 and representative vertebrate TLR sequences were used in the analysis. D. melanogaster Toll was used as an outgroup to root the tree. Sequences were aligned with MAFFT choosing L-INS-i meth...

TLR sequences of L. variegatus and S. kowalevskii used in the phylogenetic analysis. The TIR domain of each TLR is highlighted in yellow.

Complete phylogenetic analysis of B. lanceolatum TLRs. The phylogenetic tree was constructed by IQ-TREE using full-length protein sequences. This tree is a more detailed version of the tree shown in Figure 1. All the values of SH-aLRT support and ultrafast bootstrap support are shown at the tree nodes. Outgroup, mccTLRs and 6 vertebrate TLR familie...

Primers used for RT-PCR analysis.

TLR ligands used in this study.

Protein sequence identity of BlTLR and fish TLR22.

Ectodomain architecture of vertebrate TLRs and BlTLR.

Nucleotide and deduced amino acid sequences of BlTLR. Predicted transcription start site (TSS) is marked with a curved arrow. TATA box is boxed with a rectangle. The putative STAT5 and APIB transcription factor binding sites have a thick underline. The start codon (ATG), the stop codon (TAA) and the polyadenylation signal sequence (AATAAA) are in b...

Predicted domain architecture of BlTLR protein. The domain structure was predicted using the SMART program. Signal peptide (SP), leucine-rich repeat N-terminal domain (LRRNT), leucine-rich repeat (LRR), leucine rich repeat C-terminal domain (LRRCT), Transmembrane domain (TM) and Toll/interleukin-1 receptor (TIR) domain are indicated in figure. Figu...

Vertebrate and invertebrate protein sequences used in the phylogenetic analysis.

Identified DNA and putative protein sequences of TLRs in B. lanceolatum. The TIR domain of each TLR is highlighted in yellow.

Epithelial-mesenchymal interactions are crucial for the development of numerous animal structures. Thus, unraveling how molecular tools are recruited in different lineages to control interplays between these tissues is key to understanding morphogenetic evolution. Here, we study Esrp genes, which regulate extensive splicing programs and are essenti...

All vertebrate brains develop following a common Bauplan defined by anteroposterior (AP) and dorsoventral (DV) subdivisions, characterized by largely conserved differential expression of gene markers. However, it is still unclear how this Bauplan originated during evolution. We studied the relative expression of 48 genes with key roles in vertebrat...

Temporal expression of Nk2.1 during amphioxus development. Lateral views (A-F, F’), dorsal views (A’-E’), and schematic drawings (A”-F”) of the neural component of Nk2.1 gene expression pattern from 15 to 36 hours post-fertilization. Anterior is to the left except in F. Somites are indicated using red dotted lines. Scale bar = 50μm. (TIF)

Additional gene markers used in this study. Other markers with neural expression used in this study in lateral (A-G) or dorsal views (A’-G’), and drawings of the neural component of each gene expression pattern with the relative position of somites (A”-G’). Markers with no expression in the amphioxus developing CNS at this stage are showed in later...

Probes of amphioxus used for in situ hybridization. (XLSX)

Expression of key gene markers at early neural stage. (TIF)

Information on the neural expression of genes used in this study. (XLSX)

Probes of zebrafish used for in situ hybridization. (XLSX)

The vertebrate brain is arguably the most complex anatomical and functional structure in nature. During embryonic development, the central nervous system (CNS) undergoes a series of morphogenetic processes that eventually obscure the major axes of the early neural plate to our perception. Notwithstanding this complexity, the “genoarchitecture” of t...

Within the consolidated field of evolutionary development, there is emerging research on evolutionary aspects of central nervous system development and its implications for adult brain structure and function, including behaviour. The central nervous system is one of the most intriguing systems in complex metazoans, as it controls all body and mind...

Molecular fingerprinting of conserved germline and somatic “stemness” markers in different taxa have been key in defining the mechanism of germline specification (“preformation” or “epigenesis”), as well as expression domains of somatic progenitors. The distribution of molecular markers for primordial germ cells (PGCs), including vasa, nanos, and p...

During embryonic development and adult life, brain cavities and ventricles are filled with cerebrospinal fluid (CSF). CSF has attracted interest as an active signaling medium that regulates brain development, homeostasis and disease. CSF is a complex protein-rich fluid containing growth factors and signaling molecules that regulate multiple cell fu...

Cerebrospinal fluid (CSF) has attracted interest as an active signaling milieu that regulates brain development, homeostasis, and course disease. CSF is a nutrient-rich fluid, which also contains growth factors and signaling molecules that regulate multiple cell functions in the central nervous system (CNS). CSF constitution is controlled tightly a...

Mitochondrial function and dynamics are essential for neurotransmission, neural function and neuronal viability. Recently, we showed that the eutherian-specific Armcx gene cluster (Armcx1-6 genes), located in the X chromosome, encodes for a new family of proteins that localise to mitochondria, regulating mitochondrial trafficking. The Armcx gene cl...

Hox genes, with their similar roles in animals as evolutionarily distant as humans and flies, have fascinated biologists since their discovery nearly 30 years ago. During the last two decades, reports on Hox genes from a still growing number of eumetazoan species have increased our knowledge on the Hox gene contents of a wide range of animal groups...

The regulation of mitochondrial dynamics is vital in complex cell types, such as neurons, that transport and localize mitochondria in high energy-demanding cell domains. The Armcx3 gene encodes a mitochondrial-targeted protein (Alex3) that contains several arm-like domains. In a previous study we showed that Alex3 protein regulates mitochondrial ag...

Recombinant Wnt5a leads to Alex3 degradation and mitochondrial disaggregation in cells. (A,B) High-magnification micrographs illustrating that Wnt5a treatment leads to mitochondrial disaggregation. (C) Histogram showing percentage of mitochondrial phenotypes in control and Wnt5a-treated, Alex3-transfected cells. Scale Bar: 20 µm. (TIF)

Mitochondrial localization of Alex3 after co-expression of Wnts and Fz2. (A–F) Mitochondrial localization of Alex3 (green) in HEK293AD cells after co-expression with the members of the Wnt/Frizzled signaling pathway used in Figure 3 (Wnt1, Fz2, Wnt5a and Wnt11). Alex3 protein overlaps with the mitochondrial network labeled with Mitotracker (red). (...

Alex3 does not colocalize with Frizzled2-HA. Co-expression of Alex3 (green) and Frizzled2-HA (red) in HEK293T cells does not show colocalization. Nuclei are stained in blue (bisbenzimide). Scale Bar: 10 µm. (TIF)

Wnt3a treatment does not reverse Alex3 mitochondrial aggregation. Representative Alex3-transfected cells (green) treated with recombinant Wnt3a show mitochondrial aggregate phenotypes. β-catenin in red and nuclei in blue (bisbenzimide). Scale Bar: 10 µm. (TIF)

Alex3-GFP deletion constructs lacking PKC phosphorylation sites do not respond to Wnt1 and Calphostin C. (A) Co-transfection of Wnt1 with Alex3-GFP (1–106) and (1–45) deletion constructs (right panels), which lack PKC phosphorylation sites, does not lead to Alex3 protein degradation, in comparison with co-transfection with full-length Alex3-GFP pro...

Videorecording (7.5 minutes) illustrating mitochondrial dynamics in cells transfected with Alex3-GFP. (AVI)

Videorecording (7.5 minutes) illustrating mitochondrial dynamics in Alex3-GFP/Wnt1 cells treated with TPA. (AVI)

Videorecording (7.5 minutes) illustrating mitochondrial dynamics in control cells. (AVI)

Alex3 fully co-localizes with MitoTracker and MitoDsRed. (A) The mitochondrial red marker MitoTracker (red) and the mitochondrial green marker MitoGFP (green), which shares the same mitochondrial targeting sequence of MitoDsRed (from the subunit VIII of human cytochrome c oxidase), completely co-localized in HEK293T cells. Alex3-GFP (B,C) and Alex3...

Wnt5a and Calphostin C produce Alex3 protein degradation. Overexpressing Alex3 HEK293T cells treated with Wnt5a or Calphostin C and in presence of cycloheximide show a reduction in protein levels compared with cells treated only with cycloheximide. (TIF)

Videorecording (7.5 minutes) illustrating mitochondrial dynamics in Alex3-GFP/Wnt1. (AVI)

The human CERKL gene is responsible for common and severe forms of retinal dystrophies. Despite intense in vitro studies at the molecular and cellular level and in vivo analyses of the retina of murine knockout models, CERKL function remains unknown. In this study, we aimed to approach the developmental and functional features of cerkl in Danio rer...

Syntenic organization of the CERKL genomic region. Schematic view of the structure and gene organization of the 1.8 Mb genomic locus encompassing CERKL in Homo sapiens (Hsa), Xenopus tropicalis (Xtr) and Danio rerio (Dre). The discontinuous lines in the Xenopus locus represent the end of the scaffold. Conserved genes are shown in color, while empty...