A5033032163- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- Genetics, Aging, and Longevity in Model Organisms
- CRISPR and Genetic Engineering
- RNA Interference and Gene Delivery
- Mitochondrial Function and Pathology
- SARS-CoV-2 and COVID-19 Research
- Viral gastroenteritis research and epidemiology
- Genomics and Chromatin Dynamics
- ATP Synthase and ATPases Research
- Chromosomal and Genetic Variations
- Viral Infections and Immunology Research
- Pneumonia and Respiratory Infections
- Galectins and Cancer Biology
- Muscle Physiology and Disorders
- Peptidase Inhibition and Analysis
- Helicobacter pylori-related gastroenterology studies
- Advanced biosensing and bioanalysis techniques
- Genetic Neurodegenerative Diseases
- Veterinary medicine and infectious diseases
- Respiratory viral infections research
- DNA Repair Mechanisms
- Streptococcal Infections and Treatments
- RNA regulation and disease
The University of Texas at Austin
2019-2024
Stanford University
2015-2021
University of Massachusetts Chan Medical School
2011
Bilkent University
2005-2008
Elucidating the consequences of genetic differences between humans is essential for understanding phenotypic diversity and personalized medicine. Although variation in RNA levels, transcription factor binding, chromatin have been explored, little known about global translation its determinants. We used ribosome profiling, sequencing, mass spectrometry to perform an integrated analysis lymphoblastoid cell lines from a diverse group individuals. find significant RNA, translation, protein...
Viruses rely on the host translation machinery to synthesize their own proteins. Consequently, they have evolved varied mechanisms co-opt for survival. SARS-CoV-2 relies a nonstructural protein, Nsp1, shutting down translation. However, it is currently unknown how viral proteins and factors critical replication can escape global shutdown of Here, using novel FACS-based assay called MeTAFlow, we report dose-dependent reduction in both nascent protein synthesis mRNA abundance cells expressing...
ABSTRACT Characterization of shared patterns RNA expression between genes across conditions has led to the discovery regulatory networks and novel biological functions. However, it is unclear if such coordination extends translation, a critical step in gene expression. Here, we uniformly analyzed 3,819 ribosome profiling datasets from 117 human 94 mouse tissues cell lines. We introduce concept Translation Efficiency Covariation (TEC), identifying coordinated translation types. nominate...
Viruses rely on the host translation machinery to synthesize their own proteins. Consequently, they have evolved varied mechanisms co-opt for survival. SARS-CoV-2 relies a non-structural protein, Nsp1, shutting down translation. However, it is currently unknown how viral proteins and factors critical replication can escape global shutdown of Here, using novel FACS-based assay called MeTAFlow, we report dose-dependent reduction in both nascent protein synthesis mRNA abundance cells expressing...
Elucidating the consequences of genetic differences between humans is essential for understanding phenotypic diversity and personalized medicine. Although variation in RNA levels, transcription factor binding chromatin have been explored, little known about global translation its determinants. We used ribosome profiling, sequencing, mass spectrometry to perform an integrated analysis lymphoblastoid cell lines from a diverse group individuals. find significant RNA, translation, protein levels...
Interorgan communication is crucial for multicellular organismal growth, development, and homeostasis. Cell nonautonomous inhibitory cues, which limit tissue-specific growth alterations, are not well characterized due to cell ablation approach limitations. In this study, we employed the auxin-inducible degradation system in C. elegans temporally spatially modulate ribosome biogenesis, through depletion of essential factors (RPOA-2, GRWD-1, or TSR-2). Our findings reveal that embryo-wide...
The nucleolus is a large nuclear body that serves as the primary site for ribosome biogenesis. Recent studies have suggested it also plays an important role in organizing chromatin architecture. However, to establish causal relationship between nucleolar assembly and architecture, genetic tools are required disrupt In this study, we used ATAC-seq investigate changes accessibility upon specific depletion of two biogenesis components, RPOA-2 GRWD-1, model organism Caenorhabditis elegans. To...
Chromatin architecture is a fundamental mediator of genome function. Fasting major environmental cue across the animal kingdom. Yet, how it impacts on 3D organization unknown. Here, we show that fasting induces reversible and large-scale spatial reorganization chromatin in
Non-canonical intronic variants are a poorly characterized yet highly prevalent class of alterations associated with Mendelian disorders. Here, we report the first RNA expression and splicing analysis from family whose members carry non-canonical splice variant in an intron RPL11 (c.396 +3A>G). This mutation is causative for Diamond Blackfan Anemia (DBA) this despite incomplete penetrance variable expressivity. Our analyses revealed complex pattern disruptions many novel junctions RPL11....
The group of genetic ribosome biogenesis abnormalities known as ribosomopathies result from single copy loss translation machinery components and are implicated in an array disease symptoms such bone marrow failure anemia. Among four tested ribosomal protein genes to model C. elegans, we found that rps-10 exhibits a distinct phenotype characterized by reduced oxygen consumption, mitochondrial membrane potential, depletion energy indicated ATP/ADP ratios. To investigate whether the...
Germline homeostasis is essential for the accurate transmission of genetic information reproductive and evolutionary success. Ensuring germline in Caenorhabditis elegans involves preserving mitotic, transition, meiotic zones along each gonadal arm. This process an expected shift as germ cells transition from proliferation to meiosis, moving a heterochromatic mitotic zone condensed chromosome formation zone. C. exhibit simplistic composition: nucleus enveloped by partially open membrane,...
Ribosome biogenesis is an essential process that has been shown to play a role in regulating the health and lifespan of organism. Reduced ribosome biogenesis, conjunction with reduced nucleolar size linked increase lifespan. RNA Polymerase (Pol) I responsible for transcription pre-ribosomal (rRNA), integral assembly. The demand ribosomes means Pol accounts large fraction all activity cell. In this study, genomically altered lab-grown strain Caenorhabditis elegans auxin-responsive degron tag...
ABSTRACT The interplay between ribosomal protein composition and mitochondrial function is essential for sustaining energy homeostasis. Precise stoichiometric production of proteins crucial to maximize synthesis efficiency while reducing the costs cell. However, impact this balance on ATP generation, morphology remains unclear. Particularly, loss a single copy gene observed in Mendelian disorders like Diamond Blackfan Anemia common somatic tumors, yet implications imbalance dynamics are...
The interplay between ribosomal protein (RP) composition and mitochondrial function is essential for energy homeostasis. Balanced RP production optimizes synthesis while minimizing costs, but its impact on functionality remains unclear. Here, we investigated haploinsufficiency genes (rps-10, rpl-5, rpl-33, rps-23) in Caenorhabditis elegans corresponding reductions human lymphoblast cells. Significant morphological differences, upregulation of glutathione transferases, SKN-1–dependent...
ABSTRACT Inter-organ communication is a key aspect of multicellular organismal growth, development, and homeostasis. Importantly, cell-non-autonomous inhibitory cues that limit tissue specific growth alterations are poorly characterized due to limitations cell ablation approaches. Here, we report robust system investigate nutrition-independent organism-wide coordination by modulating ribosome biogenesis at distinct steps in tissue-specific reversible fashion Caenorhabditis elegans . We find...