5430 research outputs found
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Ulysses Quartet
No full textUlysses Quartet, string quartet. Celebrating debut album release: Shades of Romani Folklore : Janácek: Quartet No. 2, “Intimate Letters”; Beethoven: Quartet No. 9, Op. 59 No. 3
Photograph by Lauren Desberghttps://digitalcommons.rockefeller.edu/tri-institutional-noon-recitals/1010/thumbnail.jp
On the Origins of Genetic Novelty in Drosophila
Full text linkEvolution is at its heart the study of variation: which variants survive and even thrive across generations, and why? Behind this lies the fundamental question of the origins of novelty, for there cannot be variation without a source of new variants. Understanding how novelty emerges, then, is a crucial problem of basic relevance in evolutionary biology. In this thesis, I examine two aspects regarding the origins of novelty: first, how new proteins originate and subsequently evolve; second, how chromatin accessibility maintains evolutionary lability while remaining conserved across broad sequence divergence. The study of the origins of new genes has flourished in the genomic era with the sequencing of genomes. De novo gene birth, where a previously non-genic genomic sequence becomes genic through evolution, is a particularly exciting mechanism for the origin of new genes. While many de novo genes have been proposed to be protein-coding, and in several cases have been experimentally shown to yield protein products, their systematic study as proteins has been hampered by doubts regarding the translation of their transcripts without the experimental observation of protein products. Using a systematic, ORF-focused mass-spectrometry-first computational approach, I identify protein evidence for almost 1000 unannotated open reading frames with evidence of translation (utORFs) in the model organism Drosophila melanogaster. Using an integrative comparative genomics approach, I then identify different properties and evolutionary patterns amongst these utORFs, including their implied gene ages. My results suggest that there is substantial unappreciated diversity in de novo protein evolution: many more may exist than have been previously appreciated; there may be divergent evolutionary trajectories; and de novo proteins may be gained and lost frequently. Turning away from genes and to their regulation, I next examine the evolution of regulatory regions in the genome as part of a joint collaboration. The evolution of regulation plays a critical role in shaping the diversity of life, as the diversity of protein-coding sequences is insufficient to solely yield the observed diversity in phenotypes. Despite substantial genetic divergence, chromatin accessibility in the head and testis of Drosophila is generally conserved at the phenotypic level between species. Applying deep neural networks as a tool to investigate the sequence determinants that govern chromatin accessibility, we find that hybrid convolution-attention neural networks can predict ATAC-seq peaks using only local DNA sequences as input. This predictive capability is maintained across species, even in very distantly related ones, suggesting that these models capture conserved sequence-dependent processes that determine chromatin accessibility. Turning to examine regions with species-specific changes in chromatin accessibility, we find that their orthologous inaccessible regions in other species have unusual model outputs, suggesting that these regions may be ancestrally poised for evolution. Finally, using an array of in silico genetics experiments, we find that chromatin accessibility is simultaneously robust to random mutation and labile to extremely strong selection. Together, these results illuminate aspects regarding the origins of evolutionary novelty and suggest new directions for further experimental and computational studies. All in all, there likely does not exist a single characteristic model of evolution, but rather complex origins and diverse evolutionary mechanisms
Mechanical Manipulation of Eukaryotic Chromatin by DNA-Binding Proteins
Full text linkThe eukaryotic genome is organized in many length scales, reflecting the intricacy associated with evolution of complex biological processes. This organization serves to exert spatiotemporal control of many DNA-transacting processes such as gene expression. Despite emerging progress, the biophysical mechanism underpinning eukaryotic genome organization remains an outstanding question in the field. In this thesis, I describe mechanistic insights on genome organization and its regulation through leveraging single-molecule biophysical techniques. In Chapter 2, I characterize the dynamic interplay of Sox2 and H1 DNA binding activity. Both families constitute large classes of chromatin and DNA binding proteins that have been historically thought to be antagonistic regulators of each other, but the underlying mechanism is not well understood. Using single-molecule fluorescence-based approach, I show that Sox2 and H1 regulate each other\u27s loading rate on bare DNA and nucleosomes in a concentrationdependent fashion. In particular, H1 promotes the Sox2\u27s loading rate at low concentration but inhibits Sox2\u27s loading rate at higher concentration. Together, these findings highlight the potential importance of tuning protein concentrations in the regulation of gene expression. In Chapter 3, I characterize the mechanical effects on DNA from biomolecular condensation, which has recently emerged as an important mechanism of gene regulation. In particular, I investigate how Sox2, which constitutes an important pioneer factor implicated in the maintenance of pluripotency, forms co-condensates with DNA and chromatin components. The described results present three conceptual advances to the field: 1) protein:DNA co-condensation can generate high forces, up to ~7 pN, comparable to other reported cellular forces, 2) the intrinsically disordered regions (IDRs) are dispensable for condensate formation but necessary for high force generation, and lastly, 3) chromatin components, such as nucleosomes and linker histone H1, attenuate the force generating capacity of Sox2 condensates and reduce their mechanical effects on DNA via colocalization. The results add to the growing body of studies that the chromatin architecture can function as a mechanical sink that regulates cellular forces. In Chapter 4, I visualize the DNA compaction activity of the structural maintenance of chromosome (SMC) complex 5/6, an important ATPase implicated in regulating DNA repair and replication. Despite emerging insights on the SMC5/6 complex\u27s cellular function, the molecular mechanism behind the complex\u27s DNA binding activity is not well understood. Using singlemolecule fluorescence method, I present data showing the SMC5/6 complex can compact DNA in a tether-like mechanism without the requirement for ATP hydrolysis. Thus, this work adds a novel perspective towards understanding the molecular mechanism of the SMC5/6 complex. Together, the thesis below contributes novel mechanistic insights towards understanding genome organization and regulation. I reveal unique modes of DNA compaction spanning from transcription factors to ATPase molecular motor as well as associated regulatory mechanism. Due to the implications in diverse molecular pathways, aberrant regulation of genome organization underpins many disease processes. Thus, these findings help establish a molecular basis towards understanding many disease mechanisms, which can be potentially exploited for therapeutic avenues
Details of the Exhibit
No full textDetails of the exhibit E.G.D. Cohen: A Leader in Statistical Physics
Idea, design - Olga Nilova, Special Collections Librarian
Photograph - Lubosh Stepanekhttps://digitalcommons.rockefeller.edu/cohen-leader-in-statistical-physics/1003/thumbnail.jp
A Gain-of-Function Role of Apolipoprotein E2 in Melanoma Progression
Full text linkGenetic polymorphism of the secreted lipid transporter apolipoprotein E (APOE) plays important roles in the development of atherosclerosis and Alzheimer\u27s disease. More recently, three common APOE alleles have been implicated as modulators of melanoma progression and survival. Melanoma patients born with a copy of the APOE4 allele exhibit improved disease survival and responses to immunotherapy. Conversely, APOE2 allele carriers experience substantially worsened survival outcomes compared to APOE4 carriers and APOE3 homozygotes. These survival differences are partly governed by effects on the immune system, as the APOE4 genotype augments anti-tumor immunity. However, APOE variants also exert direct suppressive effects on melanoma cell metastatic behavior in an APOE4\u3eAPOE3\u3eAPOE2 order of potency. The molecular processes underlying the melanoma cell-intrinsic response to APOE variants are poorly characterized. In this thesis I describe the generation and characterization of a genetically engineered mouse model for melanoma that expresses each of the human APOE alleles. I show that this autochthonous model closely recapitulates the APOE2\u3eAPOE3\u3eAPOE4 order of melanoma progression observed in human patients. Transcriptomic analysis of tumors derived from this genetic model revealed upregulation of mRNA translation in APOE2 melanomas relative to APOE4 melanomas. After experimental examination of the effects of APOE variants on melanoma translational efficiency, I report the discovery that APOE2 acts in a gain-of function manner to enhance pro-tumorigenic protein synthesis in melanoma cells. Melanoma cell-specific deletion of the APOE receptor LRP1 in the genetic mouse model abolished differences in tumor growth, metastasis, and protein synthesis between the APOE2 and APOE4 genotypes, thus revealing a melanoma cell-intrinsic APOE2/LRP1 axis that serves to promote melanoma progression. Analysis of a melanoma patient RNA-Seq dataset demonstrated upregulation of mRNA translation processes in APOE2 patient tumors, thus providing clinical relevance for these findings. Altogether, this thesis identifies a potentially therapeutically targetable pathway in melanoma and reveals a novel gain-of-function role of the APOE2 allele, which may have implications for other diseases impacted by APOE genetics
Anteromedial Thalamus Gates the Selection & Stabilization of Long-Term Memories
Full text linkThe hippocampus is necessary for the initial encoding and recent storage of memories. Under the standard model of systems consolidation, it is thought that the memory trace eventually reorganizes from the hippocampus to a distributed cortical network, with the anterior cingulate cortex playing a central role in remote memory retrieval. However, little is known about the mechanisms responsible for coordinating this process. Additionally, the intermediate memory representations in the brain and the circuits that might gate and select memories for permanent storage remain unknown. To facilitate the longitudinal tracking of memory circuits in the brain, we first developed a novel virtual reality-based behavioral task for mice. We used fiber photometry to record neural activity from multiple regions across the brain throughout consolidation and identified a unique and significant neural correlate of memory in anterior thalamus that emerged in training and persisted for weeks. Inhibition of the anteromedial thalamus to anterior cingulate cortex projections during training resulted in substantial memory consolidation deficits, whereas excitation of the same projection drove the consolidation of otherwise unconsolidated memories. To gain mechanistic understanding into the role of anteromedial thalamus during consolidation, we developed a technique for imaging three brain regions simultaneously with single-cell resolution in the behaving mouse. Using this technology, we uncovered that the anteromedial thalamus rapidly forms preferential tuning to consolidated memories, and establishes inter-regional correlations that are causally required for synchronizing and stabilizing cortical representations to achieve successful memory consolidation
Bass Dining Commons Terrace
No full textBass Dining Commons Terrace at night, 2023
Photo by Juan Rodriquezhttps://digitalcommons.rockefeller.edu/river_campus/1072/thumbnail.jp
Harmony Zhu, Piano
No full textHarmony Zhu, 17-year-old pianist and composer, performed Chopin: Ballade No. 4 in F Minor, Op. 52; Chopin: Nocturne in C-sharp Minor Op. 27 No. 1; Chopin: Sonata No. 3 in B Minor, Op. 58; Scriabin: Sonata No. 2 in G-sharp Minor, Op. 19; Camille Pepin: Iridescence–glace ‘climate change cycle’; Kapustin: Variations, Op. 41
Photo Courtesy of Harmony Zhuhttps://digitalcommons.rockefeller.edu/tri-institutional-noon-recitals/1009/thumbnail.jp
Caspary Auditorium
No full textCaspary Auditorium, winter 2023
Photo by Juan Rodriguezhttps://digitalcommons.rockefeller.edu/campus/1093/thumbnail.jp
The Search for Regulatory Mutations in Gitelman Syndrome
Full text linkThe development of whole exome and whole genome sequencing technologies has allowed geneticists to gradually uncover a wide spectrum of rare, deleterious mutations with large effect sizes, which are responsible for Mendelian diseases. Roughly 70% of human genes are single copy and have orthologs across the vertebrate lineage, suggesting that they are under purifying selection. This suggests that at least 10,000 genes will have Mendelian phenotypes when mutated but have yet to be discovered1. Exhaustive research efforts have been directed at finely categorizing the coding, and more recently noncoding, genome. The actual number of large effect noncoding mutations, and of particular importance given their scarcity, mutations in functional regulatory regions have yet to be determined. Ideal prototypes to study these variants are recessive Mendelian diseases that are relatively common in the population, caused only by biallelic mutations in one gene, have virtually 100% penetrance with consistent phenotypic expressivity with recessive genotypes, and few, if any, phenotypic features in subjects with heterozygous mutant alleles. To date approximately 10 genes (SLC12A3, SLC12A1, KCNJ1, CLCNKB, BSND, MAGED2, KCNJ10, CLDN10, CLDN16, CLDN19) have been linked to recessive salt wasting disorders. Gitelman syndrome (GS) is a recessive Mendelian kidney disorder caused by deleterious mutations in SLC12A3 and has an incidence of approximately 1 in 40,0002. Clinical hallmarks of GS include hypotension, hypokalemia, hypomagnesemia, metabolic alkalosis, and hypomagnesemia. To further decipher the full contribution of regulatory mutations to Mendelian disorders, blood samples from a cohort of 387 patients referred to us by nephrologists for suspected salt-wasting disorders were subjected to whole-exome analysis and subsequent whole-genome sequencing analysis on a subset of these patients. Whole exome sequencing analysis on the 387 electrolyte-wasting subjects identified 508 deleterious coding mutations in the 10 genes linked to Mendelian electrolyte-wasting in 254 subjects. A total of 17 patients with Gitelman syndrome harbored only monoallelic, deleterious mutations in SLC12A3 and were subjected to whole genome sequencing to identify any putative large effect noncoding variants in SLC12A3. Whole genome sequencing analyses identified a total of 14 mutations outside of the coding regions in SLC12A3. These 14 mutations include 7 large deletions of two or more exons, 2 deep intronic mutations that introduce cryptic donor splice sites, 1 in-frame 6 base pair cryptic insertion at the intron-exon boundary, 3 mutations at noncanonical splice regions that disrupt conventional splicing, and 1 mutation within a putative SLC12A3 cis-regulatory site. A luciferase reporter assay revealed a drastic decrease in reporter activity for the regulatory variant and indicates this variant introduces a novel repressor site in intron 1 of SLC12A3. Collectively, whole exome and whole genome analyses identified biallelic mutations in 70% of all subjects with suspected electrolyte-wasting that likely represent causal genetic lesions, with regulatory variants only comprising ~0.2% of deleterious alleles