Norihiro Okada

• Principal Investigator at Tokyo Institute of Technology

In response to a state of stress, the body attempts to maintain protein homeostasis through intron retention (IR). In other words, by examining which genes undergo IR under stress (i.e., IR genes), it is possible to analyze what type of stress the body is experiencing (Okada et al. 2024 Front.Psychiatry). Using this principle, we re-analyzed the RN...

Background Peripheral inflammation is often associated with depressive disorders, and immunological biomarkers of depression remain a focus of investigation. Methods We performed RNA-seq analysis of RNA transcripts of human peripheral blood mononuclear cells from a case-control study including subjects with self-reported depression in the pre-symp...

BACKGROUND Peripheral inflammation is often associated with depressive disorders, and immunological biomarkers of depression remain a focus of investigation. METHODS We performed RNA-seq analysis of human peripheral blood mononuclear cell (PBMC) RNA transcripts from a case-control study including subjects with self-reported depression in the pre-s...

Our previous experiments with klotho mice (i.e., klotho knockout mice) showed that aberrant intron retention (IR) occurs in a pre-symptomatic state of aging and can be restored to the normal state by administration of Juzentaihoto (JTT), a formula of the Japanese herbal medicine (referred to as kampo; Okada et al., 2021). To explain that this pheno...

Following publication of the original article [1], it was reported that there was an error in the author name of Yuki Iwasaki. The incorrect author name is: Yuri Iwasaki. The correct author name is: Yuki Iwasaki. Furthermore, it was reported that the Given and Family names of Trieu-Duc Vu were transposed in the original publication. The author grou...

Background Aggression is an evolutionarily conserved behavior critical for animal survival. In the fish Betta splendens , across different stages of fighting interactions, fighting opponents suffer from various stressors, especially from the great demand for oxygen. Using RNA sequencing, we profiled differential alternative splicing (DAS) events in...

Intron retention (IR) is a regulatory mechanism that can retard protein production by acting at the level of mRNA processing. We recently demonstrated that IR occurs at the pre-symptomatic state during the aging process of a mouse model of aging, providing a promising biomarker for that state, and can be restored to the normal state by juzentaihoto...

We performed RNA-seq analyses of mRNA isolated from five organs, liver, bone, heart, kidney and blood at the pre-symptomatic state of klotho mice with/without administration of a Japanese traditional herbal medicine, juzentaihoto (JTT). Data of differentially expressed genes (DEG) with/without JTT was included. Intron retention (IR) is an important...

Aging-induced neuroinflammation, also known as neuroinflammaging, plays a pivotal role in emotional disturbances, including depression and anxiety, in older individuals, thereby leading to cognitive dysfunction. Although numerous studies have focused on therapeutic strategies for cognitive impairment in older individuals, little research has been p...

Siamese fighting fish Betta splendens are notorious for their aggressiveness and males of this fish have been widely used to study aggression. However, an understanding of brain transcriptome signature associated with aggression in the context of male-male interaction in this fish remains to be understood. Herein, RNA-Seq transcriptome data from 37...

Intron retention (IR) is an important regulatory mechanism that affects gene expression and protein functions. Using klotho mice at the pre-symptomatic state, we discovered that retained-introns accumulated in several organs including the liver and that among these retained introns in the liver a subset was recovered to the normal state by a Japane...

The cichlids of Lake Victoria are a textbook example of adaptive radiation, as > 500 endemic species arose in just 14,600 years. The degree of genetic differentiation among species is very low due to the short period of time after the radiation, which allows us to ascertain highly differentiated genes that are strong candidates for driving speciati...

Territorial defense involves frequent aggressive confrontations with competitors, but little is known about how brain-transcriptomic profiles change between individuals competing for territory establishment. Our previous study elucidated that when two fish Betta splendens males interact, transcriptomes across their brains synchronize in a way that...

Background The molecular basis of the incipient stage of speciation is still poorly understood. Cichlid fish species in Lake Victoria are a prime example of recent speciation events and a suitable system to study the adaptation and reproductive isolation of species. Results Here, we report the pattern of genomic differentiation between two Lake Vi...

Conspecific male animals fight for resources such as food and mating opportunities but typically stop fighting after assessing their relative fighting abilities to avoid serious injuries. Physiologically, how the fighting behavior is controlled remains unknown. Using the fighting fish Betta splendens, we studied behavioral and neurotranscriptomic c...

Background For Lake Victoria cichlid species inhabiting rocky substrates with differing light regimes, it has been proposed that adaptation of the long-wavelength-sensitive (LWS) opsin gene triggered speciation by sensory drive through color signal divergence. The extensive and continuous sand/mud substrates are also species-rich, and a correlation...

Shh signalling plays a crucial role for endoderm development. A Shh endoderm enhancer, MACS1, is well conserved across terrestrial animals with lungs. Here, we first show that eliminating mouse MACS1 causes severe defects in laryngeal development, indicating that MACS1-directed Shh signalling is indispensable for respiratory organogenesis. Extensiv...

Supplementary Figures 1-11 and Supplementary Tables 1-4

Background: For Lake Victoria cichlid species inhabiting rocky substrates with differing light regimes, it has been proposed that adaptation of the long-wavelength-sensitive (LWS) opsin gene triggered speciation by sensory drive through color signal divergence. The extensive and continuous sand/mud substrates are also species-rich, and a correlatio...

Acquisition of cis-regulatory elements is a major driving force of evolution, and there are several examples of developmental enhancers derived from transposable elements (TEs). However, it remains unclear whether one enhancer element could have been produced via cooperation among multiple, yet distinct, TEs during evolution. Here we show that an e...

Closure of the secondary palate during mouse development. Upper jaws (A) and coronal sections (B) are illustrated for E13.5–15.5 embryos. Palatal shelves are shown in magenta. (TIF)

Representative X-gal–stained E13.5 transgenic embryos. (a–i) Embryos harboring the AS3_9 construct (a) and related deletion constructs (b–i), corresponding to those in Fig 3A–3I. (j) Transgenic embryos harboring the AS3_9 construct in which a mutation was introduced in the putative Msx1-binding site, corresponding to those in Fig 3J. (TIF)

Epigenetic marks in AS3_9 from the ENCODE (A) and the Roadmap Epigenomics (B) projects. (A) The human AS3_9 region in the UCSC genome browser (hg19) showing the DNase-hypersensitive clusters and the transcription factor binding signals by the ChIP-seq analyses from the ENCODE project. (B) ChIP-seq or DNase-hypersensitive signals with scores >10 wer...

List of AmnSINE1-derived CNEs accompanied by another repetitive elements under purifying selection. The Locus ID 12 corresponds to AS3_9 enhancer. (XLSX)

X-gal staining of AS3_9-lacZ transgenic embryos. Embryos from the transient enhancer analysis (A) and the three stable lines α–γ (B) at E9.5–15.5 were stained. Scale bar: 2 mm. (TIF)

AS3_9-binding proteins and enhancer activity of the construct containing a mutation in the Msx1-binding site. (A–C) Binding of Msx1, Msx2, Gtf2ird1, and Zbtb7c to the AS3_9 sequence detected by yeast one-hybrid assay using SD/-Leu medium with (B) or without (C) antibiotic (aureobasidin A). Empty vector was used as the negative control. (D–F) Yeast...

Primer list used in this study. (XLSX)

ISH of E13.5 coronal sections for the eight genes surrounding AS3_9. (A) wnt5a, (B) erc2, (C) lrtm1, (D) cacna2d3, (E) selk, (F) actr8, (G) il17rb, and (H) chdh. Red arrowheads denote wnt5a expression in palatal shelves. (TIF)

Coronal sections (10 μm) of E14.5 (A) and E15.5 (B) embryos of AS3_9-ko mice were stained with hematoxylin and eosin. The embryos were compared among two to five littermates from eight different litters. WT: Wild type. Scale bar: 0.5 mm. (TIF)

Sequence alignments of the X6b_DNA (A), and MER117 (B) regions of AS3_9. The top line of each alignment is the consensus sequences of the TE. The putative Msx1-binding site (reverse-complement of the TAATTG motif) is denoted by a red line in (A). (TIF)

Sequence alignment of the AmnSINE1 region of AS3_9 corresponding to nucleotide positions 391–501 of its consensus sequence. The top line of the alignment shows the consensus sequences of AmnSINE1. (TIF)

Comparison of lacZ and wnt5a expression at E10.5, E13.5, and E14.5. X-gal–stained AS3_9-lacZ embryos (A,D), and ISH for lacZ (B,E) and wnt5a (C,F). Arrowheads: frontonasal region. Ventral view of the X-gal–stained upper jaw of AS3_9-lacZ (G,H), coronal sections of the X-gal–stained AS3_9-lacZ embryos (I,J), and ISH for wnt5a in coronal sections (K,...

Generation of AS3_9-deficient mice. (A) Schematic representation of wild-type and mutant alleles as well as the targeting vector. The 800-bp region containing the three TEs in AS3_9 was replaced with a Neo cassette (Pr-Neo-pA). Black bars: 5’ and 3’ probe regions used for Southern hybridization. Bl: Bln I, Bs: Bsp1407 I, E: EcoR V, and S: Sac I sit...

Isolated positive clones by yeast one-hybrid screening. In total 14 positive clones contained 12 genes, some of which are included in the same clones. (DOCX)

The lung is an important organ for air breathing in tetrapods and originated well before the terrestrialization of vertebrates. Therefore, to better understand lung evolution, we investigated lung development in the extant basal actinopterygian fish Senegal bichir (Polypterus senegalus). First, we histologically confirmed that lung development in t...

Background: Whole genome duplications (WGDs) have been proposed to have made a significant impact on vertebrate evolution. Two rounds of WGD (1R and 2R) occurred in the common ancestor of Gnathostomata and Cyclostomata, followed by the third-round WGD (3R) in a common ancestor of all modern teleosts. The 3R-derived paralogs are good models for und...

Long interspersed elements (LINEs), or non-long-terminal repeat (LTR) retrotransposons, are mobile genetic elements that exist in the genomic DNA of most eukaryotes, comprising a considerable portion of the host chromosomes. LINEs constitute endogenous mutagens that cause insertional mutations in host chromosomes and have a large impact on host gen...

Cichlid fishes in East Africa have undergone extensive adaptive radiation, which has led to spectacular diversity in their morphology and ecology. To date, genetic linkage maps have been constructed for several tilapias (riverine), Astatotilapia burtoni (Lake Tanganyika), and hybrid lines of Lake Malawi cichlids to facilitate genome-wide comparativ...

To elucidate the molecular mechanism of the integration of long interspersed elements (LINEs), we characterized the 5′ ends of more than 200 LINE de novo retrotransposition events into chicken DT40 or human HeLa cells. Human L1 inserts produced 15-bp target-site duplications (TSDs) and zebrafish ZfL2-1 inserts produced 5-bp TSDs in DT40 cells, sugg...

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity,we sequenced the genomes and transcriptomes of five lineages of African cichlids: theNile tilapia (Oreochromis niloticus), an ancestral lineage with low div...

When a population size is reduced, genetic drift may fix slightly deleterious mutations, and an increase in nonsynonymous substitution is expected. It has been suggested that past aridity has seriously affected and decreased the populations of cichlid fishes in Lake Victoria, while geographical studies have shown that the water levels in Lake Tanga...

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low d...

LINEs mobilize their own copies via retrotransposition. LINEs can be divided into two types. One is a stringent type, which constitutes a majority of LINEs. The other is a relaxed type. To elucidate the molecular mechanism of retrotransposition, we used here two different zebrafish LINEs belonging to the stringent type. By using retrotransposition...

With a remarkable increase in genomic sequence data of a wide range of species, novel tools are needed for comprehensive analyses of the big sequence data. Self-organizing map (SOM) is a powerful tool for clustering high-dimensional data on one plane. For oligonucleotide compositions handled as high-dimensional data, we have previously modified the...

Fish use olfaction to detect a variety of nonvolatile chemical signals, and thus, this sense is key to survival and communication. However, the contribution of the olfactory sense to social—especially reproductive—interactions in cichlids is still controversial. To obtain insights into this issue, we investigated the genes encoding V1Rs—possible ca...

Speciation by sensory drive can occur if divergent adaptation of sensory systems causes rapid evolution of mating traits and the resulting development of assortative mating. Previous theoretical studies have shown that sensory drive can cause rapid divergent adaptive evolution from one to two phenotypes. In this study, we examined two topics: the p...

Cichlid fishes in the African Great Lakes are known as a spectacular example of adaptive radiation in vertebrates. Four linkage maps have been constructed to identify the genes responsible for adaptation and speciation, and the genetic linkages of those genes are assumed to play an important role during adaptive evolution. However, it is difficult...

The Long interspersed element 1 (LINE1 or L1) retrotransposon constitutes 17% of the human genome. There are currently 80-100 human L1 elements that are thought to be active in any diploid human genome. These elements can mobilize into new locations of the genome, resulting in changes in genomic information. Active L1s are thus considered to be a t...

The approximately 700 species of cichlids found in Lake Victoria in East Africa are thought to have evolved over a short period of time, and they represent one of the largest known examples of adaptive radiation. To understand the processes that are driving this spectacular radiation, we must determine the present genetic structure of these species...

Coelacanths are known as "living fossils", as they show remarkable morphological resemblance to the fossil record, and belong to the most primitive lineage of living Sarcopterygii (lobe-finned fishes and tetrapods). Coelacanths may be key to elucidating the tempo and mode of evolution from fish to tetrapods. Here, we report the genome sequences of...

Fish use olfaction to sense a variety of nonvolatile chemical signals in water. However, the evolutionary importance of olfaction in species-rich cichlids is controversial. Here, we determined an almost complete sequence of the vomeronasal type 2 receptor-like (OlfC: putative amino acids receptor in teleosts) gene cluster using the bacterial artifi...

Transposable elements, including short interspersed repetitive elements (SINEs), comprise nearly half the mammalian genome. Moreover, they are a major source of conserved non-coding elements (CNEs), which play important functional roles in regulating development-related genes, such as enhancing and silencing, serving for the diversification of morp...

Coelacanths are known as "living fossils" because their morphology has changed very little from that in the fossil record. To elucidate why coelacanths have evolved so slowly is thus of primary importance in evolutionary biology. In the present study, we determined the entire sequence of the HOX cluster of the Tanzanian coelacanth (Latimeria chalum...

Reproductive isolation that prevents interspecific hybridization between closely related coexisting species maintains sympatric species diversity. One of the reproductive isolations is mate choice based on color signals (breeding color perceived by color vision). This is well known in several animal taxa, yet little is known about its genetic and m...

Although olfaction could play a crucial role in underwater habitats by allowing fish to sense a variety of nonvolatile chemical signals, the importance of olfaction in species-rich cichlids is still controversial. In particular, examining whether cichlids rely on olfaction for reproduction is of primary interest to understand the mechanisms of spec...

The zebrafish long interspersed element (LINE), ZfL2-1, which belongs to the L2 clade, contains two open reading frames, ORF1 and ORF2. ORF1 encodes a protein containing a coiled-coil motif and an esterase domain, whereas ORF2 encodes a protein containing an endonuclease and a reverse transcriptase domain. To elucidate the functional significance o...

Long interspersed elements (LINEs) are transposable elements that exist in the chromosomal DNA of most eukaryotes; as such, they have a large impact on the genome evolution of their hosts. LINEs mobilize by a mechanism called retrotransposition in which the LINE RNA is reverse-transcribed into DNA and then integrated into the host chromosome. The i...

The photosynthetic membranes of cyanobacteria and chloroplasts of higher plants have remarkably similar lipid compositions. In particular, thylakoid membranes of both cyanobacteria and chloroplasts are composed of galactolipids, of which monogalactosyldiacylglycerol (MGDG) is the most abundant, although MGDG biosynthetic pathways are different in t...

Alignment of AmnSINE1 consensus sequence with mammalian AS021 sequences. (A) Sequence alignment of the 3′ half of the AmnSINE1 consensus sequence with eight mammalian AS021 sequences. Colors in the AmnSINE1 consensus sequence represent the 5S rRNA–derived promoter (red), tRNA-derived region (yellow), Deu-domain (green), and 3′-tail region (blue). (...

LacZ expression profiling of three independent stable AS071-ΔSINE-transgenic lines. Spatiotemporally consistent lacZ expression pattern among the three independent stable AS071-ΔSINE Lines D, E, and F. LacZ expression is observed only in the dorsal midline of the diencephalon (green arrowhead) and lateral wall of the diencephalon (blue arrowhead)....

Expression of genes surrounding the AS021 locus as detected by in situ hybridization in E16 and P0 brains. P = present; N = not detected. (TIF)

AS021 drives lacZ expression in early-born glutamatergic neurons. Immunostaining for Tbr1 (red) and βgal (green) in a coronal section of an E13.5 AS021-lacZ animal. Immunostaining of the individual proteins in the boxed regions of (A) are shown in (B–D″). CP, cortical plate; IZ, intermediate zone; VZ, ventricular zone. Scale bar: 200 µm. (TIF)