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Yupeng Qiu

Bio: Yupeng Qiu is an academic researcher from Johns Hopkins University. The author has contributed to research in topics: Helicase & Homologous recombination. The author has an hindex of 6, co-authored 16 publications receiving 574 citations. Previous affiliations of Yupeng Qiu include Duke University & University of Illinois at Urbana–Champaign.

Papers
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Journal ArticleDOI
25 May 2018-Science
TL;DR: The shape of RNA can promote the formation and coexistence of the diverse array of RNA-rich liquid compartments found in a single cell and support a model in which structure-based, RNA-RNA interactions promote assembly of distinct droplets and protein-driven, conformational dynamics of the RNA maintain this identity.
Abstract: RNA promotes liquid-liquid phase separation (LLPS) to build membraneless compartments in cells. How distinct molecular compositions are established and maintained in these liquid compartments is unknown. Here, we report that secondary structure allows messenger RNAs (mRNAs) to self-associate and determines whether an mRNA is recruited to or excluded from liquid compartments. The polyQ-protein Whi3 induces conformational changes in RNA structure and generates distinct molecular fluctuations depending on the RNA sequence. These data support a model in which structure-based, RNA-RNA interactions promote assembly of distinct droplets and protein-driven, conformational dynamics of the RNA maintain this identity. Thus, the shape of RNA can promote the formation and coexistence of the diverse array of RNA-rich liquid compartments found in a single cell.

380 citations

Journal ArticleDOI
TL;DR: Characterization of nonpalpable breast lesions is improved by the addition of viscoelastic strain imaging parameters, and the differentiation of malignant and benign BI-RADS 4 or 5 tumors is especially evident with the use of the retardation time estimates, T(1).

103 citations

Journal ArticleDOI
TL;DR: A single-molecule fluorescence study of the dynamics of Rad51 filament formation and its disruption by SRS2 reveals an exquisite and highly specific mechanism by which Srs2 regulates the Rad51 filaments formation.
Abstract: Srs2 dismantles presynaptic Rad51 filaments and prevents its re-formation as an anti-recombinase. However, the molecular mechanism by which Srs2 accomplishes these tasks remains unclear. Here we report a single-molecule fluorescence study of the dynamics of Rad51 filament formation and its disruption by Srs2. Rad51 forms filaments on single-stranded DNA by sequential binding of primarily monomers and dimers in a 5'-3' direction. One Rad51 molecule binds to three nucleotides, and six monomers are required to achieve a stable nucleation cluster. Srs2 exhibits ATP-dependent repetitive motion on single-stranded DNA and this activity prevents re-formation of the Rad51 filament. The same activity of Srs2 cannot prevent RecA filament formation, indicating its specificity for Rad51. Srs2's DNA-unwinding activity is greatly suppressed when Rad51 filaments form on duplex DNA. Taken together, our results reveal an exquisite and highly specific mechanism by which Srs2 regulates the Rad51 filament formation.

85 citations

Posted ContentDOI
07 Mar 2018-bioRxiv
TL;DR: It is found that the specific secondary structure of a cyclin mRNA is required for it to assemble into distinct droplets and be excluded from other droplets containing functionally-unrelated mRNAs.
Abstract: RNA promotes liquid-liquid phase separation (LLPS) to build membrane-less compartments in cells. How distinct molecular compositions are established and maintained in these liquid compartments is unknown. Here we report that secondary structure allows mRNAs to self-associate and determines if an mRNA is recruited to or excluded from liquid compartments. The polyQ-protein Whi3 induces conformational changes in RNA structure and generates distinct molecular fluctuations depending on the RNA sequence. These data support a model in which structure-based, RNA-RNA interactions promote assembly of distinct droplets and protein-driven, conformational dynamics of the RNA maintain this identity. Thus, the shape of RNA can promote the formation and coexistence of the diverse array of RNA-rich liquid compartments found in a single cell.

69 citations

Journal ArticleDOI
TL;DR: It is demonstrated that the monomeric Chd1 remodeler shifts DNA back and forth by dynamically alternating between different segments of the nucleosome, and proposed that active interplay of the ATPase motor with the regulatory domains may promote dynamic nucleosomes structures uniquely suited for histone exchange and chromatin reorganization during transcription.

52 citations


Cited by
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Journal ArticleDOI
24 Jan 2019-Cell
TL;DR: In this article, the authors propose guidelines for rigorous experimental characterization of liquid-liquid phase separation processes in vitro and in cells, discuss the caveats of common experimental approaches, and point out experimental and theoretical gaps in the field.

1,482 citations

Journal ArticleDOI
TL;DR: The technical part of these Guidelines and Recommendations provides an introduction to the physical principles and technology on which all forms of current commercially available ultrasound elastography are based.
Abstract: The technical part of these Guidelines and Recommendations, produced under the auspices of EFSUMB, provides an introduction to the physical principles and technology on which all forms of current commercially available ultrasound elastography are based. A difference in shear modulus is the common underlying physical mechanism that provides tissue contrast in all elastograms. The relationship between the alternative technologies is considered in terms of the method used to take advantage of this. The practical advantages and disadvantages associated with each of the techniques are described, and guidance is provided on optimisation of scanning technique, image display, image interpretation and some of the known image artefacts.

1,020 citations

Journal ArticleDOI
16 Apr 2020-Cell
TL;DR: Inspired by patchy colloid theory, this work proposes a general framework by which competing networks give rise to compositionally specific and tunable condensates, while relative linkage between nodes underlies multiphase organization.

475 citations

Journal ArticleDOI
TL;DR: An overview of the molecular underpinnings of the formation and regulation of these membraneless organelles are provided and new light on neurodegenerative diseases is shone on.

463 citations

Journal ArticleDOI
01 Feb 2020
TL;DR: A perspective on the structure and function of G4s is provided with an emphasis on key molecules and methodological advances that enable the study of G 4 structures in human cells and critically examine recent mechanistic insights into G4 biology and protein interaction partners.
Abstract: Guanine-rich DNA sequences can fold into four-stranded, noncanonical secondary structures called G-quadruplexes (G4s). G4s were initially considered a structural curiosity, but recent evidence suggests their involvement in key genome functions such as transcription, replication, genome stability, and epigenetic regulation, together with numerous connections to cancer biology. Collectively, these advances have stimulated research probing G4 mechanisms and consequent opportunities for therapeutic intervention. Here, we provide a perspective on the structure and function of G4s with an emphasis on key molecules and methodological advances that enable the study of G4 structures in human cells. We also critically examine recent mechanistic insights into G4 biology and protein interaction partners and highlight opportunities for drug discovery.

422 citations