Highlighted Publications Archive

John Janetzko, PhD, Assistant Professor of Biochemistry and Molecular Genetics and Neil Kelleher (Northwestern University), are corresponding authors on a research article "Capillary Zone Electrophoresis-Mass Spectrometry of Intact G Protein Coupled Receptors Enables Proteoform Profiling" published March 27 in Analytical Chemistry. This study opens new opportunities for profiling the post-translational landscape of complex membrane protein samples towards a better understanding of drug action and disease pathogenesis.

T. Rajendra Kumar, PhD, Professor of Obstetrics and Gynecology, and Neelanjan Mukherjee, PhD, Assistant Professor of Biochemistry and Molecular Genetics, are corresponding authors of a research article, “Identification of FSH-regulated and estrous stage-specific transcriptional networks in mouse ovaries,” published February 10 by the Proceedings of the National Academy of Sciences. The study may eventually allow researchers to identify potential targets for fertility enhancement or blockade in women. Four co-authors are from our campus.

Expanding the tagging toolbox for visualizing translation live 
Ning Zhao Lab - February 2025 - Biochemical Journal

Redundant pathways for removal of defective RNA polymerase II complexes at a promoter-proximal pause checkpoint
Nova Fong & Bentley Lab - January 2025 - Molecular Cell

Nucleation and spreading maintain Polycomb domains every cell cycle
Giovana Veronezi & Ramachandran Lab – April 2024 – Cell Reports

Multiomics Signatures of Coagulopathy in a Polytrauma Swine Model Contrasted with Severe Multisystem Injured Patients
Ian LaCroix, Angelo D’Alessandro, & Hansen Lab - February 2024 - Journal of Proteome Research

Differential subcellular localization of ASPM RNA and protein
Hei-Yong Grant Lo, Matthew Taliaferro, & Taliaferro Lab - January 2024 - MicroPublication Biology

Synonymous codon usage regulates translation initiation
Chloe Barrington & Rissland Lab – December 2023 – Cell Reports

The role of midbody-associated mRNAs in regulating abscission
Katie Vaeth & Prekeris & Taliaferro Labs – December 2023 – Journal of Cell Biology

Small-molecule Ro-08-2750 interacts with many RNA-binding proteins and elicits MUSASHI2-independent phenotypes
Kathryn Walters & Mukherjee Lab – October 2023 - RNA

Compromised nonsense-mediated RNA decay results in truncated RNA-binding protein production upon DUX4 expression
Amy Campbell & Jagannathan Lab – June 2023 – Cell Reports

Z-RNA biology: A central role in the innate immune response?
Parker Nichols, Jeffrey Krall, Morkos Henen, Beat Vögeli, & Quentin Vicens - January 2023 - RNA

The molecular mechanism of sialic acid transport mediated by Sialin
Wenxin Hu & Hongjin Zheng - January 2023 - Science Advances

Proteolytic activation of human-specific Olduvai domains by the furin protease
Ashley Pacheco, Aaron Issaian, & Sikela & Hansen Labs with Vogeli Lab - January 2023 - Int J Biol Macromol

Structure and Formation of Z-DNA and Z-RNA
Jeffrey Krall, Parker Nichols, Morkos Henen, Quentin Vicens, & Beat Vogeli - January 2023 - Molecules

Pre-mRNA splicing and its co-transcriptional connections
Hossein Shenasa & David Bentley - May 2023 - Trends in Genetics

Z-RNA biology: A central role in the innate immune response?
Morkos A Henen & Beat Vögeli - December 2022 - RNA

Brief considerations on targeting RNA with small molecules
Quentin Vicens - December 2022 - Faculty Opinions

Nucleotide-level linkage of transcriptional elongation and polyadenylation
Nova Fong, Ben Erickson, & Bentley Lab - November 2022 - eLife

Xrn2 substrate mapping identifies torpedo loading sites and extensive premature termination of RNA pol II transcription
Michael Cortazar & Bentley Lab - November 2022 - Genes & Dev.

Promiscuity of response regulators for thioredoxin steers bacterial virulence
Morkos Henen & Beat Vögeli - October 2022 - Nature Communications 

The pausing zone and control of RNA polymerase II elongation by Spt5: implications for the pause-release model 
Nova Fong, Ryan Sheridan, Srinivas Ramachandran, & David Bentley - October 2022 - Molecular Cell

High-throughput identification of RNA localization elements in neuronal cells
Ankita Arora, Matthew Taliaferro, & Charlie Moffatt - September 2022 - Nucleic Acids Research

Ligand-specific conformational change drives interdomain allostery in Pin1
Morkos Henen & Beat Vogeli - August 2022 - Nature Communications 

Thoughts on how to think (and talk) about RNA structure
Quentin Vicens & Jeff Kieft - April 2022 - PNAS

Therapeutic resistance in acute myeloid leukemia cells is mediated by a novel ATM/mTOR pathway regulating oxidative phosphorylation

Hae Park, Jeff Kieft, Mark Gregory, & James DeGregori - October 2022 - ELife

 

SAM1 domain of SASH1 harbors distinctive structural heterogeneity

Morkos Henen & Beat Vögeli - October 2022 - Journal of Structural Biology

 

Atomic resolution protein allostery from the multi-state structure of a PDZ domain

Beat Vögeli - October 2022 - Nature Communications 

 

A single N6-methyladenosine site regulates lncRNA HOTAIR function in breast cancer cells
Allison Porman Swain & Johnson Lab - November 2022 - PLoS Biol

A viral RNA hijacks host machinery using dynamic conformational changes of a tRNA-like structure

Kieft Lab – November 2021 - Science

 

Identification and Development of Therapeutics for COVID-19

Greene Lab – November 2021 – mSystems

 

Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure

Greene Lab – October 2021 – mSystems

 

Cells with cancer-associated mutations overtake our tissues as we age

DeGregori Lab – October 2021 – Aging and Cancer

 

Reconstruction of Coupled Intra- and Interdomain Protein Motion from Nuclear and Electron Magnetic Resonance

Vögeli Lab – September 2021 – Journal of the American Chemical Society

 

Shared properties and singularities of exoribonuclease-resistant RNAs in viruses

Kieft Lab – July 2021 – Computational and Structural Biotechnology Journal

 

Recruitment of endoplasmic reticulum-targeted and cytosolic mRNAs into membrane-associated stress granules

Jagannathan Lab – July 2021 – RNA Journal

 

Chronic interleukin-1 exposure triggers selection for Cebpa-knockout multipotent hematopoietic progenitors

DeGregori Lab – June 2021 – Journal of Experimental Medicine

 

RNA-binding proteins regulate aldosterone homeostasis in human steroidogenic cells

Mukherjee Lab – June 2021 – RNA Journal

 

The Inherent Dynamics and Interaction Sites of the SARS-CoV-2 Nucleocapsid N-Terminal Region

Eisenmesser Lab – June 2021 – Journal of Molecular Biology

 

Modulating Enzyme Function via Dynamic Allostery within Biliverdin Reductase B

Eisenmesser Lab – May 2021 – Frontiers in Molecular Biosciences

 

Establishing RNA-RNA interactions remodels lncRNA structure and promotes PRC2 activity

Johnson Lab – April 2021 – Science Advances

 

Cooperative binding between distant transcription factors is a hallmark of active enhancers

Ramachandran Lab – April 2021 – Molecular Cell

 

Centromeres are dismantled by foundational meiotic proteins Spo11 and Rec8

Cooper Lab – March 2021 - Nature

 

Alternative RNA structures formed during transcription depend on elongation rate and modify RNA processing

Bentley Lab – February 2021 – Molecular Cell

 

Recognition of non-CpG repeats in Alu and ribosomal RNAs by the Z-RNA binding domain of ADAR1 induces A-Z junctions

Vögeli Lab - February 2021 - Nature Communications

 

The disordered Spindly C-terminus interacts with RZZ subunits ROD-1 and ZWL-1 in the kinetochore through the same sites in C. elegans

Vögeli Lab - February 2021 - JMB

Structural and mechanistic bases for a potent HIV-1 capsid inhibitor

Asturias Lab - October 2020 - Science

 

Physiologic RNA Targets and Refined Sequence Specificity of Coronavirus EndoU

Hesselberth Lab - September 2020 - RNA Journal

 

Comprehensive Chromosome End Remodeling during Programmed DNA Elimination

Davis Lab - September 2020 - Current Biology

 

The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold

Kieft Lab - August 2020 - RNA Journal

 

A somatic evolutionary model of the dynamics of aneuploid cells during hematopoietic reconstitution

DeGregori Lab - July 2020 - Scientific Reports

 

The E2 Marie Kondo and the CTLH E3 ligase clear deposited RNA binding proteins during the maternal-to-zygotic transition

Rissland Lab - June 2020 - eLife

 

COVID-19 infection alters kynurenine and fatty acid metabolism, correlating with IL-6 levels and renal status

D’Alessandro Lab - June 2020 - JCI Insight

 

FMRP promotes RNA localization to neuronal projections through interactions between its RGG domain and G-quadruplex RNA sequences

Taliaferro Lab - June 2020 - eLife

 

Identification of a Small-Molecule Inhibitor That Disrupts the SIX1/EYA2 Complex, EMT, and Metastasis

Zhao Lab - June 2020 - Cancer Research

 

The Driver of Extreme Human-Specific Olduvai Repeat Expansion Remains Highly Active in the Human Genome

Sikela Lab - January 2020 - Genetics

Control of RNA Pol II Speed by PNUTS-PP1 and Spt5 Dephosphorylation Facilitates Termination by a "Sitting Duck Torpedo" Mechanism

Bentley Lab - December 2019 - Molecular Cell

 

Control of RNA Pol II Speed by PNUTS-PP1 and Spt5 Dephosphorylation Facilitates Termination by a "Sitting Duck Torpedo" Mechanism
Bentley Lab - October 2019 - NIH

Solution NMR backbone assignment reveals interaction-free tumbling of human lineage-specific Olduvai protein domains
Vögeli Lab - October 2019 - NIH

A unified mechanism for intron and exon definition and back-splicing

Zhao Lab - September 2019 – Nature

 

Structural and functional analyses of an allosteric Eya2 phosphatase inhibitor that has on target effects in human lung cancer cells

Zhao Lab - September 2019 - Mol Cancer Ther

 

​Coding regions affect mRNA stability in human cells
Rissland Lab - September 2019 - RNA

A unified mechanism for intron and exon definition and back-splicing
Zhao Lab - September 2019 - nature

Structural and functional analyses of an allosteric Eya2 phosphatase inhibitor that has on target effects in human lung cancer cells

Zhao Lab - September 2019 - AACR

A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers
Asturias Lab - August 2019 - Cell Press

A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers
Asturias Lab - August 2019 - Cell 

Solution NMR backbone assignment reveals interaction-free tumbling of human lineage-specific Olduvai protein domains

Vögeli Lab - July 2019 - Biomolecular NMR Assignments

 

​Paired involvement of human-specific Olduvai domains and NOTCH2NL genes in human brain evolution
Davis and Sikela Labs - May 2019 - SpringerLink

​Anti-Aging Discovery Could Lead to Restorative Skin Treatments
DeGregori Lab - April 2019 - Scientific American 

​Multiple decay events target HAC1 mRNA during splicing to regulate the unfolded protein response
Hesselberth Lab - March 2019 - eLife

A Third Linear Association Between Olduvai (DUF1220) Copy Number and Severity of the Classic Symptoms of Inherited Autism​
Davis and Sikela Labs - February 2019 - Psychiatry Online 

​A transient helix in the disordered region of dynein light intermediate chain links the motor to structurally diverse adaptors for cargo transport
Vögeli Lab - January 2019 - PLOS

The comparative genomics and complex population history of Papio baboons​
Sikela Lab - January 2019 - ScienceAdvances

​Widespread backtracking by RNA Pol II is a major effector of gene activation, 5’ pause release, termination, and transcription elongation rate

Bentley Lab - November 2018 - Cell Press

Mitochondrial accumulation of amyloid beta (Aβ) peptides requires TOMM22 as a main Aβ receptor in yeast.​
Zheng Lab - August 2018 - NIH

Scientists are untangling our bodies’ genetic “double-edged swords”
Sikela Lab - June 2018 - Salon

Eya3 partners with PP2A to induce c-Myc stabilization and tumor progression

Zhao Lab - March 2018 - Nature

Transcription elongation rate affects nascent histone pre-mRNA folding and 3' end processing
Bentley Lab - February 2018 - Genes & Development 

The interplay of histone H2B ubiquitination with budding and fission yeast heterochromatin.
Johnson Lab - February 2018 - NIH

NOE-Derived Methyl Distances from a 360 kDa Proteasome Complex​
Vögeli Lab - January 2018 - NIH

Genetic bypass of essential RNA repair enzymes in budding yeast
Hesselberth Lab - December 2017 - NIH

Recruitment and allosteric stimulation of a histone-deubiquitinating enzyme during heterochromatin assembly.
Johnson Lab - December 2017 - NIH

Comparative genome analysis of programmed DNA elimination in nematodes

Davis Lab - November 2017 - Genome Research 

Genomic trade‑ofs: are autism and schizophrenia the steep price of the human brain?
Sikela Lab - November 2017 - Human Genetics 

Structure of the yeast spliceosomal postcatalytic P complex​
Zhao​ Lab - November 2017 - Science

Localization of Cdc7 Protein Kinase During DNA Replication in Saccharomyces cerevisiae​
Sclafani and Hesselberth​​ Labs - November 2017 - GSA

Sequence entropy of folding and the absolute rate of amino acid substitutions​
Pollock Lab - October 2017 - Nature

RNA Pol II Dynamics Modulate Co-transcriptional Chromatin Modification, CTD Phosphorylation, and Transcriptional Direction
Bentley Lab - May 2017 - ScienceDirect

Mediator structure and rearrangements required for holoenzyme formation
Asturias Lab - April 2017 - NIH

Changing mutational and adaptive landscapes and the genesis of cancer​​
DeGregori Lab - February 2017 - NIH

Networks of Dynamic Allostery Regulate Enzyme Function​
Eisenmesser Lab - January 2017 - NIH

Translation initiation by the hepatitis C virus IRES requires eIF1A and ribosomal complex remodeling

Kieft​ Lab - December 2016 - NIH

Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease​

Kieft​ Lab - November 2016 - NIH

A novel role for yeast casein kinases in glucose sensing and signaling
Johnston Lab - September 2016 - NIH

An RNA matchmaker protein re​gulates the activity of the long noncoding RNA HOTAIR
Johnson Lab - May 2016 - RNA

Three-way junction conformation dictates self-association of phage packaging RNAs.
Kieft Lab - May 2016 - NIH

How to write titles that ​tempt
Johnson Lab - March 2016 - GSA

Selectable one-step PCR-mediated integration of a degron for rapid depletion of endogenous human proteins.
Bentley Lab - February 2016 - NIH

DUF1220 copy number is associated with schizophrenia risk and severity: implications for understanding autism and schizophrenia as related diseases

Sikela​​  Lab - December 2015 - NIH