Výsledky vyhledávání - "Sofia A. Quinodoz"

Essential Roles for RNA in Shaping Nuclear Organization

Autor: Sofia A. Quinodoz, Mitchell Guttman

Publikováno v: Cold Spring Harbor perspectives in biology. 14(5)

It has long been proposed that nuclear RNAs might play an important role in organizing the structure of the nucleus. Initial experiments performed more than 30 years ago found that global disruption of RNA led to visible rearrangements of nuclear org

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5609a232b354ed5b5172bb50a3a418fa
https://pubmed.ncbi.nlm.nih.gov/34400555

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Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations

Autor: Lorenzo Boninsegna, Asli Yildirim, Guido Polles, Yuxiang Zhan, Sofia A. Quinodoz, Elizabeth H. Finn, Mitchell Guttman, Xianghong Jasmine Zhou, Frank Alber

Publikováno v: Nature Methods. 19:938-949

A multitude of sequencing-based and microscopy technologies provide the means to unravel the relationship between the three-dimensional organization of genomes and key regulatory processes of genome function. Here, we develop a multimodal data integr

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0d97c03d87e4f9cc46bf13af38ac2ec9
https://doi.org/10.1038/s41592-022-01527-x

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The genomic and cellular basis of biosynthetic innovation in rove beetles

Autor: Sheila A Kitchen, Thomas H Naragon, Adrian Bruckner, Mark S Ladinsky, Sofia A Quinodoz, Jean M Badroos, Joani W Viliunas, Julian M Wagner, David R. Miller, Mina Yousefelahiyeh, Igor A Antoshechkin, K Taro Eldredge, Stacy Pirro, Mitchell Guttman, Steven R Davis, Matthew L. Aardema, Joseph Parker

Publikováno v: bioRxiv

How evolution at the cellular level potentiates change at the macroevolutionary level is a major question in evolutionary biology. With >66,000 described species, rove beetles (Staphylinidae) comprise the largest metazoan family. Their exceptional ra

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6bf64983ad066dba27280e571ae7f93c
https://doi.org/10.1101/2023.05.29.542378

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3D genome organization around nuclear speckles drives mRNA splicing efficiency

Autor: Prashant Bhat, Amy Chow, Benjamin Emert, Olivia Ettlin, Sofia A. Quinodoz, Yodai Takei, Wesley Huang, Mario R. Blanco, Mitchell Guttman

Publikováno v: bioRxiv

The nucleus is highly organized such that factors involved in transcription and processing of distinct classes of RNA are organized within specific nuclear bodies. One such nuclear body is the nuclear speckle, which is defined by high concentrations

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cecb970af16454ca7ca53326a5f263fe
https://europepmc.org/articles/PMC9881923/

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Viscoelastic RNA entanglement and advective flow underlie nucleolar form and function

Autor: Joshua A. Riback, Jorine M. Eeftens, Daniel S. W. Lee, Sofia A. Quinodoz, Lien Beckers, Lindsay A. Becker, Clifford P. Brangwynne

The nucleolus facilitates transcription, processing, and assembly of ribosomal RNA (rRNA), the most abundant RNA in cells. Nucleolar function is facilitated by its multiphase liquid properties, but nucleolar fluidity and its connection to ribosome bi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::85d6b39199f2dbd50ca36188952859da
https://doi.org/10.1101/2021.12.31.474660

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Single-cell measurement of higher-order 3D genome organization with scSPRITE

Autor: Charlotte Lai, Mitchell Guttman, Matthew S. Curtis, Joanna W. Jachowicz, Mary V. Arrastia, David A. Selck, Rustem F. Ismagilov, Noah Ollikainen, Sofia A. Quinodoz

Although three-dimensional (3D) genome organization is central to many aspects of nuclear function, it has been difficult to measure at the single-cell level. To address this, we developed 'single-cell split-pool recognition of interactions by tag ex

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7d7c6dc0458405a5356326381c78b5f5
https://resolver.caltech.edu/CaltechAUTHORS:20200813-130113364

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Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription

Autor: Isabel N. Goronzy, Sofia A. Quinodoz, Joanna W. Jachowicz, Noah Ollikainen, Prashant Bhat, Mitchell Guttman

Publikováno v: Cell Reports. 41:111730

Mammalian genomes are organized into three-dimensional DNA structures called A/B compartments that are associated with transcriptional activity/inactivity. However, whether these structures are simply correlated with gene expression or are permissive

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e4a87c4a5f45edfc106f82b3b287d000
https://doi.org/10.1016/j.celrep.2022.111730

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Integrative Genome Modeling Platform reveals essentiality of rare contact events in 3D genome organizations

Autor: Guido Polles, Mitchell Guttman, Lorenzo Boninsegna, Frank Alber, Asli Yildirim, Sofia A. Quinodoz, Xianghong Jasmine Zhou, Elizabeth H. Finn

A multitude of sequencing-based and microscopy technologies provide the means to unravel the relationship between the three-dimensional (3D) organization of genomes and key regulatory processes of genome function. However, it remains a major challeng

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::f28ec20f836c4f6ab60e3ff0817ec5d2
https://doi.org/10.1101/2021.08.22.457288

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A single-cell method to map higher-order 3D genome organization in thousands of individual cells reveals structural heterogeneity in mouse ES cells

Autor: Joanna W. Jachowicz, Noah Ollikainen, David A. Selck, Sofia A. Quinodoz, Mitchell Guttman, Charlotte Lai, Mary V. Arrastia, Rustem F. Ismagilov, Matthew S. Curtis

In eukaryotes, the nucleus is organized into a three dimensional structure consisting of both local interactions such as those between enhancers and promoters, and long-range higher-order structures such as nuclear bodies. This organization is centra

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::a0a2f499c2972695df5375a922b6d438
https://doi.org/10.1101/2020.08.11.242081

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