B. A. Garcia

Chromatin profiling identifies putative dual roles for H3K27me3 in regulating transposons and cell type specific genes in choanoflagellates

The paper identifies H3K27me3's dual role in regulating transposons and cell type-specific genes in choanoflagellates, suggesting ancestral chromatin mechanisms in development.

An Unbiased Proteomic Platform for ATE1-based Arginylation Profiling

The paper introduces an unbiased proteomic platform for ATE1-based arginylation profiling, identifying 235 unique arginylation sites in human proteomes.

Defining the heterogeneous molecular landscape of lung cancer cell responses to epigenetic inhibition

The paper profiles molecular responses to HDAC inhibitors in diverse cell lines, revealing heterogeneous protein remodeling and cell-type specific effects.

Development and application of GlycanDIA workflow for glycomic analysis

The paper develops GlycanDIA, a DIA-based workflow for glycan identification and quantification, showing improved sensitivity and the ability to detect low-abundant modified glycans.

A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma

This study identifies DLK1 as a potential immunotherapeutic target in neuroblastoma through integrative proteomic, transcriptomic, and epigenomic analysis.

Comparative analysis of drug-like EP300/CREBBP acetyltransferase inhibitors

This study compares the biochemical and biological potencies of three EP300/CREBBP acetyltransferase inhibitors and demonstrates their utility in investigating epigenetic mechanisms.

Expanding the epitranscriptomic RNA sequencing and modification mapping mass spectrometry toolbox with field asymmetric waveform ion mobility and electrochemical elution liquid chromatography

This paper introduces a combined FAIMS and EMLC approach to improve RNA modification detection and sequencing in complex samples.

Post-translational modification by the Pgf glycosylation machinery modulates Streptococcus mutans physiology and virulence

This study shows that the Pgf glycosylation machinery in Streptococcus mutans modifies surface proteins, affecting biofilm formation and virulence, with phosphorylation compensating for glycosylation loss.

Permethylation of ribonucleosides provides enhanced mass spectrometry quantification of post-transcriptional modifications

This paper introduces a method to enhance RNA modification analysis using permethylation and LC-MS/MS, showing improved detection of cytosine methylation and hydroxymethylation in mouse embryonic stem cells.

A conserved long intergenic non-coding RNA containing snoRNA sequences, lncCOBRA1, affects Arabidopsis germination and development

This study identifies lncCOBRA1, a conserved lncRNA in Arabidopsis containing snoRNA domains, showing its role in germination and plant development.

Stable Isotope Tracing In Vivo Reveals A Metabolic Bridge Linking The Microbiota To Host Histone Acetylation

This study uses stable isotope tracing to show that gut microbiota supply carbon for host histone acetylation, linking microbial metabolism to host epigenetic regulation.

Structural visualization of de novo initiation of RNA polymerase II transcription

This study reports structures of RNA polymerase II initiation complexes showing TFIIH's role in promoter melting and transcription initiation.

Glycoproteomics of Haloferax volcanii reveals an extensive glycoproteome and concurrence of different N-glycosylation pathways

The paper identifies an extensive N-glycoproteome in Haloferax volcanii and shows that different N-glycosylation pathways can modify the same sites under identical culture conditions.

Structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in Nucleotide Excision Repair

The paper presents a cryo-EM structure of an NER initiation complex involving Rad4-Rad23-Rad33 and TFIIH bound to a DNA lesion, revealing DNA unwinding and translocation mechanisms.

Improved SILAC quantification with data independent acquisition to investigate bortezomib-induced protein degradation

This paper improves SILAC quantification using DIA to study bortezomib-induced protein degradation, finding enhanced accuracy and sensitivity in protein turnover models.

The propofol binding sites of prokaryotic voltage-gated sodium channels

This study identifies conserved propofol binding sites in prokaryotic voltage-gated sodium channels and shows how conformational changes at these sites mediate propofol's effects on channel function.

PAX8 orchestrates an angiogenic program through interaction with SOX17

This study identifies SOX17 as a PAX8-interacting partner and shows their role in regulating tumor angiogenesis in ovarian cancer, suggesting a new therapeutic target.

Cryo-EM Structures of Respiratory bc1-cbb3 type CIII2CIV Super-complex and Electronic Communication Between the Complexes

This paper reports the first cryo-EM structure of a bacterial respiratory bc1-cbb3 super-complex and native CIII2 conformers, revealing structural and electronic communication features between complexes.

Mechanistic insights into volatile anesthetic modulation of K2P channels

This study identifies a volatile anesthetic binding site in TREK1 K2P channels and shows its role in modulating channel activity through molecular dynamics and mutagenesis.

Viral-mediated ubiquitination impacts interactions of host proteins with viral RNA and promotes viral RNA processing

The paper identifies RNA-binding proteins as substrates of viral-mediated ubiquitination, showing that non-degradative ubiquitination enhances viral RNA processing and progeny production.

A histone-like motif in yellow fever virus contributes to viral replication

This study identifies a histone-like motif in the yellow fever virus capsid protein that mimics histone H4 and interferes with BRD4-mediated gene regulation, impacting viral replication.

The Viral Polymerase Complex Mediates the Interaction of vRNPs with Recycling Endosomes During SeV Assembly

The paper identifies viral polymerase complex components L and C as mediators of vRNP interaction with Rab11a-marked recycling endosomes during SeV assembly.

Phosphorylation of the ancestral histone variant H3.3 amplifies stimulation-induced transcription

The paper identifies phosphorylation of H3.3S31 in response to pathogen sensing in macrophages and shows its role in recruiting SETD2 to enhance transcription of inflammatory genes.

HYPERsol: flash-frozen results from archival FFPE tissue for clinical proteomics

HYPERsol enables efficient and reproducible proteome analysis from FFPE tissues, achieving results comparable to flash-frozen samples.

PFA ependymoma-associated protein EZHIP inhibits PRC2 activity through a H3 K27M-like mechanism

This study identifies EZHIP as a PRC2 inhibitor in PFA ependymomas that mimics the H3 K27M oncohistone by disrupting PRC2 activity and H3K27me3 levels.

Hydrogen-deuterium exchange coupled to top- and middle-down mass spectrometry enables high-resolution measurements of histone tail dynamics before and after nucleosome assembly

This paper uses HDX-MS/MS with ETD to study histone tail dynamics before and after nucleosome assembly, achieving high-resolution deuterium localization.