About

Professor Aleksandra Skrajna is associated with the Global and Community Health Program, which is part of both the Social Sciences Division and Physical & Biological Sciences Division. The program emphasizes interdisciplinary teaching and research, involving faculty from across all five academic divisions. The program's focus is on healthcare and public health as interdisciplinary endeavors, with students engaging in interdisciplinary classes throughout their degree programs. The faculty and staff work together to support students in their academic and career pursuits aimed at fostering a healthier world.

Research topics

• Biology
• Genetics
• Biophysics
• Computational biology
• Cell biology

Selected publications

• Nickel-NTA lipid-monolayer affinity grids allow for high-resolution structure determination by cryo-EM

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-24

  preprintOpen access1st author

  Grid preparation is a rate-limiting step in determining high-resolution structures by single particle cryogenic electron microscopy (cryo-EM). Particle interaction with the air-water interface often leads to denaturation, aggregation, or a preferred orientation within the ice. Some samples yield insufficient quantities of particles when using traditional grid making techniques and require the use of solid supports that concentrate samples onto the grid. Recent advances in grid-preparation show that affinity grids are promising tools to selectively concentrate proteins while simultaneously protecting samples from the air-water interface. One such technique utilizes lipid monolayers containing a lipid species with an affinity handle. Some of the first affinity grids used a holey carbon layer coated with nickel nitrilotriacetic acid (Ni-NTA) lipid, which allowed for the binding of proteins bearing the commonly used poly-histidine affinity tag. These studies however used complicated protocols and were conducted before the “resolution revolution” of cryo-EM. Here, we provide a straight-forward preparation method and systematic analysis of Ni-NTA lipid monolayers as a tool for high-resolution single particle cryo-EM. We found that lipid affinity grids concentrate particles away from the air-water interface in thin ice (∼30 nm). We determined a 2.6 Å structure of the human nucleosome, showing this method is amenable to high-resolution structure determination. Furthermore, we determined a 3.1 Å structure of a sub-100 kDa protein demonstrating that this technique is amenable to proteins across biological size ranges. Lipid monolayers are therefore an easily extendable tool for most systems and help alleviate common problems such as low yield, disruption by the air-water interface, and thicker ice.

  PublisherOA PDFDOI

• Post-translational modification of H2B C-terminal helix regulates nucleosome interactions and chromatin signaling

  Nucleic Acids Research · 2025-09-04 · 1 citations

  articleOpen access

  Histone H2B contains a highly conserved C-terminal (H2B αC) helix that has been implicated in chromatin interactions and dynamics. The H2B αC helix comprising residues 105-125 is positioned adjacent to a major site of nucleosome interactions called the acidic patch. Despite individual structural studies highlighting interactions between chromatin proteins and the H2B αC helix, the general role of the helix in mediating nucleosome recognition has not been explored. Moreover, many post-translational modifications (PTMs) have been identified within the H2B αC helix, but significant gaps exist in our understanding of their regulatory potential. In this study, we employed nucleosome affinity proteomics using a library of nucleosomes with mutations or PTMs of the H2B αC helix to investigate contributions to nucleosome binding. Our work uncovers new spatial patterns of H2B αC helix engagement across the proteome. We also demonstrate that H2B K120 mono-ubiquitylation (H2B K120ub) within the H2B αC helix broadly disrupts nucleosome binding, phenocopying mutation of the acidic patch, while differentially regulating acidic patch-dependent chromatin functions. In contrast, lysine acetylation results in more subtle position-specific changes, highlighting a more general role of H2B αC helix PTMs in tuning acidic patch recognition.

  PublisherDOI

• Nickel-NTA lipid-monolayer affinity grids allow for high-resolution structure determination by cryo-EM

  Journal of Structural Biology · 2025-10-11

  articleOpen access1st authorCorresponding
  PublisherOA PDFDOI

• APC/C-mediated ubiquitylation of extranucleosomal histone complexes lacking canonical degrons

  Nature Communications · 2025-03-15 · 3 citations

  articleOpen access1st authorCorresponding

  Non-degradative histone ubiquitylation plays a myriad of well-defined roles in the regulation of gene expression and choreographing DNA damage repair pathways. In contrast, the contributions of degradative histone ubiquitylation on genomic processes has remained elusive. Recently, the APC/C has been shown to ubiquitylate histones to regulate gene expression in pluripotent cells, but the molecular mechanism is unclear. Here we show that despite directly binding to the nucleosome through subunit APC3, the APC/C is unable to ubiquitylate nucleosomal histones. In contrast, extranucleosomal H2A/H2B and H3/H4 complexes are broadly ubiquitylated by the APC/C in an unexpected manner. Using a combination of cryo-electron microscopy (cryo-EM) and biophysical and enzymatic assays, we demonstrate that APC8 and histone tails direct APC/C-mediated polyubiquitylation of core histones in the absence of traditional APC/C substrate degron sequences. Taken together, our work implicates APC/C-nucleosome tethering in the degradation of diverse chromatin-associated proteins and extranucleosomal histones for the regulation of transcription and the cell cycle and for preventing toxicity due to excess histone levels. The APC/C ubiquitylates histones to regulate gene expression in pluripotent cells. Here, the authors pair cryo-EM and biochemical and biophysical assays to show that instead of modifying nucleosome-incorporated histones, the APC/C ubiquitylates extranucleosomal histone complexes through a mechanism that bypasses canonical substrate degrons.

  PublisherOA PDFDOI

• PELP1 coordinates the modular assembly and enzymatic activity of the rixosome complex

  Science Advances · 2025-07-25 · 2 citations

  articleOpen access

  The rixosome is a large multisubunit complex that initiates RNA decay during critical nuclear transactions including ribosome assembly and heterochromatin maintenance. The overall architecture of the complex remains undefined because several subunits contain intrinsically disordered regions (IDRs). Here, we combined structural and functional approaches to establish PELP1 as the central scaffold of the rixosome upon which the enzymatic subunits modularly assemble. The C-terminal half of PELP1 is composed of a proline-rich IDR that mediates association with the AAA-ATPase MDN1, histones, and the SUMO-specific protease SENP3. The PELP1 IDR contains a glutamic acid-rich region that we establish can chaperone the histone octamer in vitro. Last, the x-ray structure of a small linear motif (SLiM) from the PELP IDR bound to SENP3 reveals how PELP1 allosterically activates SUMO protease activity. This work provides an integrated structural model for understanding the rixosome's dynamic architecture and how it modularly coordinates several cellular functions.

  PublisherDOI

• Abstract 1997 APC/C-mediated ubiquitylation of extranucleosomal histone complexes lacking canonical degrons

  Journal of Biological Chemistry · 2025-05-01

  articleOpen access

  Non-degradative histone ubiquitylation plays a myriad of welldefined roles in the regulation of gene expression and choreographing DNA damage repair pathways.In contrast, the contributions of degradative histone ubiquitylation on genomic processes has remained elusive.Recently, the 1.2 MDa E3 ubiquitin ligase, known as the Anaphase-Promoting Complex/Cyclosome (APC/C), has been shown to ubiquitylate histones to regulate gene expression in pluripotent cells, but the molecular mechanism is unclear.Here we show that despite directly binding to the nucleosome through subunit APC3, the APC/C is unable to ubiquitylate nucleosomal histones.In contrast, extranucleosomal H2A/H2B and H3/H4 complexes are broadly ubiquitylated by the APC/C in an unexpected manner.Using a combination of cryo-electron microscopy (cryo-EM) and biophysical and enzymatic assays, we demonstrate that APC8 and histone tails direct APC/Cmediated polyubiquitylation of core histones in the absence of traditional APC/C substrate degron sequences.Taken together, our work implicates APC/C-nucleosome tethering in the degradation of diverse chromatin-associated proteins and extranucleosomal histones for the regulation of transcription and the cell cycle and for preventing toxicity due to excess histone levels.

  PublisherOA PDFDOI

• Exploring the Use of Lipid-Monolayers Affinity Grids for CryoEM Structural Determination of Protein Complexes at a Multi-User Core Facility

  Microscopy and Microanalysis · 2024-07-01

  article1st authorCorresponding
  PublisherDOI

• Time Resolved-Fluorescence Resonance Energy Transfer platform for quantitative nucleosome binding and footprinting

  UNC Libraries · 2024-08-14 · 4 citations

  articleOpen access

  Quantitative analysis of chromatin protein-nucleosome interactions is essential to understand regulation of genome-templated processes. However, current methods to measure nucleosome interactions are limited by low throughput, low signal-to-noise, and/or the requirement for specialized instrumentation. Here, we report a Lanthanide Chelate Excite Time-Resolved Fluorescence Resonance Energy Transfer (LANCE TR-FRET) assay to efficiently quantify chromatin protein-nucleosome interactions. The system makes use of commercially available reagents, offers robust signal-to-noise with minimal sample requirements, uses a conventional fluorescence microplate reader, and can be adapted for high-throughput workflows. We determined the nucleosome-binding affinities of several chromatin proteins and complexes, which are consistent with measurements obtained through orthogonal biophysical methods. We also developed a TR-FRET competition assay for high-resolution footprinting of chromatin protein-nucleosome interactions. Finally, we set up a TR-FRET competition assay using the LANA peptide to quantitate nucleosome acidic patch binding. We applied this assay to establish a proof-of-principle for regulation of nucleosome acidic patch binding by methylation of chromatin protein arginine anchors. Overall, our TR-FRET assays allow facile, high-throughput quantification of chromatin interactions and are poised to complement mechanistic chromatin biochemistry, structural biology, and drug discovery programs.

  PublisherDOI

• Structural basis of paralog-specific KDM2A/B nucleosome recognition

  UNC Libraries · 2024-08-14

  articleOpen access1st authorCorresponding
  PublisherDOI

• Structural basis of paralog-specific KDM2A/B nucleosome recognition

  Nature Chemical Biology · 2023-02-16 · 27 citations

  articleOpen access
  PublisherOA PDFDOI

Frequent coauthors

• Robert K. McGinty

  18 shared

• Zbigniew Domiński

  University of North Carolina at Chapel Hill

  11 shared

• Michał Dadlez

  Institute of Biochemistry and Biophysics, Polish Academy of Sciences

  10 shared

• William F. Marzluff

  University of North Carolina at Chapel Hill

  8 shared

• Dennis Goldfarb

  Washington University in St. Louis

  8 shared

• Cheng Yang

  Ningxia Medical University

  7 shared

• Gabrielle R. Budziszewski

  Hauptman-Woodward Medical Research Institute

  5 shared

• Holly C. Simmons

  University of Pittsburgh

  5 shared

Education

• PhD, Biophysics

  Institute of Biochemistry and Biophysics

  2016

• B.S., Biophysics

  University of Warsaw

  2015

• M.S., Molecular Biology

  University of Warsaw

  2011

• B.S., Molecular Biology

  University of Warsaw

  2009

Awards & honors

• Forbeck Scholar Award (2025)
• Postdoctoral Award for Research Excellence, UNC Chapel Hill…
• American Cancer Society Postdoctoral Fellowship (2019-2022)