Highlighted Publications Archive

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