FOXM1 expression reverts aging chromatin profiles through repression of the senescence-associated pioneer factor AP-1

Aging is characterized by changes in gene expression, some of which can drive deleterious cellular phenotypes and senescence. The transcriptional activation of senescence genes has been mainly attributed to epigenetic shifts, but the changes in chromatin accessibility and its underlying mechanisms remain largely elusive in natural aging. Here, we profiled chromatin accessibility in human dermal fibroblasts (HDFs) from individuals with ages ranging from neonatal to octogenarian. We found that AP-1 binding motifs are prevalent in elderly-specific accessible chromatin regions while neonatal-specific regions are highly enriched for TEAD binding motifs. We further show that TEAD4 and FOXM1 share a conserved transcriptional regulatory landscape controlled by a not previously described and age-dependent enhancer that loses accessibility with aging and whose deletion drives senescence. Finally, we demonstrate that FOXM1 ectopic expression in elderly cells partially resets chromatin accessibility to a youthful state due to FOXM1's repressive function on several members of the AP-1 complex, which is known to trigger the senescence transcriptional program. These results place FOXM1 at a top hierarchical level in chromatin remodeling required to prevent senescence.

Single-cell Transcriptomic Studies Unveil Potential Nodes of the Notochord Gene Regulatory Network

Transcription factors (TFs) are DNA-binding proteins able to modulate the timing, location, and levels of gene expression by binding to regulatory DNA regions. Therefore, the repertoire of TFs present in the genome of a multicellular organism and the expression of variable constellations of TFs in different cellular cohorts determine the distinctive characteristics of developing tissues and organs. The information on tissue-specific assortments of TFs, their cross-regulatory interactions, and the genes/regulatory regions targeted by each TF is summarized in gene regulatory networks (GRNs), which provide genetic blueprints for the specification, development, and differentiation of multicellular structures. In this study, we review recent transcriptomic studies focused on the complement of TFs expressed in the notochord, a distinctive feature of all chordates. We analyzed notochord-specific datasets available from organisms representative of the three chordate subphyla, and highlighted lineage-specific variations in the suite of TFs expressed in their notochord. We framed the resulting findings within a provisional evolutionary scenario, which allows the formulation of hypotheses on the genetic/genomic changes that sculpted the structure and function of the notochord on an evolutionary scale.

Evolutionary origin of the chordate nervous system revealed by amphioxus developmental trajectories

The common ancestor of all vertebrates had a highly sophisticated nervous system, but questions remain about the evolution of vertebrate neural cell types. The amphioxus, a chordate that diverged before the origin of vertebrates, can inform vertebrate evolution. Here we develop and analyse a single-cell RNA-sequencing dataset from seven amphioxus embryo stages to understand chordate cell type evolution and to study vertebrate neural cell type origins. We identified many new amphioxus cell types, including homologues to the vertebrate hypothalamus and neurohypophysis, rooting the evolutionary origin of these structures. On the basis of ancestor-descendant reconstruction of cell trajectories of the amphioxus and other species, we inferred expression dynamics of transcription factor genes throughout embryogenesis and identified three ancient developmental routes forming chordate neurons. We characterized cell specification at the mechanistic level and generated mutant lines to examine the function of five key transcription factors involved in neural specification. Our results show three developmental origins for the vertebrate nervous system: an anterior FoxQ2-dependent mechanism that is deeply conserved in invertebrates, a less-conserved route leading to more posterior neurons in the vertebrate spinal cord and a mechanism for specifying neuromesoderm progenitors that is restricted to chordates. The evolution of neuromesoderm progenitors may have led to a dramatic shift in posterior neural and mesodermal cell fate decisions and the body elongation process in a stem chordate.

Conservation of cis-Regulatory Syntax Underlying Deuterostome Gastrulation

Throughout embryonic development, the shaping of the functional and morphological characteristics of embryos is orchestrated by an intricate interaction between transcription factors and cis-regulatory elements. In this study, we conducted a comprehensive analysis of deuterostome cis-regulatory landscapes during gastrulation, focusing on four paradigmatic species: the echinoderm Strongylocentrotus purpuratus, the cephalochordate Branchiostoma lanceolatum, the urochordate Ciona intestinalis, and the vertebrate Danio rerio. Our approach involved comparative computational analysis of ATAC-seq datasets to explore the genome-wide blueprint of conserved transcription factor binding motifs underlying gastrulation. We identified a core set of conserved DNA binding motifs associated with 62 known transcription factors, indicating the remarkable conservation of the gastrulation regulatory landscape across deuterostomes. Our findings offer valuable insights into the evolutionary molecular dynamics of embryonic development, shedding light on conserved regulatory subprograms and providing a comprehensive perspective on the conservation and divergence of gene regulation underlying the gastrulation process.

FISH for All: A Fast and Efficient Fluorescent In situ Hybridization (FISH) Protocol for Marine Embryos and Larvae

In situ hybridization is one the most commonly used techniques for developmental and evolutionary biology and has extensively contributed to the identification of distinct cell types and cell states, as well dissecting several molecular mechanisms involved in physiological processes. Moreover, it has been used as a tool to compare distinct gene expression patterns and, therefore, genetic programs across animal species. Nowadays, the predominance of transcriptomics in science has imposed the need to establish a reliable, fast and easy whole mount in situ hybridization protocol. Here we describe a fluorescent in situ hybridization protocol that is rapid, accurate and applicable in a great variety of marine species.

Innovation Through Heterochrony: An Amphioxus Perspective on Telencephalon Origin and Function

Heterochrony has played a key role in the evolution of invertebrate larval types, producing “head larvae” in diverse taxa, where anterior structures are accelerated and specialized at the expense of more caudal ones. For chordates, judging from amphioxus, the pattern has been more one of repeated acceleration of adult features so that they function earlier in development, thus converting the ancestral larva, whether it was a head larva or not, into something progressively more chordate-like. Recent molecular data on gene expression patterns in the anterior nerve cord of amphioxus point to a similar process being involved in the origin of the telencephalon. As vertebrates evolved, a combination of acceleration and increasing egg size appears here to have allowed the development of a structure that would originally have emerged only gradually in the post-embryonic phase of the life history to be compressed into embryogenesis. The question then is what, in functional terms, makes the telencephalon so important to the survival of post-embryonic ancestral vertebrates that this was adaptively advantageous. A better understanding of the function this brain region performs in amphioxus may help provide the answer.

Identification and expression profiles of Fox transcription factors in the Yesso scallop (Patinopecten yessoensis)

The forkhead box (Fox) gene family is a family of transcription factors that play important roles in a variety of biological processes in vertebrates, including early development and cell proliferation and differentiation. However, at present, studies on the mollusk Fox family are relatively lacking. In the present study, the Fox gene family of the Yesso scallop (Patinopecten yessoensis) was systematically identified. In addition, the expression profiles of the Fox gene family in early development and adult tissues were analyzed. The results showed that there were 26 Fox genes in P. yessoensis. Of the 26 genes, 24 belonged to 20 subfamilies. The Fox genes belonging to the I, Q1, R and S subfamilies were absent in P. yessoensis. The other 2 genes formed 2 independent clades with the Fox genes of other mollusks and protostomes. They might be new members of the Fox family and were named FoxY and FoxZ. P. yessoensis contained a FoxC-FoxL1 gene cluster similar in structure to that of Branchiostoma floridae, suggesting that the cluster might already exist in the ancestors of bilaterally symmetrical animals. The gene expression analysis of Fox showed that most of the genes were continuously expressed in multiple stages of early development, suggesting that Fox genes might be widely involved in the regulation of embryo and larval development of P. yessoensis. Nine Fox genes were specifically expressed in certain tissues, such as the nerve ganglia, foot, ovary, testis, and gills. For the 9 genes that were differentially expressed between the testis and ovary, their expression levels were analyzed during the 4 developmental stages of gonads. The results showed that FoxL2, FoxE and FoxY were highly expressed in the ovary during all developmental stages, while FoxZ was highly expressed in the testis during all developmental stages. The results suggested that these genes might play an important role in sex maintenance or gametogenesis. The present study could provide a reference for evolutionary and functional studies of the Fox family in metazoans.

Cilia-driven asymmetric Hedgehog signalling determines the amphioxus left-right axis by controlling Dand5 expression

Cilia rotation-driven nodal flow is crucial for the left-right (L-R) break in symmetry in most vertebrates. However, the mechanism by which the flow signal is translated to asymmetric gene expression has been insufficiently addressed. Here, we show that Hedgehog (Hh) signalling is asymmetrically activated (L<R) in the region in which initial asymmetric Dand5 expression is detected. Upregulation of Hh signalling on the left side of wild-type embryos induces ectopic Dand5 expression on the left side, and the unilateral recovery of Hh signalling in Hh homozygous mutants induces Dand5 expression in the Hh signal recovery side. Immunofluorescence analysis results revealed that Hh fusion protein is asymmetrically enriched in the anterior-right paraxial mesoderm at the early neurula stage. Inhibiting embryonic cilia motility using methylcellulose (MC) blocks Hh protein enrichment on the right hand side and randomizes Dand5 expression and organ positioning along the L-R axis. These findings present a model showing that cilia movement is crucial for the symmetry breaks in amphioxus through asymmetric Hh protein transport. The resultant asymmetric Hh signalling provides a clue into the induction of asymmetric Dand5 expression.This article has an associated 'The people behind the papers' interview.

The expression of FoxG1 in the early development of the European river lamprey Lampetra fluviatilis demonstrates significant heterochrony with that in other vertebrates

FoxG1, a member of the Fox/Forkhead family of winged helix transcription factors, plays key roles in the induction and spatial compartmentalization of the telencephalon in vertebrates. Loss- and gain-of-function experiments have established FoxG1 as a maintenance factor for neural progenitors and a crucial player in the specification of the ventral telencephalon (subpallium). For the first time in evolution, the telencephalon appeared in the ancestors of vertebrates, including cyclostomes. However, although FoxG1 homologues are present in cyclostomes (i.e., in lampreys and hagfishes), no systematic study of the spatial-temporal expression of FoxG1 during the embryonic development of these animals has been carried out. Given these findings, we have now studied FoxG1 spatial-temporal expression patterns in the early development of the European river lamprey Lampetra fluviatilis. We show that in contrast to other vertebrates, in which the expression of FoxG1 begins during neurulation, the expression of this gene in L. fluviatilis starts after neurulation, first at stage 21 (early head protrusion) in the area of the otic placodes and then, beginning from stage 22, in the telencephalon. Such heterochrony of FoxG1 expression in the lamprey may reflect the fact that in this basally divergent representative of vertebrates, telencephalon specification occurs relatively late. This heterochrony could be related to the evolutionary history of the telencephalon, with a recent appearance in vertebrates as an extension to more ancient anterior brain regions. Another peculiarity of FoxG1 expression in lamprey, compared to other vertebrates, is that it is not expressed in the lamprey optic structures.

Gene profiling of head mesoderm in early zebrafish development: insights into the evolution of cranial mesoderm

Background

The evolution of the head was one of the key events that marked the transition from invertebrates to vertebrates. With the emergence of structures such as eyes and jaws, vertebrates evolved an active and predatory life style and radiated into diversity of large-bodied animals. These organs are moved by cranial muscles that derive embryologically from head mesoderm. Compared with other embryonic components of the head, such as placodes and cranial neural crest cells, our understanding of cranial mesoderm is limited and is restricted to few species.

Results

Here, we report the expression patterns of key genes in zebrafish head mesoderm at very early developmental stages. Apart from a basic anterior–posterior axis marked by a combination of pitx2 and tbx1 expression, we find that most gene expression patterns are poorly conserved between zebrafish and chick, suggesting fewer developmental constraints imposed than in trunk mesoderm. Interestingly, the gene expression patterns clearly show the early establishment of medial–lateral compartmentalisation in zebrafish head mesoderm, comprising a wide medial zone flanked by two narrower strips.

Conclusions

In zebrafish head mesoderm, there is no clear molecular regionalisation along the anteroposterior axis as previously reported in chick embryos. In contrast, the medial–lateral regionalisation is formed at early developmental stages. These patterns correspond to the distinction between paraxial mesoderm and lateral plate mesoderm in the trunk, suggesting a common groundplan for patterning head and trunk mesoderm. By comparison of these expression patterns to that of amphioxus homologues, we argue for an evolutionary link between zebrafish head mesoderm and amphioxus anteriormost somites.

Electronic supplementary material

The online version of this article (10.1186/s13227-019-0128-3) contains supplementary material, which is available to authorized users.