Nature Search

Biomimetic synthesis and optimization of cyclic peptide antibiotics

Rahul M. Kohli
Christopher T. Walsh
Michael D. Burkart
Research08 Aug 2002
Nature

Volume: 418, P: 658-661
On the public dissemination and open sourcing of ultrasound resources, datasets and deep learning models

Mohammad Alsharid
Xiaoqing Guo
J. Alison Noble
ResearchOpen Access24 Nov 2025
npj Digital Medicine

Volume: 8, P: 1-15
Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects

Simultaneous single-cell profiling of 5hmC and 5mC shows their unique regulatory roles.

Emily B. Fabyanic
Peng Hu
Hao Wu
Research28 Aug 2023
Nature Biotechnology

Volume: 42, P: 960-974
Peptide cyclization catalysed by the thioesterase domain of tyrocidine synthetase

John W. Trauger
Rahul M. Kohli
Christopher T. Walsh
Research14 Sept 2000
Nature

Volume: 407, P: 215-218
The LexA–RecA* structure reveals a cryptic lock-and-key mechanism for SOS activation

Here, using cryo-EM, the authors reveal the mechanism by which RecA filamented on single-stranded DNA binds to and induces LexA cleavage, the key signal governing the bacterial DNA damage response pathway implicated in antibiotic resistance.

Michael B. Cory
Allen Li
Rahul M. Kohli
Research16 May 2024
Nature Structural & Molecular Biology

Volume: 31, P: 1522-1531
Direct enzymatic sequencing of 5-methylcytosine at single-base resolution

Wang et al. developed a bisulfite-free method termed DM-Seq that leverages an unnatural enzyme–substrate pair coupled with a DNA deaminase to sequence 5-methylcytosine at base resolution in sparse DNA samples, circumventing the limitations of chemical deamination methods.

Tong Wang
Johanna M. Fowler
Rahul M. Kohli
Research15 Jun 2023
Nature Chemical Biology

Volume: 19, P: 1004-1012
Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies

RNA base-editors are often used in methods for RNA binding protein (RBP) target discovery. Here the authors present a new RBP target discovery method, PRINTER, and suggest optimal RNA base-editors for dual-RBP studies, emphasizing the importance of matching rBEs’ editing biases with RBPs’ binding preferences.

Hugo C. Medina-Munoz
Eric Kofman
Gene W. Yeo
ResearchOpen Access29 Jan 2024
Nature Communications

Volume: 15, P: 1-17
Efficient engineering of human and mouse primary cells using peptide-assisted genome editing

Peptide-assisted genome editing enables efficient single and multiplex editing in hematopoietic cells.

Zhen Zhang
Amy E. Baxter
Junwei Shi
Research24 Apr 2023
Nature Biotechnology

Volume: 42, P: 305-315
Controllable genome editing with split-engineered base editors

The development of split-engineered base editors (seBEs) enables small-molecule control over DNA deaminase activity, decreasing off-target effects and offering a generalizable solution for temporal control over precise genome editing.

Kiara N. Berríos
Niklaus H. Evitt
Rahul M. Kohli
Research18 Oct 2021
Nature Chemical Biology

Volume: 17, P: 1262-1270
High-performance CRISPR-Cas12a genome editing for combinatorial genetic screening

Reliable, multiplexed gene editing to uncover synergies between targets remains challenging. Here, the authors engineer AsCas12a and the crRNA to improve double knockout for synthetic sick/lethal interaction genetic screening.

Rodrigo A. Gier
Krista A. Budinich
Junwei Shi
ResearchOpen Access13 Jul 2020
Nature Communications

Volume: 11, P: 1-9
Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase

A bisulfite-free sequencing method yields high-confidence 5hmC profiles in low-input samples.

Emily K Schutsky
Jamie E DeNizio
Rahul M Kohli
Research08 Oct 2018
Nature Biotechnology

Volume: 36, P: 1083-1090
AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation

AID/APOBEC deaminases, which convert cytosine bases to uracils in DNA and RNA, have recently been assigned a role in epigenetic regulation as components of DNA demethylation pathways. A systematic study shows that AID/APOBEC enzymes preferentially deaminate unmodified cytosine over its C5-modified forms, calling into question the plausibility of deaminase-mediated DNA demethylation pathways.

Christopher S Nabel
Huijue Jia
Rahul M Kohli
Research08 Jul 2012
Nature Chemical Biology

Volume: 8, P: 751-758
Mechanisms for targeted, purposeful mutation revealed in an APOBEC–DNA complex

Targeted deamination of cytosine bases in DNA by AID/APOBEC-family enzymes is critical for proper immune function, but it also poses risks to genomic integrity. New structures reported by Harris, Aihara and colleagues offer the first glimpses into the enzyme–DNA complex and reveal both expected and unexpected insights into the DNA-binding mode involved in targeting purposeful mutation.

Emily K Schutsky
Zachary M Hostetler
Rahul M Kohli
News & Views06 Feb 2017
Nature Structural & Molecular Biology

Volume: 24, P: 97-98
Grand Challenge Commentary: The chemistry of a dynamic genome

In the postsequencing era, chemical biology is uniquely situated to investigate genomic DNA alterations arising through epigenetic modifications, genetic rearrangements or active mutation. These transformations significantly expand nature's diversity and may profoundly alter our view of DNA's coding potential.

Rahul M Kohli
Comments & Opinion15 Nov 2010
Nature Chemical Biology

Volume: 6, P: 866-868
Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine

Saturation mutagenesis, molecular modeling and biochemical analysis revealed that active site interactions involving Thr1372 of TET2 are responsible for controlling its proficiency for stepwise oxidation of 5-methylcytosine residues within DNA.

Monica Yun Liu
Hedieh Torabifard
Rahul M Kohli
Research05 Dec 2016
Nature Chemical Biology

Volume: 13, P: 181-187
The strength and pattern of natural selection on gene expression in rice

Phenotypic selection analysis is used to estimate the type and strength of selection that acts on more than 15,000 transcripts in rice (Oryza sativa), which provides insight into the adaptive evolutionary role of selection on gene expression.

Simon C. Groen
Irina Ćalić
Michael D. Purugganan
Research12 Feb 2020
Nature

Volume: 578, P: 572-576
Disruption of TET2 promotes the therapeutic efficacy of CD19-targeted T cells

Genetically engineered T cells that induced remission in a patient with chronic lymphocytic leukaemia were found to have disruption of the TET2 gene, which caused T cell changes that potentiated their anti-tumour effects.

Joseph A. Fraietta
Christopher L. Nobles
J. Joseph Melenhorst
Research30 May 2018
Nature

Volume: 558, P: 307-312
A vitamin-C-derived DNA modification catalysed by an algal TET homologue

An algal TET dioxygenase homologue, CMD1, uses vitamin C as a glycerol donor to modify 5-methylcytosine and helps to regulate gene transcription in response to high light levels.

Jian-Huang Xue
Guo-Dong Chen
Guo-Liang Xu
Research01 May 2019
Nature

Volume: 569, P: 581-585
TET enzymes, TDG and the dynamics of DNA demethylation

Rahul M. Kohli
Yi Zhang
Reviews23 Oct 2013
Nature

Volume: 502, P: 472-479
Modular affinity-labeling of the cytosine demethylation base elements in DNA

Fanny Wang
Osama K. Zahid
Adam R. Hall
ResearchOpen Access20 Nov 2020
Scientific Reports

Volume: 10, P: 1-9
CYBA (p22^phox) variants associate with blood pressure and oxidative stress markers in hypertension: a replication study in populations of diverse altitudes

Rahul Kumar
Samantha Kohli
MA Qadar Pasha
Research19 Mar 2015
Hypertension Research

Volume: 38, P: 498-506

Search

Biomimetic synthesis and optimization of cyclic peptide antibiotics

On the public dissemination and open sourcing of ultrasound resources, datasets and deep learning models

Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects

Peptide cyclization catalysed by the thioesterase domain of tyrocidine synthetase

The LexA–RecA* structure reveals a cryptic lock-and-key mechanism for SOS activation

Direct enzymatic sequencing of 5-methylcytosine at single-base resolution

Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies

Efficient engineering of human and mouse primary cells using peptide-assisted genome editing

Controllable genome editing with split-engineered base editors

High-performance CRISPR-Cas12a genome editing for combinatorial genetic screening

Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase

AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation

Mechanisms for targeted, purposeful mutation revealed in an APOBEC–DNA complex

Grand Challenge Commentary: The chemistry of a dynamic genome

Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine

The strength and pattern of natural selection on gene expression in rice

Disruption of TET2 promotes the therapeutic efficacy of CD19-targeted T cells

A vitamin-C-derived DNA modification catalysed by an algal TET homologue

TET enzymes, TDG and the dynamics of DNA demethylation

Modular affinity-labeling of the cytosine demethylation base elements in DNA

CYBA (p22^phox) variants associate with blood pressure and oxidative stress markers in hypertension: a replication study in populations of diverse altitudes

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