Maternal starvation primes progeny response to nutritional stress.

Organisms adapt to environmental changes in order to survive. Mothers exposed to nutritional stresses can induce an adaptive response in their offspring. However, the molecular mechanisms behind such inheritable links are not clear. Here we report that in Drosophila, starvation of mothers primes the progeny against subsequent nutritional stress. We found that RpL10Ab represses TOR pathway activity by genetically interacting with TOR pathway components TSC2 and Rheb. In addition, starved mothers produce offspring with lower levels of RpL10Ab in the germline, which results in higher TOR pathway activity, conferring greater resistance to starvation-induced oocyte loss. The RpL10Ab locus encodes for the RpL10Ab mRNA and a stable intronic sequence RNA (sisR-8), which collectively repress RpL10Ab pre-mRNA splicing in a negative feedback mechanism. During starvation, an increase in maternally deposited RpL10Ab and sisR-8 transcripts leads to the reduction of RpL10Ab expression in the offspring. Our study suggests that the maternally deposited RpL10Ab and sisR-8 transcripts trigger a negative feedback loop that mediates intergenerational adaptation to nutritional stress as a starvation response.

Circular sisRNA identification and characterisation.

Stable Intronic Sequence RNA (sisRNA) is a relatively new class of non-coding RNA. Found in many organisms, these sisRNA produced from their host genes are generally involved in regulatory roles, controlling gene expression at multiple levels through active involvement in regulatory feedback loops. Large scale identification of sisRNA via genome-wide RNA sequencing has been difficult, largely in part due to its low abundance. Done on its own, RNA sequencing often yields a large mass of information that is ironically uninformative; the potential sisRNA reads being masked by other highly abundant RNA species like ribosomal RNA and messenger RNA. In this review, we present a practical workflow for the enrichment of circular sisRNA through the use of transcriptionally quiescent systems, rRNA-depletion, and RNase R treatment prior to deep sequencing. This workflow allows circular sisRNA to be reliably detected. We also present various methods to experimentally validate the circularity and stability of the circular sisRNA identified, as well as a few methods for further functional characterisation.

Q&A with Jun Wei Pek and Amanda Yunn Ee Ng.

Investigator Jun Wei Pek (J.P.) and graduate student Amanda Yunn Ee Ng (A.Y.) spoke to Cell Reports about their scientific journeys and love of science, their work on gene expression regulation during reproductive development, and challenges encountered during the pandemic.

Genetic compensation between ribosomal protein paralogs mediated by a cognate circular RNA.

Inter-regulation between related genes, such as ribosomal protein (RP) paralogs, has been observed to be important for genetic compensation and paralog-specific functions. However, how paralogs communicate to modulate their expression levels is unknown. Here, we report a circular RNA involved in the inter-regulation between RP paralogs RpL22 and RpL22-like during Drosophila spermatogenesis. Both paralogs are mutually regulated by the circular stable intronic sequence RNA (sisRNA) circRpL22(NE,3S) produced from the RpL22 locus. RpL22 represses itself and RpL22-like. Interestingly, circRpL22 binds to RpL22 to repress RpL22-like, but not RpL22, suggesting that circRpL22 modulates RpL22's function. circRpL22 is in turn controlled by RpL22-like, which regulates RpL22 binding to circRpL22 to indirectly modulate RpL22. This circRpL22-centric inter-regulatory circuit enables the loss of RpL22-like to be genetically compensated by RpL22 upregulation to ensure robust male germline development. Thus, our study identifies sisRNA as a possible mechanism of genetic crosstalk between paralogous genes.

VAP-mediated membrane-tethering mechanisms implicate ER-PM contact function in pH homeostasis.

Vesicle-associated membrane protein (VAMP)-associated proteins (VAPs) are highly conserved endoplasmic reticulum (ER)-resident proteins that establish ER contacts with multiple membrane compartments in many eukaryotes. However, VAP-mediated membrane-tethering mechanisms remain ambiguous. Here, focusing on fission yeast ER-plasma membrane (PM) contact formation, using systematic interactome analyses and quantitative microscopy, we predict a non-VAP-protein direct binding-based ER-PM coupling. We further reveal that VAP-anionic phospholipid interactions may underlie ER-PM association and define the pH-responsive nature of VAP-tethered membrane contacts. Such conserved interactions with anionic phospholipids are generally defective in amyotrophic lateral sclerosis-associated human VAPB mutant. Moreover, we identify a conserved FFAT-like motif locating at the autoinhibitory hotspot of the essential PM proton pump Pma1. This modulatory VAP-Pma1 interaction appears crucial for pH homeostasis. We thus propose an ingenious strategy for maintaining intracellular pH by coupling Pma1 modulation with pH-sensory ER-PM contacts via VAP-mediated interactions.

Plasma Membrane Furrows Control Plasticity of ER-PM Contacts.

The plasma membrane (PM) forms extensive close junctions with the cortical endoplasmic reticulum (cER) in many cell types, ranging from yeast to mammals. How cells modulate structural plasticity of ER-PM contacts to accommodate space-demanding cortical events is largely unknown. Here, we report a role for eisosome-driven PM furrows in regulating ER-PM contact plasticity in fission yeast. We demonstrate that eisosome-coated PM invaginations function to stabilize local ER-PM contacts and attenuate cER remodeling dynamics through electrostatic Scs2-Pil1 interactions. We also identify divergent roles of ER-shaping proteins in controlling cER remodeling capacity and ER-PM contact plasticity. Furthermore, we show that eisosome organization is responsive to PM tension variations during active PM remodeling, which may enable adaptive control of ER-PM contact plasticity to potentially coordinate with space-demanding PM events. We thus propose a cellular strategy of modulating membrane contact plasticity by deploying sensory elements at contact sites.

ER-PM Contacts Restrict Exocytic Sites for Polarized Morphogenesis.

Spatial control of exocytosis underlies polarized cell morphogenesis. In rod-shaped fission yeast, exocytic vesicles are conveyed along the actin cytoskeleton by myosin V motors toward growing cell ends [1, 2], the major sites for exocytosis. However, actomyosin-based vesicle delivery is dispensable for polarized secretion and cylindrical cell shape of fission yeast [3]. Thus, additional mechanisms should function in the spatial confinement of exocytosis. Here we report a novel role of endoplasmic reticulum (ER)-plasma membrane (PM) contacts in restricting exocytic sites for polarized fission yeast morphogenesis. We show that fission yeast cells deficient in both ER-PM contacts and actomyosin-based secretory vesicle transport display aberrant globular cell shape due to delocalized exocytosis. By artificially manipulating the strength and extent of ER-PM contacts in wild-type and mutant cells that exhibit induced ectopic exocytosis, we demonstrate that exocytosis and ER-PM contact formation are spatially incompatible. Furthermore, extensive ER-PM junctions at the non-growing lateral cell cortex prevent the PM from exocytic vesicle tethering and hence attenuate growth potential at cell sides. We thus propose that ER-PM contacts function as a new morphogenetic module by limiting exocytosis to growing cell tips in fission yeast. A similar mechanism could apply to other cell types with prominent ER-PM contacts.

Germline Stem Cell Heterogeneity Supports Homeostasis in Drosophila.

Adult and embryonic stem cells exhibit fluctuating gene expression; however, the biological significance of stem cell heterogeneity is not well understood. We show that, in Drosophila, female germline stem cells (GSCs) exhibit heterogeneous expression of a GSC differentiation-promoting factor Regena (Rga). The Drosophila homolog of human SON, dsn, is required to maintain GSC heterogeneity by suppressing sustained high levels of Rga. Reducing the expression of Rga in dsn mutants restores GSC heterogeneity and self-renewal. Thus, GSC heterogeneity is linked to GSC homeostasis.

DIP1 modulates stem cell homeostasis in Drosophila through regulation of sisR-1.

Stable intronic sequence RNAs (sisRNAs) are by-products of splicing and regulate gene expression. How sisRNAs are regulated is unclear. Here we report that a double-stranded RNA binding protein, Disco-interacting protein 1 (DIP1) regulates sisRNAs in Drosophila. DIP1 negatively regulates the abundance of sisR-1 and INE-1 sisRNAs. Fine-tuning of sisR-1 by DIP1 is important to maintain female germline stem cell homeostasis by modulating germline stem cell differentiation and niche adhesion. Drosophila DIP1 localizes to a nuclear body (satellite body) and associates with the fourth chromosome, which contains a very high density of INE-1 transposable element sequences that are processed into sisRNAs. DIP1 presumably acts outside the satellite bodies to regulate sisR-1, which is not on the fourth chromosome. Thus, our study identifies DIP1 as a sisRNA regulatory protein that controls germline stem cell self-renewal in Drosophila.Stable intronic sequence RNAs (sisRNAs) are by-products of splicing from introns with roles in embryonic development in Drosophila. Here, the authors show that the RNA binding protein DIP1 regulates sisRNAs in Drosophila, which is necessary for germline stem cell homeostasis.