Jose M. Eirin-Lopez

Florida International University | FIU · Department of Biological Sciences

Histone variants play a critical role in chromatin structure and epigenetic regulation. These "deviant" proteins have been historically considered as the evolutionary descendants of ancestral canonical histones, helping specialize the nucleosome structure during eukaryotic evolution. Such view is now challenged by two major observations: first, can...

Okadaic acid (OA) and dinophysistoxins (DTXs) are the main toxins responsible for diarrhetic shellfish poisoning (DSP) intoxications during harmful algal blooms (HABs). Although the genotoxic and cytotoxic responses to OA have been evaluated in vitro, the in vivo effects of these toxins have not yet been fully explored. The present work fills this...

Background. Harmful Algal Blooms (HABs) responsible for Diarrhetic Shellfish Poisoning (DSP) represent a major threat for human consumers of shellfish. The biotoxin Okadaic Acid (OA), a well-known phosphatase inhibitor and tumor promoter, is the primary cause of acute DSP intoxications. Although several studies have described the molecular effects...

Histone variants are non-allelic protein isoforms that play key roles in diversifying chromatin structure. The known number of such variants has greatly increased in recent years, but the lack of naming conventions for them has led to a variety of naming styles, multiple synonyms and misleading homographs that obscure variant relationships and comp...

Reef-building corals are increasingly threatened by the warming climate, necessitating the development of tools to monitor their responses to environmental stress. Furthermore, scalable methods of identifying resilient corals are a particular conservation priority. Techniques commonly used to quantify the severity of coral bleaching can be invasive...

The plastic ability for a range of phenotypes to be exhibited by the same genotype allows organisms to respond to environmental variation and may modulate fitness in novel environments. Differing capacities for phenotypic plasticity within a population, apparent as genotype by environment interactions (GxE), can therefore have both ecological and e...

Age information is often non‐existent for most shark populations due to a lack of measurable physiological and morphological traits that can be used to estimate age. Recently, epigenetic clocks have been found to accurately estimate age for mammals, birds, and fish. However, since these clocks rely, among other things, on the availability of refere...

NAD metabolism is essential for all forms of life. Compartmental regulation of NAD+ consumption, especially between the nucleus and the mitochondria, is required for energy homeostasis. However, how compartmental regulation evolved remains unclear. In the present study, we investigated the evolution of the macrodomain-containing histone variant mac...

There is a growing focus on the role of DNA methylation in the ability of marine invertebrates to rapidly respond to changing environmental factors and anthropogenic impacts. However, genome-wide DNA methylation studies in non-model organisms are currently hampered by limited understanding of methodological biases. Here we compare three methods for...

Algal symbiont shuffling in favor of more thermo-tolerant species has been shown to enhance coral resistance to heat-stress. Yet, the mechanistic underpinnings and long-term implications of these changes are poorly understood. This work studied the modifications in coral DNA methylation, an epigenetic mechanism involved in coral acclimatization, in...

The methyltransferase like (METTL) proteins constitute a family of seven-beta-strand methyltransferases with S-adenosyl methionine binding domains that modify DNA, RNA, and proteins. Methylation by METTL proteins contributes to the epigenetic, and in the case of RNA modifications, epitranscriptomic regulation of a variety of biological processes. D...

Sharks serve as key predators in coastal areas, with several species using near shore habitats as nursery refuges. With many shark species threatened or endangered, it is now critical to increase the knowledge of how anthropogenic activities impact these populations. This study is the first attempt at characterizing epigenetic modifications in elas...

The apparent ability of corals to acquire and maintain enhanced stress tolerance through a dose-dependent environmental memory, which may persist for multiple years, has critical implications for coral reef conservation research. Such responses are variable across coral species and environmental stressors, with primed corals exhibiting a modified r...

Lipids are excellent biomarkers for assessing coral stress, although staghorn coral data (Acropora cervicornis) is lacking. Lipid extraction is the most critical step in lipidomic assessments, usually performed using carcinogenic solvents. Efficient alternative using less toxic methods, such as the BUME method using butanol and methanol as extracti...

There is a growing focus on the role of DNA methylation in the ability of marine invertebrates to rapidly respond to changing environmental factors and anthropogenic impacts. However, genome-wide DNA methylation studies in non-model organisms are currently hampered by limited understanding of methodological biases. Here we compare three methods for...

Epigenetic modifications such as DNA methylation have been shown to participate in plastic responses to environmental change in a wide range of organisms, including scleractinian corals. Unfortunately, the current understanding of the links between environmental signals, epigenetic modifications, and the subsequent consequences for acclimatory phen...

Age constitutes a critical parameter for the study of animal populations, providing information about development, environmental effects, survival, and reproduction. Unfortunately, age estimation is not only challenging in large, mobile and legally protected species, but often involves invasive sampling methods. The present work investigates the as...

Protamines are small, highly specialized, arginine-rich, intrinsically disordered chromosomal proteins that replace histones during spermiogenesis in many organisms. Previous evidence supports the notion that, in the animal kingdom, these proteins have evolved from a primitive replication-independent histone H1 involved in terminal cell differentia...

Marine organisms' persistence hinges on the capacity for acclimatization and adaptation to the myriad of interacting environmental stressors associated with global climate change. In this context, epigenetics-mechanisms that facilitate phenotypic variation through genotype-environment interactions-are of great interest ecologically and evolutionari...

Nutrient pollution and thermal stress constitute two of the main drivers of global change in the coastal oceans. While different studies have addressed the physiological effects and ecological consequences of these stressors in corals, the role of acquired modifications in the coral epigenome during acclimatory and adaptive responses remains unknow...

Periwinkles of the family Littorinidae (Children, 1834) are common members of seashore littoral communities worldwide. Although the family is composed of more than 200 species belonging to 18 genera, chromosome numbers have been described in only eleven of them. A molecular cytogenetic analysis of nine periwinkle species, the rough periwinkles Litt...

Although epigenetics is still a relatively new discipline, its development during the last 10 years has revolutionized the current understanding of genome structure and function. The present chapter provides an insight on the exciting field of environmental epigenetics (i.e., the cause-effect relationships between environmental signals and epigenet...

Bivalve molluscs constitute a ubiquitous taxonomic group playing key functions in virtually all ecosystems, and encompassing critical commercial relevance. Along with a sessile and filter-feeding lifestyle in most cases, these characteristics make bivalves model sentinel organisms routinely used for environmental monitoring studies in aquatic habit...

The nucleoplasmin family of histone chaperones is identified by a pentamer-forming domain and multiple acidic tracts that mediate histone binding and chaperone activity. Within this family, a novel domain organization was recently discovered that consists of an N-terminal nucleoplasmin-like (NPL) domain and a C-terminal FKBP peptidyl-proline isomer...

The genotoxic and cytotoxic effects of Diarrhetic Shellfish Poisoning (DSP) toxins have been widely investigated in bivalve molluscs, representing the main vectors of these compounds in the Atlantic coast of Europe. DSP toxins are produced by Harmful Algal Blooms (HABs) of Dinophysis and Prorocentrum dinoflagellates, being subsequently accumulated...

Massive algal proliferations known as Harmful Algal Blooms (HABs) represent one of the most important threats to coastal areas. Among them, the so-called Florida Red Tides (FRTs, caused by blooms of the dinoflagellate Karenia brevis and associated brevetoxins) are particularly detrimental in the southeastern U.S., causing high mortality rates and a...

Yeast nucleosomes are known to be intrinsically less stable than those from higher eukaryotes. This difference presents significant challenges for the production of yeast nucleosome core particles (NCPs) and chromatin for in vitro analyses. Using recombinant yeast, human and chimeric histone proteins we demonstrate that three divergent amino acids...

Histones are the fundamental constituents of the eukaryotic chromatin, facilitating the physical organization of DNA in chromosomes and participating in the regulation of its metabolism. The H2A family displays the largest number of variants among core histones, including the renowned H2A.X, macroH2A, H2A.B (Bbd), and H2A.Z. This latter variant is...

Epigenetics is the study of heritable changes in gene expression resulting from modifications in chromatin structure, without involving changes in the genetic information stored in DNA. In addition to their critical role in regulating cell differentiation and development, epigenetic modifications have also been linked to human diseases, most notabl...

Background: Diarrhetic Shellfish Poisoning (DSP) Harmful Algal Blooms (HABs) represent a major threat for human consumers of shellfish. The biotoxin Okadaic Acid (OA), a well-known phosphatase inhibitor and tumor promoter, is the main responsible of acute DSP intoxications. Although several studies have described the molecular effects of high OA co...

Background: Diarrhetic Shellfish Poisoning (DSP) Harmful Algal Blooms (HABs) represent a major threat for human consumers of shellfish. The biotoxin Okadaic Acid (OA), a well-known phosphatase inhibitor and tumor promoter, is the main responsible of acute DSP intoxications. Although several studies have described the molecular effects of high OA co...

The gene doublesex, which is placed at the bottom of the sex-determination gene cascade, plays the ultimate discriminatory role for sex determination in insects. In all insects where this gene has been characterized, the dsx premessenger RNA (pre-mRNA) follows a sex-specific splicing pattern, producing male-and female-specific mRNAs encoding the ma...

Okadaic acid (OA) is the predominant biotoxin responsible for diarrhetic shellfish poisoning (DSP) syndrome in humans. While its harmful effects have been extensively studied in mammalian cell lines, the impact on marine organisms routinely exposed to OA is still not fully known. Few investigations available on bivalve molluscs suggest less genotox...

The gene doublesex, which is placed at the bottom of the sex determination gene cascade, plays the ultimate discriminatory role for sex determination in insects. In all insects where this gene has been characterized, the dsx pre-mRNA follows a sex-specific splicing pattern producing male- and female-specific mRNAs encoding the male-DSXM and female-...

In insects, the sex determination cascade is composed of genes that interact with each other in a strict hierarchical manner, constituting a coadapted gene complex built in reverse order from bottom to top. Accordingly, ancient elements at the bottom are expected to remain conserved ensuring the correct functionality of the cascade. In the present...

High mobility group (HMG)-N proteins are a family of small nonhistone proteins that bind to nucleosomes (N). Despite the amount of information available on their structure and function, there is an almost complete lack of information on the molecular evolutionary mechanisms leading to their exclusive differentiation. In the present work, we provide...

The extraordinary progress experienced by sequencing technologies and bioinformatics has made the development of omic studies virtually ubiquitous in all fields of life sciences nowadays. However, scientific attention has been quite unevenly distributed throughout the different branches of the tree of life, leaving molluscs, one of the most diverse...

Harmful Algal Blooms (HABs) constitute one of the most important sources of contamination in the oceans, producing high concentrations of potentially harmful biotoxins that are accumulated across the food chains. One such biotoxin, Okadaic Acid (OA), is produced by marine dinoflagellates and subsequently accumulated within the tissues of filtering...

This work presents the results of applying two clustering techniques to gene expression data from the mussel Mytilus galloprovincialis. The objective of the study presented in this paper was to cluster the different genes involved in the experiment, in order to find those most closely related based on their expression patterns. A self-organising ma...

Okadaic Acid (OA) constitutes the main active principle in Diarrhetic Shellfish Poisoning (DSP) toxins produced during Harmful Algal Blooms (HABs), representing a serious threat for human consumers of edible shellfish. Furthermore, OA conveys critical deleterious effects for marine organisms due to its genotoxic potential. Many efforts have been de...

Supplementary Materials (PDF, 526 KB)

The study of chromatin constitutes one of the most active research fields in life sciences, being subject to constant revisions that continuously redefine the state of the art in its knowledge. As every other rapidly changing field, chromatin biology requires clear and straightforward educational strategies able to efficiently translate such a vast...

Recent reviews have focused on the structure and function of histone chaperones involved in different aspects of somatic cell chromatin metabolism. One of the most dramatic chromatin remodeling processes takes place immediately after fertilization and is mediated by egg histone storage chaperones. These include members of the nucleoplasmin (NPM2/NP...

For quite some time, scientists have wondered how multigene families come into existence. Over the last several decades, a number of genomic and evolutionary mechanisms have been discovered that shape the evolution, structure and organization of multigene families. While gene duplication represents the core process, other phenomena such as pseudoge...

Histone variants are used by the cell to build specialized nucleosomes, replacing canonical histones and generating functionally specialized chromatin domains. Among many other processes, the specialization imparted by histone H2A (H2A.X and H2A.Z) variants to the nucleosome core particle constitutes the earliest response to DNA damage in the cell....

Marine biotoxins synthesized by Harmful Algal Blooms (HABs) represent one of the most important sources of contamination in marine environments as well as a serious threat to fisheries and aquaculture-based industries in coastal areas. Among these biotoxins Okadaic Acid (OA) is of critical interest as it represents the most predominant Diarrhetic S...

Despite their relatively arginine-rich composition, protamines exhibit a high degree of structural variation. Indeed, the primary structure of these histone H1-related sperm nuclear basic proteins (SNBPs) is not random and is the depository of important phylogenetic information. This appears to be the result of their fast rate of evolution driven b...

The evolution of sex remains a hotly debated topic in evolutionary biology. In particular, studying the origins of the molecular mechanisms underlying sexual reproduction and gametogenesis (its fundamental component) in multicellular eukaryotes has been difficult due to the rapid divergence of many reproductive proteins, pleiotropy, and by the fact...

We would like to express our gratitude to all the authors and reviewers that contributed to the successful completion of this Issue.

Percentage similarity among the insect Tra2 proteins. Comparison of the Tra2 proteins of the insects so far characterised. A. obliqua was used as the reference species for the Anastrepha species.

Percentage similarity among the Anastrepha Tra2 proteins. Comparison of the Tra2 proteins of Anastrepha species.

Number of nucleotides that compose the exons and introns of gene tra-2 of A. obliqua, C. capitata and D. melanogaster. Exons (boxes) and introns (lines) are not drawn to scale.

Amino acid alignment of the Tra2 protein in the analysed species. The different protein domains are indicated as follows: RS-rich regions in grey background, RNA recognition motif (RRM) in green background, and linker region in yellow background. The RNP-1 and RNP-2 elements are indicated in open black boxes.

Evolutionary parameters of the Tra2 proteins from insects. Average numbers of amino acid (pAA), total nucleotide (pNT), synonymous (pS) and non-synonymous (pN) nucleotide differences per site, codon bias (Effective Number of Codons, ENC) and Z-test of selection in complete tra-2 genes and independent tra-2 domains from insects. SE, standard error;...

In the tephritids Ceratitis, Bactrocera and Anastrepha, the gene transformer provides the memory device for sex determination via its auto-regulation; only in females is functional Tra protein produced. To date, the isolation and characterisation of the gene transformer-2 in the tephritids has only been undertaken in Ceratitis, and it has been show...

In higher eukaryotes, the gene family encoding the 5S ribosomal RNA (5S rRNA) has been used (together with histones) to showcase the archetypal example of a gene family subject to concerted evolution. However, recent studies have revealed conspicuous features challenging the predictions of this model, including heterogeneity of repeat units, the pr...

The rich diversity within each of the five histone families (H1, H2A, H2B, H3, and H4) can hardly be reconciled with the notion of homogenizing evolution. The prevalence of birth-and-death long-term evolution over concerted evolution has already been demonstrated in the linker histone H1 family as well as for the H2A, H3, and H4 core histone famili...

GenBank Accession numbers for the histone variants H2A.Z-1 and H2A.Z-2 used in the present work. The ANNOTATION field denotes: gene sequences newly isolated from draft genomes (in silico), gene sequences predicted as either H2A.Z-1 or H2A.Z-2 from databases and draft/complete genomes data (Pred), sequences defined either as H2A.Z-1 or H2A.Z-2 by th...

Nucleotide alignment of H2A.Z-1 and H2A.Z-2 proximal promoter sequences from representative mammals (human, rhesus monkey and mouse). Regulatory sequences in H2A.Z-1 are indicated by solid boxes in yellow (TATA box), green (GC box) and blue (CAAT box). Regulatory elements in H2A.Z-2 are underlined in red (SP1 TP1 binding sites) and purple (c-Myc bi...

Nucleotide alignment of H2A.Z-1 and H2A.Z-2 upstream promoter region sequences from representative mammals (human, rhesus monkey and mouse). Regulatory elements in H2A.Z-1 are indicated by solid boxes in red (GC boxes), blue (CAAT boxes), purple (c-Myc binding sites), and by an open box (BGP1 RS1 binding site). Regulatory elements in H2A.Z-2 are un...