Benjamin T. Donovan

U2AF regulates the translation and localization of nuclear-encoded mitochondrial mRNAs

Gloria R. Garcia, Murali Palangat, Josquin Moraly, Benjamin T. Donovan et autres

The mechanisms underlying molecular targeting to mitochondria remain enigmatic, yet this process is crucial for normal cellular function. The RNA-binding proteins U2AF1 and U2AF2 form a heterodimer (U2AF) that shuttles between the nucleus and cytoplasm, regulating splicing in the nucleus and translation …

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Granulocyte maturation and splicing defects in DDX41-mutated leukemia

Ira Lignugaris Kraft, Jérémy Scutenaire, Ayush T. Raman, Trinh Hoc-Tran Pham et autres

Abstract Deleterious germ line DEAD-box helicase 41 (DDX41) variants cause an inherited predisposition to adult-onset acute myeloid leukemia (AML) accounting for ~5% of cases. DDX41 encodes a DEAD-box type RNA helicase potentially involved in RNA processing, ribosomal biogenesis, metabolism, cell cycle progression, …

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U2AF regulates the translation and localization of nuclear-encoded mitochondrial mRNAs

Gloria R. Garcia, Murali Palangat, Josquin Moraly, Benjamin T. Donovan et autres

The mechanisms underlying molecular targeting to mitochondria remain enigmatic, yet this process is crucial for normal cellular function. The RNA-binding proteins U2AF1 and U2AF2 form a heterodimer (U2AF) that shuttles between the nucleus and cytoplasm, regulating splicing in the nucleus and translation …

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REAL-TIME VISUALIZATION OF SPLICEOSOME ASSEMBLY REVEALS BASIC PRINCIPLES OF SPLICE SITE SELECTION

Benjamin T. Donovan, Bixuan Wang, Gloria R. Garcia, Stephen M. Mount et autres

ABSTRACT The spliceosome is a megadalton protein-RNA complex which removes introns from pre-mRNA, yet the dynamic early assembly steps have not been structurally resolved. Specifically, how the spliceosome selects the correct 3’ splice site (3’SS) amongst highly similar non-functional sites is not …

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Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome-depleted regions

Benjamin T. Donovan, Hengye Chen, Priit Eek, Zhiyuan Meng et autres

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Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome depleted regions.

Benjamin T. Donovan, Michael Guy Poirier

This dataset includes all time traces from single-molecule experiments as well as raw gel images used in the manuscript. All time traces from single-molecule experiments and can be viewed using vbFRET (https://vbfret.sourceforge.net/).

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Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome depleted regions.

Benjamin T. Donovan, Michael Guy Poirier

This dataset includes all time traces from single-molecule experiments as well as raw gel images used in the manuscript. All time traces from single-molecule experiments and can be viewed using vbFRET (https://vbfret.sourceforge.net/).

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The nucleosome unwrapping free energy landscape defines distinct regions of transcription factor accessibility and kinetics

Benjamin T. Donovan, Yi Luo, Zhiyuan Meng, Michael Guy Poirier

Transcription factors (TF) require access to target sites within nucleosomes to initiate transcription. The target site position within the nucleosome significantly influences TF occupancy, but how is not quantitatively understood. Using ensemble and single-molecule fluorescence measurements, we investigated the targeting and occupancy …

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The Nucleosome Unwrapping Free Energy Landscape Defines Distinct Regions of Transcription Factor Accessibility and Kinetics

Benjamin T. Donovan

Raw single-molecule time traces of Gal4 binding to the nucleosome. These data can be viewed using ebFRET (http://ebfret.github.io/)

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Regulating gene expression through control of transcription factor multivalent interactions

Benjamin T. Donovan, Daniel R. Larson

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Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome depleted regions

Benjamin T. Donovan, Hengye Chen, Priit Eek, Zhiyuan Meng et autres

SUMMARY Nucleosomes drastically limit transcription factor (TF) occupancy, while pioneer transcription factors (PFs) somehow circumvent this nucleosome barrier. In this study, we compare nucleosome binding of two conserved S. cerevisiae basic helix-loop-helix (bHLH) TFs, Cbf1 and Pho4. A Cryo-EM structure of Cbf1 …

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Live‐cell imaging reveals the interplay between transcription factors, nucleosomes, and bursting

Benjamin T. Donovan, Anh Huynh, David A. Ball, Heta Patel et autres

Transcription factors show rapid and reversible binding to chromatin in living cells, and transcription occurs in sporadic bursts, but how these phenomena are related is unknown. Using a combination of in vitro and in vivo single‐molecule imaging approaches, we directly correlated binding …

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