For over a century, biologists have used test tubes and petri dishes to investigate life. By studying bacteria in laboratory conditions, generations of scientists have amassed a wealth of biological knowledge. However, simple experimental systems remove complexity, leading us to question how our knowledge translates to the natural world. Approaches combining microfluidics and molecular biology have made rapid progress, filling this gap by reintroducing experimental complexity. In our review, we highlight how microfluidics has shifted and enhanced our understanding of several core molecular microbiology processes. In Section 1, we follow the journey of bacterial cells as they colonize surfaces, emphasizing that this is not a linear process. In Section 2, we explore how the interplay of physical, chemical, and biological features impacts surface-attached communities. Along the way, we highlight how using microfluidics captures bacterial behavior that classical approaches overlook, often revealing unexpected and counterintuitive outcomes.
Dicer has long been viewed as the RNAse III enzyme that generates small regulatory RNAs to drive RNA interference (RNAi) machinery and posttranscriptional gene silencing. However, a growing body of evidence reveals that Dicer's functional landscape extends far beyond its canonical role in the cytoplasmic RNAi pathway. In this review, we delineate the classical, RNAse III-dependent small RNA processing activities from an expanding set of noncanonical functions in which Dicer operates independently of RNAi outputs. We highlight emerging principles that underlie these functions, including structural and regulatory principles, with a focus on nuclear functions, posttranslational regulation, and noncanonical substrates. We then explore how Dicer intersects with genome integrity pathways, transcriptional programs, and cellular response to DNA damage. Finally, we propose an integrated conceptual framework in which Dicer acts as a multifunctional regulator of chromatin architecture and genome stability, as we consider how perturbations of these pathways contribute to disease.
Meiosis is a specialized cell division essential for sexual reproduction, generating haploid gametes through two consecutive nuclear divisions following a single round of DNA replication. During an extended meiotic prophase I, chromosomes undergo elaborate rearrangements, such as pairing, synapsis, and recombination, culminating in crossovers that physically link homologs for accurate segregation. Errors in these processes cause aneuploidy, a leading contributor to infertility, miscarriage, and congenital disorders. These chromosomal events must be precisely coordinated with cell cycle transitions through signaling pathways involving cell cycle and DNA damage checkpoint kinases, as well as ubiquitin-mediated regulation. These pathways control the timing and levels of programmed DNA double-strand breaks, monitor synapsis and crossover formation, and enforce surveillance checkpoints that eliminate defective cells. This review examines how signaling networks orchestrate chromosome dynamics during meiotic prophase, highlighting conserved principles and organism-specific adaptations that ensure faithful genetic transmission across generations.
Multicellularity necessitated the evolution of cellular diversity and specialization, yet across organisms, the retention of cellular plasticity within defined physiological contexts is a recurring principle. Here, we examine early-diverging metazoans to reevaluate the evolutionary logic of stemness. Rather than viewing stem cells as exceptional, we argue that cellular plasticity represents a deeply conserved attribute of early life. The ability of cells to remain responsive, multipotent, and regenerative under ecological or physiological contexts challenges the notion of cellular identity. We integrate evidence across three layers: evolutionary origins of cellular plasticity, systemic physiological axes that govern stem cell behavior, and metabolic and epigenetic mechanisms that execute fate decisions. This synthesis reveals that stemness is not a default cellular state but a licensed state, permitted when organism-level physiological signals align with local tissue demands. Within this framework, regeneration, age-associated decline, and cancer emerge as evidence of how effectively systemic governance regulates cellular plasticity across multicellular life.
Transposable elements (TEs), originally characterized in maize, are ubiquitous features of eukaryotes and replicate within genomes independent of the host replication cycle. This replicative advantage can result in genomes that are almost entirely composed of these selfish genetic elements. Most mutations caused by TE insertions are harmful, and all eukaryotes have evolved mechanisms to limit TE replication. This process requires the careful distinction between self and nonself, or host versus TE. Eukaryotic genome defense commonly relies on Argonaute proteins that block the TE replication cycle, guided by small RNAs that detect harmful TE transcripts. Because no system of immunity is perfect, genes can be caught in the crossfire and inappropriately silenced. Here, mainly focusing on maize and Drosophila, we discuss how off-target small RNA silencing can arise. This genomic immunity can shape TE evolutionary dynamics, establish novel modes of adaptation and epigenetic inheritance, and establish evolutionary feedback that shapes the evolution of gene silencing itself.
Predictable environmental cues, such as daily and seasonal cycles of light and temperature, are integrated by circadian clocks in both plants and animals to coordinate metabolism, physiology, growth, development, and behavior with optimal times of day and year. This temporal coupling enables organisms to anticipate recurring environmental changes and maintain adaptive alignment between internal biological processes and the external environment. However, the accelerating pace of environmental change, including increased environmental variability and altered cue reliability, threatens this circadian alignment, potentially disrupting historically beneficial and adaptive relationships across taxa. In this review, we provide a cross-taxonomic synthesis of circadian regulation of output traits, highlighting conserved and taxa-specific mechanisms that rely on this synchronization. We provide context on how these timing processes may be reshaped or compromised in increasingly dynamic and less predictable environments.
In this review, we discuss three meiotic checkpoints-the DNA damage response, the pachytene checkpoint, and the spindle checkpoint-and highlight their similarities and differences across diverse systems. Cell cycle checkpoints play a unique and important role during meiosis by enforcing dependencies within the complex choreography that governs chromosome behavior during meiotic prophase and chromosome segregation. However, meiotic checkpoints can exhibit dramatic variations in their stringency, especially when compared with mitotic checkpoints. This range in stringency likely reflects the mechanistic trade-offs associated with the unique goals of meiosis, as well as the evolutionary constraints and innovations inherent to the process.
A cell functions as a metabolic economy that parses information on nutrient availability and internal metabolic flux and then converts that to state outcomes that maintain or shift homeostasis. Here, we discuss how the nutrient-signaling machinery in cells follows an hourglass (or bow tie) design architecture, using modular signal integrators. In eukaryotic cells, this architecture is exemplified by two evolutionarily conserved, core complexes: mechanistic target of rapamycin complex 1 (mTORC1)/TORC1 and AMP-activated protein kinase (AMPK). This bow-tie design of core signal integrators enables cells to condense, fan-in, and integrate noisy metabolic information. These integrators then meaningfully transduce this condensed information into durable cell state transitions by fanning-out resource allocations toward distinct outputs that are all within the possibilities of the existing metabolic economy. Through this design, cells can incorporate diverse metabolite- or flux-sensing modules, secondary integrators, and localization or higher-order assemblies to alter response kinetics over time and space. We discuss how these inherent design constraints result in robust yet versatile cellular decision-making that can drive cell-to-cell heterogeneity. Finally, we highlight how genetic mutations in this machinery disrupt information processing through the bow tie, shifting homeostasis toward disease states.
In eukaryotes, ribosomal RNA genes (rDNA) encode the major ribosomal RNA molecules and are typically organized into a distinctive genomic structure involving tandem repetition of a polycistronic coding region. Here, we review eukaryotic rDNA organization, emphasizing the extensive, but not absolute, conservation of the canonical organization across eukaryotes. We describe exceptions to both the canonical gene structure and tandem organization and discuss important questions and hypotheses raised by this conserved organization, which is also tolerant of alternatives. Furthermore, we examine variations in rDNA copy/array number and their implications, including whether variants are likely to be adaptive, a passive consequence of ongoing cellular processes, or the outcome of interrepeat competition within rDNA arrays. Finally, we describe how recent technological advances offer great promise for overcoming the barriers imposed by the repetitive nature of rDNA and thus for improving our understanding of this fascinating region of the genome.
Centromeres are essential chromosomal loci specified epigenetically by CENP-A chromatin, yet they undergo rapid sequence turnover, structural remodeling, and occasional repositioning. In this review, we integrate recent advances enabled by long-read genome assemblies and high-resolution chromatin mapping to synthesize current understanding of centromere organization across taxa. We examine how satellite repeats, transposable elements, molecular drive, and meiotic conflict generate extreme centromere diversity. We further explore how DNA methylation and H3K9me3 heterochromatin constrain CENP-A positioning, stabilize centromeric domains, and shape boundary dynamics during centromere drift, duplication, and de novo formation. Together, these perspectives show how centromeres accommodate evolutionary change while preserving the stringent requirements of faithful chromosome segregation.
Nonessential, supernumerary B chromosomes have been an intriguing anomaly known to researchers for over a century. B chromosomes were first identified in insects and have since been discovered in hundreds of species across many different taxa. Their prevalence has made it difficult to strictly define the nature of a B chromosome due to the variety of sizes, genetic compositions, and segregation behaviors; however, with modern molecular technologies, the impact, origin, and evolutionary trajectory of these B chromosomes are coming into focus. In this review, we consolidate what is currently known about B chromosomes, including their life cycle and evolutionary trajectory, the impact of B chromosomes on their host, and how B chromosomes are transmitted to the next generation. We highlight several prominent B chromosome model systems that have led to significant advances in B chromosome biology, serving as a prologue for the exciting future of the B chromosome field and its many unknowns.
Genomic imprinting is an epigenetic phenomenon in which chromosome behavior or gene expression depends on whether an allele was paternally or maternally inherited. Imprinting is commonly associated with a placenta or an analogous organ during embryo development; however, imprinting occurs in diverse species across animal and plant life, including those that lack a placenta. Common epigenetic modifications are associated with genome imprinting across these groups, although the exact mechanisms vary across taxa. There are also commonalities surrounding the evolutionary selection for imprinting. The most well-known hypothesis is parental conflict theory, which proposes that imprinting resolves conflict over the maternal allocation of resources to the developing embryo. Shared mechanisms and functions of imprinting across diverse groups suggest that parental epigenetic asymmetries may be an inherent characteristic of sexual reproduction in species where the sperm and egg differ in size and form.
Telomeres are sequences at chromosome ends that distinguish the natural end from a DNA break. Telomeres shorten at each round of cell division because the replisome cannot completely copy both DNA strands to the very end. This shortening is counterbalanced by telomerase, which adds telomeric sequences de novo onto telomeres. The balance of shortening and lengthening is regulated to establish an equilibrium distribution of telomere lengths. If the equilibrium is perturbed, short telomeres trigger a DNA damage response that leads to cellular senescence or cell death. In humans, short telomeres cause age-related degenerative disease, while long telomeres protect against senescence and allow the continued growth of cancer cells. To target the telomere in human disease, we need a more complete understanding of how telomere length is regulated. Here, we describe pathways that regulate telomere length with a focus on the fundamental mechanisms established over the last 40 years in the yeast Saccharomyces cerevisiae.
The naked mole-rat (Heterocephalus glaber) defies mammalian norms with lifelong fertility and postnatal oogenesis. Unlike most mammals, which experience reproductive senescence due to depletion of a finite ovarian follicle pool, naked mole-rat queens maintain fertility for their entire 30+-year lifespan through multiple mechanisms, including postnatal oogenesis, an exceptionally large ovarian reserve, and maintenance of primordial germ cells into adulthood. This review explores the unique reproductive biology of naked mole-rats within the context of their eusocial lifestyle, examining how social suppression of reproduction in subordinates, the role of very-high-molecular-weight hyaluronan (vHMW-HA) in cancer resistance and tissue maintenance, and the maintenance of germline stem cell populations contribute to their extraordinary reproductive longevity. We discuss the evolutionary advantages of eusociality, mechanisms of reproductive suppression and activation, and the potential of naked mole-rats as a research model for understanding ovarian aging and developing fertility-preserving therapies in humans.
Decades of research into the noncoding transcriptome have unveiled a complex, multilayered web of molecular interactions that govern gene expression, protein synthesis, and cellular function, challenging the once-presumed linear simplicity of the flow of genetic information. In bacteria, highly diverse small RNAs (sRNAs) play a crucial role in gene expression, often acting at the heart of large regulatory networks to modulate cellular processes through direct base-pairing interactions with target messenger RNAs (mRNAs). The expression of most sRNAs is tightly controlled at the level of transcription, but RNA sponges have recently emerged as an additional layer of regulation restricting sRNA activity and abundance. By titrating sRNAs and influencing their interactions with target mRNAs and RNA-binding proteins, RNA sponges contribute to the fine-tuning of global gene expression networks. In addition, the integration of RNA sponges into functional loops promotes elegant crosstalk between major regulons at the posttranscriptional level.
Cochlear hair cells are epithelial cells that are not replaced when lost, leading to permanent hearing loss. The lack of spontaneous regeneration of hair cells is a rarity in epithelial tissues, including hair cell epithelia. Evolutionary considerations may explain why hair cell regenerative capacity of mammals was lost during the evolution of the cochlea. In parallel, at the molecular level, studies using transgenesis and developmental biology have revealed some of the key signaling molecular players that govern the development of hair cells and their neighboring supporting cells and provided candidates for manipulating the system to induce regeneration. Gene transfer technology using viruses showed proof of principle for the ability to induce the transdifferentiation of supporting cells to new hair cells, but the outcome is inconsistent and of low quantity and poor quality. Further use of modern sequencing technology should reveal additional details of gene expression and its regulation in the process of regenerating hair cell organs such as in fish, birds, and mammalian balance organs. Sequence data generated from supporting cells in mature ears with hair cell lesions, at the level of gene expression and its epigenetic regulation, will assist in designing these therapeutic interventions. Still, rebuilding a perfect new cochlea to provide normal hearing in profoundly deaf ears remains a formidable challenge.
The MAP3K dual-leucine zipper kinases are stress-sensing signaling molecules that have important roles in neuronal development and maintenance, traumatic injury, and neurodegeneration. These kinases activate signal transduction cascades and elicit distinct cellular phenotypes in response to a variety of physiological and pathological stimuli. Studies from animal and cellular models have supported their conserved functions and also highlight context and cell-type specificity. This review focuses on recent findings on the molecular landscape associated with these kinases and discusses key themes of the DLK function network in the mammalian nervous system.
Nucleus-forming jumbo bacteriophages display a surprisingly intricate replication cycle inside of bacterial host cells, challenging the long-standing paradigm of prokaryotic simplicity. The phage nucleus encloses phage DNA in a protein shell, strictly uncouples transcription from translation, and facilitates selective protein import and messenger RNA (mRNA) export, serving the same major functions as the eukaryotic nucleus. Infection of host cells by these phages begins with the formation of a transcriptionally active membrane-bound early phage infection vesicle, demonstrating that these phages are capable of constructing subcellular compartments composed of lipids and proteins. Here, we review the current body of literature revealing the complexities of nucleus-forming phages and the history of the major discoveries. Studies of these phages are revealing new insights into basic principles of subcellular organization, viral speciation, and intracellular viral competition.
The natural world is full of valuable lessons about genetic adaptation as organisms respond to changing conditions around them. Deciphering these changes is a major goal of evolutionary genetics. Advances have been made through phylogenomic approaches using the wealth of closely related genome sequences in mammals. These studies bring us lessons about the adaptive capacity allowed by the evolutionary process as well as the underlying genetic mechanisms controlling important traits. Diverse methods are now routinely used to identify the genetic basis of these adaptations. These reveal new functions of genes and regulatory regions that have responded to changes in lifestyle, such as aquatic life and flight, as well as major life history axes, such as lifespan. Phylogenomic studies have been equally revealing of specific traits that evolve in response to different selective pressures, such as hair formation and vocal learning. These approaches continue to develop to overcome challenges inherent in information-poor regulatory regions to find changes to gene regulatory networks as well. The development of these approaches is expected to accelerate as new tools, such as machine learning models, are incorporated and deployed on ever denser phylogenies containing new interesting traits.
The brain has a remarkable ability to adapt its function in response to both environmental and internal cues. The cellular composition of the brain is largely static after birth; thus, persistent experience-dependent changes in brain function depend on altered programs of gene expression that result in the plasticity of circuit connectivity and network function. High-throughput sequencing studies have comprehensively cataloged stimulus-dependent programs of gene expression in the brain. The current challenge is to integrate this information in the context of specific cells and circuits to understand the mechanisms by which transcriptional regulation coordinates adaptive plasticity of the brain and behavior. Here, I review molecular genetics studies that reveal how neuronal activity-regulated gene products orchestrate intricate cellular and intercellular adaptations in response to changes in patterns of brain activity. I also discuss examples of genetic mutations that impair experience-dependent transcriptional plasticity in the context of neurodevelopmental disorders.
