Author

B. E. Nickels

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biochemistry· 5 Microbiology· 2 Plant Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 8 Organism:E. coli· 5 Research Focus:chromatin & epigenetic regulation· 4 Assay:DNA methylation· 3 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Research Focus:gene regulatory network inference· 2 Organism:Arabidopsis· 1

Frequent Co-Authors

R. H. Ebright· 5 shared I. O. Vvedenskaya· 4 shared D. M. Taylor· 3 shared J. T. Winkelman· 3 shared Y. Zhang· 3 shared C. Pukhrambam· 2 shared J. B. Kinney· 2 shared J. G. Bird· 2 shared

Activity by Year

2017-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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5 shared papersBiochemistry

R. H. Ebright

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Author profile →

8 papers

Recent·Most cited

Structural and mechanistic basis of σ-dependent transcriptional pausing

C. Pukhrambam, V. Molodtsov, M. Kooshkbaghi, A. Tareen, H. Vu, K. S. Skalenko, M. Su, Y. Zhou, J. T. Winkelman, J. B. Kinney, R. H. Ebright, B. E. Nickels

This paper identifies the structural basis of σ-dependent transcriptional pausing by showing that it involves backtracked or scrunched states of RNA polymerase, depending on the presence of GreB.

bioRxiv · Jan 24, 2022Biochemistry

Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli

K. S. Skalenko, L. Li, Y. Zhang, I. O. Vvedenskaya, J. T. Winkelman, A. Cope, D. M. Taylor, P. Shah, R. H. Ebright, J. B. Kinney, Y. Zhang, B. E. Nickels

The paper identifies promoter sequence determinants and structural basis of primer-dependent transcription initiation in E. coli using MASTER and biochemical studies.

bioRxiv · Apr 6, 2021Biochemistry

A Spatiotemporal Molecular Switch Governs Plant Asymmetric Cell Division

X. Guo, C. H. Park, Z.-y. Wang, B. E. Nickels, J. Dong

The paper identifies BSL protein phosphatase polarization as a spatiotemporal molecular switch governing asymmetric cell division in Arabidopsis stomatal stem cells.

bioRxiv · Sep 5, 2020Plant Biology

Functional determinants of a small protein repressor controlling a broadly conserved bacterial sensor kinase

S. S. Yadavalli, T. Goh, J. N. Carey, G. Malengo, S. Vellappan, B. E. Nickels, V. Sourjik, M. Goulian, J. Yuan

This study investigates how mutations in MgrB affect its ability to inhibit PhoQ, revealing key residues and regions critical for its function.

Journal of Bacteriology · Jul 27, 2020Peer-reviewedMicrobiology

XACT-seq comprehensively defines the promoter-position and promoter-sequence determinants for initial-transcription pausing

J. T. Winkelman, C. Pukhrambam, I. O. Vvedenskaya, Y. Zhang, D. M. Taylor, P. Shah, R. H. Ebright, B. E. Nickels

XACT-seq identifies promoter-position and sequence determinants for initial-transcription pausing in Escherichia coli by measuring RNAP-active-center position relative to DNA with single-nucleotide resolution.

bioRxiv · Dec 21, 2019Biochemistry

Detection of Spacer Precursors Formed In Vivo During Primed CRISPR Adaptation

A. A. Shiriaeva, E. Savitskaya, K. A. Datsenko, I. O. Vvedenskaya, I. Fedorova, N. Morozova, A. Metlitskaya, A. Sabantsev, B. E. Nickels, K. Severinov, E. Semenova

The paper develops a method to detect spacer precursors formed during primed CRISPR adaptation in vivo and identifies their structural and functional characteristics.

bioRxiv · Mar 30, 2019Microbiology

Mitochondrial RNA capping: highly efficient 5’-RNA capping with NAD+ and NADH by yeast and human mitochondrial RNA polymerase

J. G. Bird, U. Basu, D. Kuster, A. Ramachandran, E. Grudzien-Nogalska, M. Kiledjian, D. Temiakov, S. S. Patel, R. H. Ebright, B. E. Nickels

The paper shows mitochondrial RNA polymerases in yeast and human cells efficiently cap RNA with NAD+ and NADH, linking metabolism to mitochondrial gene expression.

bioRxiv · Oct 1, 2018Biochemistry

“CapZyme-Seq” comprehensively defines promoter-sequence determinants for RNA 5’ capping with NAD+

I. O. Vvedenskaya, J. G. Bird, Y. Zhang, Y. Zhang, X. Jiao, I. Barvik, L. Krasny, M. Kiledjian, D. M. Taylor, R. H. Ebright, B. E. Nickels

The paper introduces CapZyme-Seq to detect NCIN-capped RNA and identifies a consensus promoter sequence for NAD+ capping in E. coli.

bioRxiv · Dec 29, 2017Biochemistry