A5052827656- RNA Research and Splicing
- RNA modifications and cancer
- MicroRNA in disease regulation
- RNA Interference and Gene Delivery
- Cancer-related molecular mechanisms research
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- Advanced biosensing and bioanalysis techniques
- RNA regulation and disease
- CRISPR and Genetic Engineering
- Genetics and Neurodevelopmental Disorders
- Single-cell and spatial transcriptomics
- Chromatin Remodeling and Cancer
- Nanopore and Nanochannel Transport Studies
University of California, Los Angeles
2014-2024
University of California System
2023
Delft University of Technology
2011-2016
Seoul National University
2006-2014
Institute for Basic Science
2014
DGCR8/Pasha is an essential cofactor for Drosha, a nuclear RNase III that cleaves the local hairpin structures embedded in long primary microRNA transcripts (pri-miRNAs) eukaryotes. Although our knowledge of pri-miRNA processing has significantly advanced recent years, precise role DGCR8 this pathway remains unclear. In present study, we dissect domains contribute to pri-miRNAs and subcellular localization DGCR8. Drosha stabilized through interaction between its middle domain conserved...
The RNA-binding protein TRBP is a central component of the Dicer complex. Despite decade biochemical and structural studies, essential functionality in microRNA (miRNA) biogenesis remains unknown. Here we show that an integral cofactor for time-efficient processing RNA-crowded environments. We competed pre-miRNA with large amount cellular RNA species found Dicer-TRBP, but not alone, resilient. To apprehend mechanism this substrate selectivity, use single-molecule fluorescence. real-time...
Synaptic function in neurons is modulated by local translation of mRNAs that are transported to distal portions axons and dendrites. The metastasis‐associated lung adenocarcinoma transcript 1 ( MALAT1 ) broadly expressed across cell types, almost exclusively as a nuclear long noncoding RNA. We found differentiating neurons, portion Malat1 RNA redistributes the cytoplasm. Depletion using antisense oligonucleotides (ASOs) stimulates expression particular pre- postsynaptic proteins, implicating...
Development of embryonic stem cells (ESCs) into neurons requires intricate regulation transcription, splicing, and translation, but how these processes interconnect is not understood. We found that polypyrimidine tract binding protein 1 (PTBP1) controls splicing DPF2, a subunit BRG1/BRM-associated factor (BAF) chromatin remodeling complexes. Dpf2 exon 7 inhibited by PTBP1 to produce the DPF2-S isoform early in development. During neuronal differentiation, loss allows inclusion DPF2-L...
Steps of mRNA maturation are important gene regulatory events that occur in distinct cellular locations. However, transcriptomic analyses often lose information on the subcellular distribution processed and unprocessed transcripts. We generated extensive RNA-seq data sets to track across locations mouse embryonic stem cells, neuronal progenitor postmitotic neurons. find disparate patterns RNA enrichment between cytoplasmic, nucleoplasmic, chromatin fractions, with some genes maintaining more...
Significance MicroRNAs repress genes controlling important decisions in animal development, but miRNA production and their interaction with larger genetic programs of development are not well understood. We found that the initial transcript an neuronal miRNA, miR-124, is expressed much earlier than mature functional miRNA. Conversion this primary RNA into its active form blocked by binding protein PTBP1, whose down-regulation upon differentiation allows miR-124 expression. To understand need...
AbstractMicroRNAs (miRNAs) are endogenous antisense regulators that trigger endonucleolytic mRNA cleavage, translational repression, and/or decay. miRNA-mediated gene regulation is important for numerous biological pathways, yet the underlying mechanisms still under rigorous investigation. Here we identify human UPF1 (hUPF1) as a protein contributes to RNA silencing. When hUPF1 knocked down, miRNA targets upregulated. The depletion of also increases off-target messages small interfering RNAs...
Abstract Synaptic function is modulated by local translation of mRNAs that are transported to distal portions axons and dendrites. The Metastasis-associated lung adenocarcinoma transcript 1 ( MALAT1 ) broadly expressed across cell types, almost exclusively as a nuclear non-coding RNA. We found in differentiating neurons, portion Malat1 RNA redistributes the cytoplasm. Depletion from neurons stimulated expression particular pre- post-synaptic proteins, implicating their regulation. Neuronal...
Fluorescence in situ hybridization (FISH) is a widely used tool for quantifying gene expression and determining the location of RNA molecules cells. We present an improved method FISH probe production that yields high-purity probes with wide range fluorophores using standard laboratory equipment at low cost. The modifies earlier protocol uses terminal deoxynucleotidyl transferase to add fluorescently labeled nucleotides synthetic deoxyoligonucleotides. In our protocol, amino-11-ddUTP joined...
ABSTRACT Development of embryonic stem cells (ESCs) into neurons requires intricate regulation transcription, splicing, and translation, but how these processes interconnect is not understood. We found that polypyrimidine tract binding protein 1 (PTBP1) alters splicing DPF2, a subunit BAF chromatin remodeling complexes. Dpf2 exon 7 inhibited by PTBP1 to produce the DPF2-S isoform early in development. During neuronal differentiation, loss allows resulting longer DPF2-L isoform. Gene...
Abstract Fluorescence In Situ Hybridization (FISH) is a widely used tool for quantifying gene expression and determining the location of RNA molecules in cells. Here, we present an improved method FISH probe production that yields high purity probes with wide range fluorophores using standard laboratory equipment at low cost. The modifies earlier protocol uses terminal deoxynucleotidyl transferase to add fluorescently labeled nucleotides synthetic deoxyoligonucleotides. our protocol,...
Abstract MicroRNA-124 is expressed in neurons, where it represses genes inhibitory for neuronal differentiation, including the RNA binding protein PTBP1. PTBP1 maintains non-neuronal splicing patterns of mRNAs that switch to isoforms upon differentiation. We find pri-miR-124-1 mouse embryonic stem cells (mESCs) mature miR-124 absent. binds this precursor upstream miRNA stem-loop inhibit expression vivo , and DROSHA cleavage vitro . This new function repressing biogenesis adds an additional...
SUMMARY To globally assess the distribution and processing of gene transcripts across subcellular compartments, we developed extensive RNA-seq datasets both polyA+ total RNA from chromatin, nucleoplasm cytoplasm mouse ESC, neuronal progenitors, neurons. We identified protein-coding genes whose polyadenylated were more abundant in chromatin than cytoplasm. defined introns exhibiting cotranscriptional splicing, complete intron retention cytoplasmic RNA, many retained nucleoplasmic but absent...
The process of alternative splicing is tightly regulated by RNA binding proteins that bind to corresponding cis‐acting elements and influence the assembly spliceosomal components at adjacent splice sites. Many these occur as gene families, with family members generally sharing high amino acid sequence identity domain structure yet targeting overlapping but distinct sets exons. PTBP1 (polypyrimidine tract protein 1) PTBP2 2) are paralogous proteins. well characterized a repressor. PTBP2,...