A5003631055- Immunotherapy and Immune Responses
- vaccines and immunoinformatics approaches
- Viral-associated cancers and disorders
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Advanced biosensing and bioanalysis techniques
- Chromosomal and Genetic Variations
- Monoclonal and Polyclonal Antibodies Research
- Animal Virus Infections Studies
- Studies on Chitinases and Chitosanases
- DNA Repair Mechanisms
- RNA Interference and Gene Delivery
- Ubiquitin and proteasome pathways
- Microtubule and mitosis dynamics
- Genomics and Chromatin Dynamics
- SARS-CoV-2 and COVID-19 Research
- 14-3-3 protein interactions
- T-cell and Retrovirus Studies
- Nuclear Structure and Function
- CRISPR and Genetic Engineering
- Protist diversity and phylogeny
- Advanced Proteomics Techniques and Applications
- Circular RNAs in diseases
- Bacterial Genetics and Biotechnology
Rockefeller University
2015-2024
Jackson Laboratory
2006
Brown University
2006
The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, peripheral regions can exhibit considerable variation within and between species. One such structure cage-like basket. crucial roles mRNA surveillance chromatin organization, an architectural has remained elusive. Using in-cell cryo-electron tomography subtomogram analysis, we explored NPC's structural variations basket across fungi...
Post-translational modifications (PTMs) (e.g., acetylation, methylation, and phosphorylation) play crucial roles in regulating the diverse protein-protein interactions involved essentially every cellular process. While significant progress has been made to detect PTMs, profiling mediated by these PTMs remains a challenge. Here, we report method that combines photo-cross-linking strategy with stable isotope labeling cell culture (SILAC)-based quantitative mass spectrometry identify...
The basket of the nuclear pore complex (NPC) is generally depicted as a discrete structure eight protein filaments that protrude into nucleoplasm and converge in ring distal to NPC. We show yeast proteins Mlp1p Mlp2p are necessary components they also embed NPC within dynamic network, whose extended interactome includes spindle organizer, silencing factors, proteasome, key messenger ribonucleoproteins (mRNPs). Ultrastructural observations indicate reduces chromatin crowding around central...
The emergence of SARS-CoV-2 variants threatens current vaccines and therapeutic antibodies urgently demands powerful new therapeutics that can resist viral escape. We therefore generated a large nanobody repertoire to saturate the distinct highly conserved available epitope space spike, including S1 receptor binding domain, N-terminal S2 subunit, identify sites may reflect novel mechanisms neutralization. Structural mapping functional assays show indeed these stable monovalent nanobodies...
Abstract Improved biomarkers are needed for early cancer detection, risk stratification, treatment selection, and monitoring response. Although proteins can be useful blood-based biomarkers, many have limited sensitivity or specificity these applications. Long INterspersed Element-1 (LINE-1) open reading frame 1 protein (ORF1p) is a transposable element overexpressed in carcinomas high-risk precursors during carcinogenesis with negligible expression normal tissues, suggesting ORF1p could...
Specific mammalian genes functionally and dynamically associate together within the nucleus. Yet, how an array of many along chromosome sequence can be spatially organized folded is unknown. We investigated 3D structure a well-annotated, highly conserved 4.3-Mb region on mouse 14 that contains four clusters separated by gene “deserts.” In nuclei, this forms multiple, nonrandom “higher order” structures. These structures are based distribution pattern in primary marked preferential...
ABSTRACT Sindbis virus (SINV) is the prototype member of Alphavirus genus, whose members cause severe human diseases for which there no specific treatment. To ascertain host factors important in replication SINV RNA genome, we generated a expressing nsP4, viral RNA-dependent polymerase, with an in-frame 3×Flag epitope tag. Proteomic analysis nsP4-containing complexes isolated from cells infected tagged revealed 29 associated proteins. Of these, 10 proteins were only at later time infection...
Long Interspersed Nuclear Element-1 (LINE-1, L1) is a mobile genetic element active in human genomes. L1-encoded ORF1 and ORF2 proteins bind L1 RNAs, forming ribonucleoproteins (RNPs). These RNPs interact with diverse host proteins, some repressive others required for the lifecycle. Using differential affinity purifications, quantitative mass spectrometry, next generation RNA sequencing, we have characterized nucleic acids associated distinctive, enzymatically macromolecular complexes. Among...
Abstract Early eukaryotic ribosome biogenesis involves large multi-protein complexes, which co-transcriptionally associate with pre-ribosomal RNA to form the small subunit processome. The precise mechanisms by two of largest complexes—UtpA and UtpB—interact nascent are poorly understood. Here, we combined biochemical structural biology approaches ensembles RNA–protein cross-linking data elucidate essential functions both complexes. We show that UtpA contains a composite RNA-binding site...
Significance Virion proteomics represents a powerful and unbiased approach to gain insights into the process of virus assembly host factors important for infection. For hepatitis C (HCV), it is known that infectious virions are assembled alongside endogenous lipoproteins give rise chimeric lipoviral particle. Host-derived apolipoproteins coat exterior circulating particles, making veiled pathogen. The protein composition HCV remains, however, undefined. Here, using MS, we identified novel...
Long interspersed element-1 (LINE-1, L1) is the major driver of mobile DNA activity in modern humans. When expressed, LINE-1 loci produce bicistronic transcripts encoding two proteins essential for retrotransposition, ORF1p and ORF2p. Many types human cancers are characterized by L1 promoter hypomethylation, transcription, protein expression, somatic retrotransposition. ORF2p encodes endonuclease reverse transcriptase activities required Its expression poorly tissues cell lines.We report...
An efficient and reliable procedure for the capture of affinity-tagged proteins associated complexes from human cell lines is reported. Through multiple optimizations, high yield low background affinity-purifications are achieved modest quantities cells expressing endogenous-level tagged proteins. Isolations triple-FLAG GFP-tagged fusion involved in RNA metabolism presented.
Dissecting and studying cellular systems requires the ability to specifically isolate distinct proteins along with co-assembled constituents of their associated complexes. Affinity capture techniques leverage high affinity, specificity reagents target interest from cell extracts. coupled mass spectrometry (MS)-based proteomic analyses has enabled isolation characterization a wide range endogenous protein Here, we outline effective procedures for affinity complexes, highlighting best...
Nuclear RNA metabolism is influenced by protein complexes connecting to both RNA-productive and -destructive pathways. The ZC3H18 binds the cap-binding complex (CBC), universally present on capped RNAs, while also associating with nuclear exosome targeting (NEXT) complex, linking decay. To dissect function, we conducted interaction screening mutagenesis of protein, which revealed a phosphorylation-dependent isoform. Surprisingly, modified region associates core histone proteins. Further...
The 11-subunit eukaryotic replicative helicase CMG (Cdc45, Mcm2-7, GINS) tightly binds Mcm10, an essential replication protein in all eukaryotes. Here we show that Mcm10 has a potent strand-annealing activity both alone and complex with CMG. CMG-Mcm10 unwinds then reanneals single strands soon after they have been unwound vitro. Given the DNA damage replisome instability associated loss of function, examined effect on fork regression. Fork regression requires unwinding pairing newly...