Author

Katherine E. Berry

Mount Holyoke CollegeORCID 0000-0002-9452-0239Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:experimental assay· 6 Organism:E. coli· 5 Organism:bacteria (other)· 1 Research Focus:cell signaling & trafficking· 1 Research Focus:cell type annotation· 1 Research Focus:chromatin & epigenetic regulation· 1 Research Focus:differential expression· 1 Assay:multiome· 1

Frequent Co-Authors

Chandra M. GraveliD· 4 shared Cynthia Mira SharmaiD· 2 shared Ewa M. SteiniD· 2 shared Manasa NarayaniD· 2 shared Mikołaj OlejniczakiD· 2 shared Nay Won LettiD· 2 shared Sahil SharmaiD· 2 shared Hannah LeBlanciD· 1 shared

Activity by Year

2020-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

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4 shared papersMolecular Biology

Chandra M. GravelORCID

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Author profile →

6 papers

Recent·Most cited

Interdependent mode of RNA recognition by the interacting KH-domain proteins KhpA and KhpB

Manasa Narayan, Sahil Sharma, Thorsten Bischler, Nay Won Lett, Tom Gräfenhan, Sander Granneman, Katherine E. Berry, Mona Alzheimer, Cynthia Mira Sharma

This study shows KhpA and KhpB in Campylobacter jejuni depend on each other for RNA recognition, with KhpA using a KH domain and KhpB an atypical R3H domain.

bioRxiv · Oct 12, 2026 · PreprintMicrobiology

Genetic detection of RNA-protein interactions using a bacterial three-hybrid assay

Chandra M. Gravel, Katherine E. Berry

The paper describes a bacterial three-hybrid assay protocol for detecting RNA-protein interactions and assessing RBP mutations in Escherichia coli.

bioRxiv · Jul 1, 2026 · PreprintMolecular Biology

Molecular genetic characterization of bacterial KH-domain proteins

Kaylee Nguyen, Nay Won Lett, Chandra M. Gravel, Sungeun Jo, Yiling Shi, Manasa Narayan, Sahil Sharma, Cynthia Mira Sharma, Katherine E. Berry

The paper characterizes the molecular interactions of KH-domain proteins KhpA and KhpB across bacterial species, revealing conserved protein-protein interactions and species-specific RNA-binding behaviors.

bioRxiv · Mar 17, 2026 · PreprintMolecular Biology

Improved constructs for bait RNA display in a bacterial three-hybrid assay

Linh D. Nguyen, Hannah LeBlanc, Katherine E. Berry

This paper introduces improved RNA constructs for the bacterial three-hybrid assay to enhance detection of RNA-protein interactions by using short GC clamps and non-terminating RNA sequences.

Scientific Reports · Jan 30, 2025Peer-reviewedMolecular Biology

Biochemical and genetic dissection of the RNA-binding surface of the FinO domain of Escherichia coli ProQ

Ewa M. Stein, Suxuan Wang, Katherine G. Dailey, Chandra M. Gravel, Shiying Wang, Mikołaj Olejniczak, Katherine E. Berry

This study identifies key RNA-binding residues in E. coli ProQ's FinO domain through genetic and biochemical assays, revealing conserved and variable residues involved in RNA interactions.

RNA · Aug 22, 2023Peer-reviewedMolecular Biology

Determinants of RNA recognition by the FinO domain of the Escherichia coli ProQ protein

Ewa M. Stein, Joanna Kwiatkowska, Maciej M. Basczok, Chandra M. Gravel, Katherine E. Berry, Mikołaj Olejniczak

This study identifies RNA sequence determinants recognized by the FinO domain of E. coli ProQ, showing specificity for Rho-independent terminators and interactions with Hfq.

Nucleic Acids Research · Jun 1, 2020Peer-reviewedMolecular Biology