A5069330800- RNA Research and Splicing
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- RNA Interference and Gene Delivery
- MicroRNA in disease regulation
- Cancer-related gene regulation
- Molecular Biology Techniques and Applications
- Biomedical Text Mining and Ontologies
- DNA Repair Mechanisms
- Topic Modeling
- Circular RNAs in diseases
- Pluripotent Stem Cells Research
- MXene and MAX Phase Materials
- Genomics and Chromatin Dynamics
- Angiogenesis and VEGF in Cancer
- Synthetic Organic Chemistry Methods
- Ubiquitin and proteasome pathways
- Extracellular vesicles in disease
- Protein Degradation and Inhibitors
- DNA and Nucleic Acid Chemistry
- Advanced Text Analysis Techniques
- 3D Printing in Biomedical Research
- Cancer-related molecular mechanisms research
Nagoya University
2021-2025
Nagoya City University
2011-2023
Columbia University
2014-2020
Koichi Ogami1,4, Patricia Richard1, Yaqiong Chen1, Mainul Hoque2, Wencheng Li2, James J. Moresco3, John R. Yates III3, Bin Tian2 and L. Manley1 1Department of Biological Sciences, Columbia University, New York, York 10027, USA; 2Department Microbiology, Biochemistry, Molecular Genetics, Rutgers Jersey Medical School, Newark, 07103, 3Department Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA Corresponding author: jlm2{at}columbia.edu ↵4 Present address:...
Polyadenylation of mRNA precursors is mediated by a large multisubunit protein complex. Here we show that RBBP6 (retinoblastoma-binding 6), identified initially as an Rb- and p53-binding protein, component this complex functions in 3′ processing vitro vivo. associates with other core factors, interaction unusual ubiquitin-like domain, DWNN (“domain no name”), required for activity. The also expressed, via alternative RNA processing, small single-domain (isoform 3 [iso3]). Importantly, iso3,...
The nuclear RNA exosome is an essential and versatile machinery that regulates maturation degradation of a huge plethora species. past two decades have witnessed remarkable progress in understanding the whole picture its substrates structural basis functions. In addition to itself, recent studies focusing on associated co-factors been elucidating how directed towards specific substrates. Moreover, it has gradually realized loss-of-function subunits affect multiple biological processes, such...
Abstract Most eukaryotic genes produce alternative polyadenylation (APA) isoforms. Here we report that, unlike previously characterized cell lineages, differentiation of syncytiotrophoblast (SCT), a type critical for hormone production and secretion during pregnancy, elicits widespread transcript shortening through APA in 3’UTRs introns. This global change is observed multiple vitro trophoblast models, single cells from placentas at different stages pregnancy. Strikingly, the unrelated to...
Translation of 5′ terminal oligopyrimidine (TOP) mRNAs encoding the protein synthesis machinery is strictly regulated by an amino-acid-sensing mTOR pathway. However, its regulatory mechanism remains elusive. Here, we demonstrate that TOP mRNA translation positively correlates with poly(A) tail length under active/amino-acid-rich conditions, suggesting are post-transcriptionally controlled tail-length regulation. Consistent this, dynamically fluctuates in response to amino acid availability....
MicroRNAs (miRNAs) are ~22-nucleotide small non-coding RNAs that play critical roles in gene regulation. The discovery of miRNAs Caenorhabditis elegans 1993 by the research groups Victor Ambros and Gary Ruvkun opened a new era RNA research. Typically, act as negative regulators expression binding to complementary sequences within 3′ untranslated regions their target mRNAs. This interaction results translational repression and/or destabilization. levels activities fine-tuned multiple factors,...
Abstract Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of large offline gold-standard benchmark documents that cover variety research fields such newly search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we established RElevant LIterature SearcH consortium consisting more than 1500 scientists from 84 countries, who collectively annotated...
Oncogene-induced DNA replication stress (RS) and consequent pathogenic R-loop formation are known to impede S phase progression. Nonetheless, cancer cells continuously proliferate under such high-stressed conditions through incompletely understood mechanisms. Here, we report taurine upregulated gene 1 (TUG1) long noncoding RNA (lncRNA), which is highly expressed in many types of cancers, as an important regulator intrinsic cells. Under RS conditions, TUG1 rapidly via activation the ATR-CHK1...
MicroRNA-122 (miR-122) is highly expressed in hepatocytes, where it plays an important role regulating cholesterol and fatty acid metabolism, also a host factor required for hepatitis C virus replication. miR-122 selectively stabilized by 3' adenylation mediated the cytoplasmic poly(A) polymerase GLD-2 (also known as PAPD4 or TENT2). However, unclear how specifically stabilizes miR-122. Here, we show that QKI7 KH domain-containing RNA binding (QKI-7), one of three isoforms QKI proteins,...
Combinatorial gene regulation by multiple microRNAs (miRNAs) is widespread and closely spaced target sites often act cooperatively to achieve stronger repression ("neighborhood" miRNA cotargeting). While cotarget are suggested be more conserved implicated in developmental control, the pathological significance of cotargeting remains elusive.
The RNA helicase Mtr4 is a versatile protein that crucial component of several distinct surveillance complexes. Here we describe novel complex contains Mtr4, but has role from any those previously described. We found association with the human homolog fission yeast Nrl1, NRDE-2, defines function for in DNA damage response pathway. provide biochemical evidence and NRDE-2 are part same show both proteins play by maintaining low double-strand break levels. Importantly, Mtr4/NRDE-2 does not...
Poly(A) tail metabolism contributes to post-transcriptional regulation of gene expression. Here, we present a protocol for analyzing intact mRNA poly(A) length using nanopore direct RNA sequencing, which excludes truncated RNAs from the measurement. We describe steps preparing recombinant eIF4E mutant protein, purifying m7G- capped RNAs, library preparation, and sequencing. Resulting data can be used not only expression profiling estimation but also detecting alternative splicing...
Micro RNA s are small noncoding that regulate translation and mRNA stability by binding target in complex with Argonaute ( AGO ) proteins. interacts a member of the TNRC 6 family proteins to form micro RNP complex, which recruits CCR 4‐ NOT accelerate deadenylation inhibits translation. primarily repress but have been shown enhance specific type reporter various experimental systems: G0 quiescent mammalian cells, Xenopus laevis oocytes, Drosophila embryo extracts, HeLa cells. In all cases...
Endothelial cells (ECs) and endothelial progenitor (EPCs) play crucial roles in maintaining vascular health homeostasis. Both cell types have been used regenerative therapy as well various vitro models; however, the properties of primary human ECs EPCs are dissimilar owing to differences genetic backgrounds sampling techniques. Human induced pluripotent stem (hiPSCs) an alternative source EPCs. However, low purity differentiated from hiPSCs, purification via antigen-antibody reaction, which...
ABSTRACT Occasionally, cells must adapt to an inimical growth conditions like amino acid starvation (AAS) by downregulating protein synthesis. A class of transcripts containing 5’terminal oligopyrimidine (5’TOP) motif encodes translation-related proteins such as ribosomal (RPs) and elongation factors, therefore, their translation is severely repressed during AAS conserve energy 1 . The RNA-binding LARP1 transduces signaling TOP gene expression controlling stability mRNAs 2-6 When released...
The 2′-5′-oligoadenylate synthetase (OAS)/RNase L system protects hosts against pathogenic viruses through cleavage of the exogenous single-stranded RNA. In this system, an evolutionally conserved RNA quality control factor Dom34 (known as Pelota (Pelo) in higher eukaryotes) forms a surveillance complex with RNase to recognize and eliminate manner dependent on translation. Here, we newly identified that ATP-binding cassette sub-family E member 1 (ABCE1), which is also known inhibitor (RLI),...
During early embryonic development, the RNA-binding protein CPEB mediates cytoplasmic polyadenylation and translational activation through a combinatorial code defined by cy-toplasmic element (CPE) present in maternal mRNAs. However, non-neuronal somatic cells, accelerates deadenylation to repress translation of target, including c-myc mRNA, an ill-defined cis-regulatory mechanism. Using RNA mutagenesis electrophoretic mobility shift assays, we demonstrated that combination tandemly arranged...