Biology subjects

Berlin, S.

Publications and source records attributed to Berlin, S..

6 recordsLinked to original sources

bioRxiv2025

Epigenetic inheritance of complex learning abilities in the mammalian brain

For several decades, the question of whether cognitive and learning capacities can be inherited through non-genetic mechanisms has been the subject of ongoing debate. Here, we provide the first evidence of transgenerational inheritance of enhanced ability to learn complex tasks in the mammalian rodent brain. These inherited learning enhancements are not limited to specific stimuli, sensory modalities, or learning paradigms. Using behavioral, cellular biophysical, methylomics, genetics and molecular methods, we find that the inherited epigenetic modifications reflect an enhanced neuronal learning state, driven by increased intrinsic neuronal excitability in most pyramidal neurons in the relevant neuronal networks. This enhancement is mediated by persistent downregulation of the muscarinic M-current and is associated with widespread changes in DNA methylation, notably within coding genes associated with the M-current, the Kv7 pathway, in the hippocampi of trained F0 rats, as well as in non-coding RNAs in their sperm samples. Remarkably, a significant portion of these DNA methylation changes were also observed in the hippocampi of their untrained F1 offspring. These findings suggest that complex learning abilities can be inherited in the mammalian brain, as the offspring of trained rodents are born with the biophysical modifications that enable them to become super-learners, the exact change that occurs in their parents brains only after the rule learning.

neuroscience↗

bioRxiv2024

Targeting FUS-ALS aggregation with Proteasome Inhibitors

ALS, Amyotrophic lateral sclerosis, a devastating neurodegenerative disease (ND) with no cure, is often caused by abnormal cytosolic aggregation of RNA-binding proteins, the most well-known of which are TDP-43 and FUS. The proteasome is considered one of the major systems that degrades misfolded, including ND-associated, proteins, thereby acting to reduce aggregation, while inhibition of the proteasome increases aggregation. Unexpectedly, we found that proteasome inhibitor treatment significantly reduced ALS-associated mutant FUS aggregation in cells and in primary neurons. This is in sharp contrast to most other ND-associated aggregating proteins, including Huntingtin and TDP-43, for which proteasome inhibitors enhanced aggregation. We further found that this inhibitory effect is dependent on the transcription factor HSF1, suggesting that the underlying mechanism of this effect is transcriptionally-mediated. Since heat shock treatment did not show any effect on FUS aggregation, we hypothesized that proteasome inhibitors elicit a transcriptional program distinct of that of heat shock, which is protective of FUS aggregation. We identified BAG3, a co-chaperone that cooperates with HSP70 in reducing FUS aggregation, as a significant mediator of this effect. We therefore propose BBB-permeable proteasome inhibitors as a potential therapy specific to ALS-FUS.

molecular biology↗

bioRxiv2023

A novel polycistronic method tailored for engineering split GECIs

We assessed the feasibility of using stop-codons as means to obtain polycistronic expression in eukaryotic cells. We show robust bicistronic expression of different open reading frames (ORFs), when these are cloned in-sequence and simply separated by stop codons (in-or out-of-frame), in heterologous expression systems and primary neurons. We further find this method to support polycistronic expression of three stop-codon-separated ORFs in vivo, which guided us to develop a technicolor Genetically-Encoded Functional Rainbow Indicators (GEFRIs) for monitoring cellular morphology and neuronal firing, concomitantly. These findings guided us to develop a new technique we denote SPLIT--Stop-codon mediated Polycistronic Induction in HeTerologous expression systems-- for rapid and easy development of fragmented proteins by the sole use of stop codons. We validated the SPLIT method by generating several new split-GFP variants, then engineer a palette of functional split-GCaMP6s variants and, lastly, generate a split ca2+-probe localized at ER and mitochondria junctions, denoted split-MEGIC. With the use of the probe, we show presence and activity of mito-ER contact sites within individual dendritic spines. Split-MEGIC can thereby be imaged by two-photon excitation in vivo in mice brains and, by standard confocal microscope in transgenic zebrafish larvae. Together, we explore non-canonical translation mechanisms and show these to be highly pervasive in various cell types in vitro and in vivo. We harness translation re-initiation to express multiple ORFs, to engineer rainbow indicators and to swiftly produce functional split-proteins and probes.

neuroscience↗

bioRxiv2022

Two extreme Loss-of-Function GRIN2B-mutations are detrimental to tri-heteromeric NMDAR-function, but rescued by pregnanolone-sulfate

Mutations within various N-methyl-D-aspartate receptor (NMDAR) subunits are tightly associated with severe pediatric neurodevelopmental disorders and encephalopathies (here denoted GRINopathies), for which there are no treatments. NMDARs are tetrameric receptors and can be found at the membrane of neurons in various compositions, namely in di- or tri-heteromeric forms. The GluN2B subunit appears very early in development and, therefore, prenatally this subunit is predominantly found within di-heteromeric receptors, exclusively composed of the GluN1 and GluN2B subunits. Postnatally, however, the GluN2A subunit undergoes rapid increase in expression, giving rise to the appearance of tri-heteromers containing the GluN1, GluN2A and GluN2B-subunits. The latter are emerging as the principal receptor-type postnatally. Despite more than a decade of research of numerous GRINopathies, not much is known regarding the effect of GRIN variants when these are assembled within tri-heteromers. Here, we have systematically examined how two de novo GRIN2B variants (G689C and G689S) affect the function of di- and tri-heteromers. We show that whereas a single mutated subunit readily instigates a dominant negative effect over glutamate affinity of tri-heteromers, it does not dominate other features of the receptor, notably potentiation by pregnanolone-sulfate (PS). This led us to explore PS as a potential treatment for these two severe loss-of-function (LoF) mutations in cultured neurons, in which case we indeed find that the neurosteroid rescues current amplitudes. Together, we present the first report to examine LoF GRIN2B mutations in the context of di- and tri-heteromeric receptors. We also provide the first demonstration of the positive outcome of the use of a GRIN2B-relevant potentiator in the context of tri-heteromers. Our results highlight the importance of examining how different mutations affect features in various receptor subtypes, as these could not have been deduced from observations performed on purely di-heteromers. Together, our study contributes to the ongoing efforts invested towards understanding the pathophysiology of GRINopathies as well as provides insights towards a potential treatment.

neuroscience↗

bioRxiv2021

Differential roles for DNAJ isoforms in HTT-polyQ and mutant FUS aggregation modulation revealed by chaperone network screens

Protein aggregation is a hallmark of many neurodegenerative diseases1,2. In order to cope with misfolding and aggregation, cells have evolved an elaborate network of molecular chaperones, composed of different families3. But while chaperoning mechanisms for different families are well established, functional and regulatory diversification within chaperone families is still largely a mystery4,5. Here we decided to explore chaperone functional diversity, through the lens of pathological aggregation. We revealed that different naturally-occurring isoforms of DNAJ chaperones showed differential effects on different types of aggregates. We performed a chaperone screen for modulators of two neurodegeneration-related aggregating proteins, the Huntingtons disease-related HTT-polyQ, and the ALS-related mutant FUS (mutFUS). The screen identified known modulators of HTT-polyQ aggregation6,7, confirming the validity of our approach. Surprisingly, modulators of mutFUS aggregation were completely different than those of HTT-polyQ. Interestingly, different naturally-occurring isoforms of DNAJ chaperones had opposing effects on HTT-polyQ vs. mutFUS aggregation. We identified a complex of the full length (FL) DNAJB14 and DNAJB12 isoforms which substantially alleviated mutFUS aggregation, in an HSP70-dependent manner. Their naturally occurring short isoforms were unable to form the complex, nor to interact with HSP70, and lost their ability to reduce mutFUS aggregation. In contrast, the short isoform of DNAJB12 significantly alleviated HTT-polyQ aggregation, while DNAJB12-FL aggravated HTT-polyQ aggregation. Finally, we demonstrated that full-length DNAJB14 ameliorated mutFUS aggregation compared to DNAJB14-short in primary neurons. Together, our data unraveled distinct molecular properties required for aggregation protection in different neurodegenerative diseases, and revealed a new layer of complexity of the chaperone network elicited by naturally occurring J-protein isoforms, highlighting functional diversity among the DNAJ family.

molecular biology↗

bioRxiv2019

Single-molecule genome assembly of the Basket Willow, Salix viminalis, reveals earliest stages of sex chromosome expansion

Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes and this leads to a range of non-adaptive modifications causing the gradual degeneration and gene loss on the sex-limited chromosome. However, because studies on sex chromosomes have primarily focused on old and highly differentiated sex chromosomes, the causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear. Here, we use long- and short-read single molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W divergence, largely the result of the accumulation of single nucleotide polymorphisms in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although a few genes present on the Z have already been lost from the W. Furthermore, we use multiple lines of evidence to test for inversions, which have long been assumed to halt recombination between the sex chromosomes. Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation.

evolutionary biology↗