Digital Commons Network^™

Starspot Inference Using Light Curve Inversion Techniques, Mohammad Refat

Dissertations, Theses, and Capstone Projects

Star spots are patches that are dark or bright on the surface of a star. They are tightly correlated to the magnetic activity of stars. One of the reasons we want to study star spots is to better understand where the active latitude of stars are located, which helps us understand planet habitability around low mass stars. The Starry package is a set of tools that can map the surface of stars and exoplanets using time series data, with spherical harmonics. Butterpy is a package that allows for the simulation of starspot evolution and their lightcurves. Fleck is a package …

Mechanisms Of Sleep Regulation In Drosophila Melanogaster, Anfal A. Abuhilal

Dissertations, Theses, and Capstone Projects

Sleep is a fundamental biological need, and sufficient sleep is required for physical and mental well-being. Sleep is regulated by two biological mechanisms: sleep-wake homeostasis and circadian rhythm. Circadian rhythms are near 24-h rhythms in behavior and physiology that are generated by endogenous mechanisms. In mammals, the suprachiasmatic nucleus (SCN) is the central circadian pacemaker, which is known to receive a significant amount of serotonergic input that likely modulates sleep rhythms. In addition to circadian modulation, sleep is subject to homeostatic regulation. Several neuromodulators have been proposed as mediators of sleep homeostasis. Serotonin has been implicated in sleep drive and …

Flotsam And Jetsam: The Role Of Mlb Integration In The Wreckage Of The Negro Leagues, Nastasia Pollas

Dissertations, Theses, and Capstone Projects

“We are the ship, all else the sea.” Adapted from a Frederick Douglass speech, this quote by Rube Foster became the slogan of the Negro Leagues, illustrating the resolve and determination to prosper alone during a time of segregation. Setting aside long-standing rivalry and strife, Black baseball teams united under a shared vision of forming the first professional Black baseball league.

This paper examines how Giddens' structuration theory, connecting social structures with individual actions, can explain both the development and success of the league under segregation and its eventual demise during integration.

How To Form A Gravitational-Wave Source: Quantifying Intermediate Evolutionary Stages In Isolated Binary Stellar Evolution, Ana Lam

Dissertations, Theses, and Capstone Projects

Gravitational-wave (GW) detections from double compact object (DCO) mergers provide crucial observational constraints for understanding massive stars across cosmic time. Coupled with these observations, binary population synthesis simulations become powerful tools for probing the formation, evolution, and ultimate fates of their progenitors---massive binary stars. However, complex evolutionary pathways, shaped by key intermediate stages such as mass transfer phases and supernovae, present a significant challenge to assess their impact. To address this, we develop a framework to quantify the influence of intermediate evolutionary stages on GW sources. By combining Sankey diagrams with survival factors, we systematically investigate how intermediate stages influence …

Britten’S Violin Concerto And His Early Period—Score Analysis And Pacifist Narrative, Magdalena Filipczak

Dissertations, Theses, and Capstone Projects

This dissertation presents a comprehensive study of Benjamin Britten’s Violin Concerto, Op. 15, using the work as a lens through which to examine the composer’s early period. Rather than treating the concerto as a purely technical or stylistic artifact, the study situates it within the broader context of Britten’s formative years, his early artistic circles, the political tensions of the 1930s, and his evolving pacifist stance.

The final third of the dissertation offers a detailed formal and interpretative analysis of the full orchestral score, tracing an expressive arc across the entire work by identifying an idée fixe motif and following …

Refining Orbits And Revealing Origins: A Study Of Giant Exoplanets Around Low-Mass Stars, Angeli Sandoval

Dissertations, Theses, and Capstone Projects

The study of gas giants around low-mass stars offers important insight into planet formation. Core accretion models predict that these planets should have a low likelihood of forming due to the limited disk masses of their host low-mass stars. However, NASA space missions such as Kepler and TESS have revealed an emerging population of Saturn- and Jupiter-like planets around M-dwarfs (referred to as giant exoplanets orbiting M-dwarfs or GEMS) that challenge these expectations. This thesis investigates the detection, confirmation, and analysis of GEMS through pipeline development and a detailed analysis of two systems.

In Chapter 1, I provide background information …

Structural Characterization Of A Tarantula Toxin And Its Interactions With Lipid Bilayers And Voltage-Gated Sodium Channels, Krishnakoli Adhikary

Dissertations, Theses, and Capstone Projects

Voltage-gated ion channels are membrane protein complexes. They allow the selective flow of their respective ions down an electrochemical gradient through a central ion conduction pore surrounded by four voltage-sensing domains (VSDs). Various neurological and cardiovascular diseases are caused by mutations in voltage-gated ion channels (VGICs). One of the biggest challenges today is addiction to opioid medication. Coming up with non-opioid drug leads can be a real blessing for society. This is where voltage-gated sodium channel research comes in. Na_v1.7, Na_v1.8, and Na_v1.9 are responsible for pain sensations. Loss or gain of function in …

Processing Of Diphthongs By Turkish English Bilinguals: An Erp Study, Ecem Kopuz

Dissertations, Theses, and Capstone Projects

This study examines how native phonological experience influences the brain’s response to speech sounds in Turkish-English late bilinguals and English monolinguals. We asked whether neural responses reflecting encoding of auditory information would be sensitive to language specific experience. Using event-related potentials (ERPs), and specifically, the Acoustic Change Complex (ACC) we measured neural responses to four stimuli, /u/, /ua/, /iu/, and /ia/, where vowel quality changes for three of these. A change from /u/ to /a/ or /i/ to /a/ within a syllable (as in [ua] and [ia]) represents a clear vowel quality shift. All participants were expected to show sensitivity …

Liberated Learning Spaces: A Visual Playlist, Tarilyn R. Little

Dissertations, Theses, and Capstone Projects

Liberation can be defined as “the act of setting free” or “being free from limits on thoughts and behavior.” Both an action and a state of being, liberation has long been centered as a key function of education, particularly for those who live in historically and systemically marginalized identities. Despite the long-standing existence of liberation-focused pedagogies and activism aimed at transforming schools and students’ lived experiences, educational institutions in the United States have struggled to live out these ideals, often sustaining and replicating systems and practices of oppression. Drawing on historical and contemporary conversations in education and psychology, Liberated Learning …

Crisis Narratives And The Vicissitudes Of Haitian Foodways: A Critical Comparison Of Three Food Items, Marc S. Gabriel

Dissertations, Theses, and Capstone Projects

Polities and media external to Haiti direct a lot of narrative focus on the country being the source of its own protracted crises. This represents a powerful narrative hegemony that casts the post-colonial nation as a zone of perpetual disasters or crisis. To maintain that narrative domination over Haiti, opportunistic observers of Haiti’s media spectacles of crisis only need to atomize the country’s newest crisis or natural disaster from the history that situates it. The elision of the Haitian memory – a memory of structural adjustment programs, systematic displacement, foreign-sponsored paramilitary violence, erosion of peasant foodways and agriculture – from …

Satellite-Host Galaxy Co-Evolution With Next-Generation Regulator Models, Austen Gabrielpillai

Dissertations, Theses, and Capstone Projects

The evolution of satellites galaxies is an unsolved problem in galaxy formation. Recent observations such as the SAGA and ELVES surveys find tension in HI contents and star formation of satellites around their central host galaxies when compared to our own local environment, the Milky Way. These processes are potentially highly influenced by the host's circumgalactic medium (CGM), and to constrain these cases requires accurate and fast modeling of satellites-host interactions. In this work, we present our methodology for evolving z = 0 surviving satellites alongside their central galaxy in sapphire, a CGM regulator co-evolution model of galaxy formation. …

Non-Perturbative Aspects Of Gauge Theories Through A Complex Parametrization, Antonina Maj

Dissertations, Theses, and Capstone Projects

This dissertation explores a complex matrix parametrization of four-dimensional non-Abelian gauge theories as a means of gaining analytical insights into (3+1)-dimensional QCD. The low-energy scale of non-Abelian gauge theories remains an elusive area of research even after decades of work. A key challenge lies in identifying physical, gauge-invariant degrees of freedom that are relevant to non-perturbative phenomena. In this dissertation we develop a complex parametrization of gauge fields on which gauge transformations act homogeneously, thereby enabling a manifestly gauge-invariant analytical formulation of the theory.

Chapter one constructs the complex gauge-invariant parametrization for gauge theories living on both complex projective space …

Investigation Of Motor Neuronal And Circuit Level Mechanistic Determinants Of Spinal Excitability Following Cst Injury, Thelma Bethea

Dissertations, Theses, and Capstone Projects

The corticospinal tract (CST) is the primary descending motor pathway in mammals, essential for precise, dexterous movements, especially in humans and nonhuman primates. Damage to the CST, such as from spinal cord injury (SCI), impairs skilled motor function and triggers maladaptive changes including aberrant proprioceptive afferent sprouting and increased spinal excitability. These changes are closely linked to both muscle weakness and the development of hyperreflexia, compounding the functional deficits. Animal models of SCI are valuable for investigating mechanisms of injury and recovery, though traditional models often limit the ability to isolate circuit-specific contributions. To address this, I employed selective unilateral …

The Georgian Of Heritage Speaker Children, Cass Lowry

Dissertations, Theses, and Capstone Projects

This dissertation presents three research articles united in the goal of describing the Georgian language as it is spoken by heritage speakers in the Brooklyn diaspora. The Georgian heritage speaker subjects recruited for these studies were children due to immigration patterns at the time when experimental data was collected. Their production of morphosyntactic inflection and pronouns is compared to adult and child homeland speakers.

Heritage speakers of Georgian demonstrate the following divergences from homeland and standard language comparisons. Nominal case inflection is most affected in heritage production, as heritage speakers use a default case or collapse Georgian's split-ergative and inverse …

Digital Odyssey: Navigating Culture, Structure, And Agency In The Transformation Of A Public University, Lisa Santa-Coloma

Dissertations, Theses, and Capstone Projects

Digital transformation broadly refers to the process of enacting digital technologies to fundamentally change how an organization creates value, enhancing the customer experience, increasing efficiency, and achieving a sustained competitive advantage. Current industry research estimates that over 90 percent of large organizations globally are undertaking digital transformation initiatives, yet a surprisingly low percentage of them report a resulting lift in revenue or improved efficiency. This trend is particularly pronounced in the education sector, where universities, navigating the pressure of lower enrollment rates following the global pandemic and the impact of disruptive technology such as artificial intelligence and online learning platforms, …

Quantum Entanglement Correlations In The Proton On The Light-Front, Eric Kolbusz

Dissertations, Theses, and Capstone Projects

In this work we gather results on information theory applied to proton tomography. We start by analyzing the quantum entanglement of momentum, spin-flavor, and color degrees of freedom (d.o.f.) in the leading valence-quark state of the proton on the light front using standard information theoretical tools, leveraging model wavefunctions by Brodsky and Schlumpf to obtain numerical predictions. Light-cone perturbation theory allows us to introduce the one-gluon correction in the sub-leading Fock state and study the entanglement of the gluonic d.o.f. We find weak entanglement in the spatial d.o.f. of the valence quarks, and significantly stronger entanglement in the analogous d.o.f. …

Predicting Clinical Success Of Ct-Based Functional Drained Liver Volume Assessment In Malignant Biliary Obstruction, Ethan Y Lin, Bruno C Odisio, Koustav Pal, Iwan Paolucci, Ryan P Kempen, Nicolas Cardenas, Paige Reed, Ketan Y Shah, Ahmed Awad, Rahul A Sheth, David Fuentes, Alda Tam

Faculty, Staff and Student Publications

Purpose

To compare the predictive accuracy of subjective versus objective assessment of three-dimensional functional drained liver volume (fDLV) for clinical success after percutaneous transhepatic biliary drainage (PTBD).

Materials and Methods

This retrospective study included patients with malignant biliary obstruction and hyperbilirubinemia who underwent de novo PTBD between January 2016 and February 2017. Clinical success was defined as achieving total bilirubin level less than 1.8 mg/dL (30.8 μmol/L) within 30 days after PTBD. Seven interventional radiologists independently categorized subjective fDLV into four groups: less than 30%, 30%–50%, 51%–75%, and greater than 75% of the total liver volume. Objective fDLV was calculated …

Author Correction: Oncolytic Dnx-2401 Virotherapy Plus Pembrolizumab In Recurrent Glioblastoma: A Phase 1/2 Trial, Farshad Nassiri, Vikas Patil, Leeor S Yefet, Olivia Singh, Jeff Liu, Rachel M A Dang, Takafumi N Yamaguchi, Mariza Daras, Timothy F Cloughesy, Howard Colman, Priya U Kumthekar, Clark C Chen, Robert Aiken, Morris D Groves, Shirley S Ong, Rohan Ramakrishna, Michael A Vogelbaum, Simon Khagi, Thomas Kaley, Jason M Melear, David M Peereboom, Analiz Rodriguez, Maxim Yankelevich, Suresh G Nair, Vinay K Puduvalli, Kenneth Aldape, Andrew Gao, Álvaro López-Janeiro, Carlos E De Andrea, Marta M Alonso, Paul Boutros, Joan Robbins, Warren P Mason, Adam M Sonabend, Roger Stupp, Juan Fueyo, Candelaria Gomez-Manzano, Frederick F Lang, Gelareh Zadeh

Faculty, Staff and Student Publications

No abstract provided.

Designing An Electronic Patient-Reported Outcomes Information Infrastructure Supported By The Re-Aim Implementation Framework, Amy C Moreno, Angela Peek, Toshiko S Stein, Kevin R Shook, Sara M Ali, Laia Humbert-Vidan, Aileen Chen, Miriam Lango, Anna Lee, Michael Spiotto, William H Morrison, Adam S Garden, Jack Phan, Steven J Frank, Katherine Hutcheson, David I Rosenthal, Clifton D Fuller, G Brandon Gunn

Faculty, Staff and Student Publications

Objective: Patient-reported outcomes (PROs) contain valuable information that can be leveraged by providers to perform timely interventions and improve quality of life and survival. However, the implementation of electronic PROs (ePROs) remains a challenge from technical and evaluation perspectives. Our objective was to construct a robust electronic health record (EHR)-integrated ePRO information infrastructure founded on RE-AIM (reach-effectiveness-adoption-implementation-maintenance) principles.

Materials and methods: We used Epic Systems as our EHR platform to build the MD Anderson Symptom Index Head and Neck Module (MDASI-HN) for release to all patients undergoing evaluation and/or treatment in our HN Radiation Oncology clinics. RE-AIM metrics were established …

In Situ Programming Of The Tumor Microenvironment To Alleviate Immunosuppression For Pancreatic Cancer Immunotherapy, Man Sun, Huan Zhang, Yarui Ma, Simiao Wang, Jiayi Chen, Yaxin Cui, Yun Zhang, Siyuan Hu, Dan Zhou, Pengchen Zhang, Yahui Liu, Betty Y S Kim, Wen Jiang, Xiaobing Wang, Zhaogang Yang

Faculty, Staff and Student Publications

Recent studies have highlighted the pivotal role of the cGAS‐STING pathway in cancer immunotherapy. However, clinical trials with cGAS‐STING pathway agonists have faced setbacks thanks to their short biological half‐life, lack of tumor specificity, and potential to promote tumor immune evasion. To address these challenges, a novel exosome‐based drug delivery platform, termed cmExoaCD11b is developed, designed to precisely target and reprogram the tumor microenvironment (TME) in situ for pancreatic cancer immunotherapy. cmExoaCD11b is engineered to encapsulate high copy numbers of IL‐12 mRNA and 2′3’‐cGAMP (cGAMP) and is functionalized with CD11b antibodies for targeted delivery to macrophages. Notably, cmExoaCD11b facilitated the …

Leveraging Existing Cohort Studies Of Mexican Women To Better Understand Hispanic Health And Cancer Risk, Dalia Stern, Liliana Gomez-Flores-Ramos, Britton Trabert, V Wendy Setiawan, Loïc Le Marchand, Henry Gomez, Paul A Scheet, Humberto Parada, Amber Pirzada, Martin Lajous, Leslie V Farland

Faculty, Staff and Student Publications

Background: Hispanics have been historically underrepresented in epidemiologic cancer research. Existing cohort studies focused on recruiting Hispanic participants have been relatively small, making studying cancer outcomes challenging. Therefore, we aimed to compare the distribution of cancer risk factors among Hispanic women of Mexican heritage (HWMH) participating in existing cohorts to explore the possibility of future data pooling efforts.

Methods: We used baseline data of HWMH from three US-based studies, the Mexican American Cohort (MAC; n = 19,797; 2001-2017), the Multiethnic Cohort (MEC; n = 18,007; 1993-1996), and the Hispanic Community Health Study/Study of Latinos (HCHS/SOL; n = 4,022; 2008-2011), and …

Sex Disparities In Chlamydia And Gonorrhea Treatment In Us Adult Emergency Departments: A Systematic Review And Meta-Analysis, Rachel E Solnick, Rahi Patel, Ethan Chang, Carmen Vargas-Torres, Maaz Munawar, Carlin Pendell, Judith E Smith, Ethan Cowan, Keith E Kocher, Roland C Merchant

Faculty, Staff and Student Publications

BACKGROUND: Empiric antibiotic treatment for gonorrhea (GC) and chlamydia (CT) is common in U.S. emergency departments (EDs) due to the delayed availability of test results. Local studies have identified sex-based disparities in sexually transmitted infection (STI) care, with females potentially receiving less empiric treatment than males. This study evaluates how STI treatment aligns with laboratory-confirmed results to quantify potential overtreatment and undertreatment rates and investigates sex differences for these outcomes.

METHODS: We conducted a preregistered (PROSPERO #241429) systematic review and meta-analysis of studies published between January 2010 and January 2025 in U.S. EDs, excluding studies conducted exclusively in pediatric settings. …

Corrigendum To " Igf-1r Inhibitors In Cancer: A Review Of Available Evidence And Future Outlook" [Crit Rev Oncol/Hematol 214 (2025) 104809], Deniz Can Guven, Jibran Ahmed, Bettzy Stephen, Aung Naing

Faculty, Staff and Student Publications

No abstract provided.

Which Score For What? Operationalizing Standardized Cognitive Test Performance For The Assessment Of Change, Cristan Farmer, Audrey Thurm, Tanvi Das, E Martina Bebin, Jonathan A Bernstein, Elizabeth Berry-Kravis, Joseph D Buxbaum, Charis Eng, Thomas Frazier, Antonio Y Hardan, Alexander Kolevzon, Darcy A Krueger, Julian A Martinez-Agosto, Hope Northrup, Craig M Powell, Latha Valluripalli Soorya, Joyce Y Wu, Mustafa Sahin, Developmental Synaptopathies Consortium

Faculty, Staff and Student Publications

Developmental domains, such as cognitive, language, and motor, are key concepts of interest in longitudinal studies of intellectual and developmental disabilities (IDD). Normative scores (e.g., IQ) are often used to operationalize performance on standardized tests of these concepts, but it is the interval-distributed person-ability scores that are intended for the assessment of within-individual change. Here we illustrate the use and interpretation of several Stanford Binet, 5th Edition score types (IQ, extended IQ, Z-normalized raw score, developmental quotient, raw sum score, age equivalent, and ability score) using data from two longitudinal studies of rare genetic conditions associated with IDD. We found …

Analysis Of Hospital Costs For Robotic And Open Pancreatectomy Incurred During The Implementation Of A Robotic Pancreatectomy Program At A Cancer Center, Heather G Lyu, Yuki Hirata, Pamela W Lu, Jess E Maxwell, Rebecca A Snyder, Michael P Kim, Hop Tran Cao, Ching-Wei D Tzeng, Matthew H G Katz, Naruhiko Ikoma

Faculty, Staff and Student Publications

Background: Costs associated with robotic pancreatectomy compared to those of open pancreatectomy are assumed to be high but are not well known, particularly during the initial implementation of the robot.

Study design: Patients who underwent pancreatectomy for any diagnosis from January 2017 to August 2021 were identified retrospectively. Total hospital cost was calculated using intraoperative, inpatient, and outpatient costs within 30 days of surgery. The ratio of the total cost of each pancreatectomy to the average cost of all operations at our center was used to represent cost without sharing proprietary financial data. Propensity score matching was performed to account …

Correction: Imaging In Pelvic Exenteration-A Multidisciplinary Practice Guide From The Esgar-Sar-Esur-Pelvex Collaborative Group, Stephanie Nougaret, Doenja M J Lambregts, Geerard L Beets, Regina G H Beets-Tan, Lennart Blomqvist, David Burling, Quentin Denost, Maria A Gambacorta, Benedetta Gui, Ann Klopp, Yulia Lakhman, Kate E Maturen, Riccardo Manfredi, Iva Petkovska, Luca Russo, Atul B Shinagare, James A Stephenson, Damian Tolan, Aradhana M Venkatesan, Aaron J Quyn, Rosemarie Forstner

Faculty, Staff and Student Publications

No abstract provided.

Trop2 Expression In Salivary Gland Adenoidcystic Carcinoma (Acc) According To Histologic Subtype: Therapeutic Implications, Juliana Mota Siqueira, Yoshitsugu Mitani, Mario L Marques-Piubelli, Camilla Oliveira Hoff, Flavia Bonini, Luana Guimaraes De Sousa, Mutsumi Mitani, Giovanna Lopes Carvalho, Fabio Daumas Nunes, Leandro Luongo Matos, Shiaw-Yih Lin, Michael T Spiotto, Ehab Y Hanna, Daniel J Mcgrail, Adel K El-Naggar, Renata Ferrarotto

Faculty, Staff and Student Publications

Background: Adenoid cystic carcinoma (ACC) is a common salivary gland carcinoma with high recurrence and distant metastasis rates. Currently, there is no standard systemic treatment available. TROP2 is a transmembrane glycoprotein involved in the oncogenesis of several tumors that can be therapeutically targeted by a TROP2-antibody-drug conjugate (ADC). We aimed to characterize TROP2 expression in ACC and assess TROP2 as a potential therapeutic target.

Methods: TROP2 immunohistochemistry was performed in a tissue microarray including 165 ACC of salivary gland. The tumors were grouped according to the histological pattern as non-solid, solid + non-solid, or solid. TROP2 protein expression in ACC …

Wuse-Oil Compound 03 Mitigates Radiation-Induced Oral Mucositis By Modulating Oral Microbiota To Mediate Tlr4/Nf-Κb Pathway And Inhibit M1 Macrophage Polarization, Liqun Jia, Rong Huang, Chen Chen, Feng Teng, Tian Gu, Huafeng Liu, Li Ma, Ye Feng, Jingyi Long, Zihan Jin, Dong Li, Dongmei Chen, Yanni Lou

Faculty, Staff and Student Publications

Background: Radiation-induced oral mucositis (RIOM) is a prevalent condition among patients with head and neck cancer undergoing radiotherapy. It is characterized by a high incidence and severe symptoms that significantly compromise patients' quality of life. Currently, there exists no consensus regarding an effective treatment modality. Wuse-oil Compound 03 (WC03), a Traditional Chinese Herbal Medicine, demonstrates potential in managing RIOM.

Purpose: This study aims to investigate the efficacy of WC03 in treating RIOM through the modulation of oral microbiota and associated biological pathways.

Study design: Mechanism study experimental design.

Methods: A rat model of RIOM was established via radiation exposure. WC03 …

Mucinous Cystic Neoplasms Of The Pancreas And Liver Share A Similar Dna Methylation Profile With Mucinous Ovarian Tumors, Zoe Leoni, Teodor G Calina, Tobias Janik, Elena Grafenhorst, Eliane T Taube, Christopher Cm Neumann, Baoqing Chen, Elena I Braicu, Jalid Sehouli, Thomas Malinka, Wenzel Schöning, Johann Pratschke, George A Calin, David S Klimstra, Jamal K Benhamida, Irene Esposito, Markus Möbs, David Horst, Simon Schallenberg, David Capper, Mihnea P Dragomir

Faculty, Staff and Student Publications

The origin of mucinous cystic neoplasms (MCNs) remains a major challenge in hepato-pancreato-biliary pathology. These cystic tumors are defined by their mucinous epithelium and ovarian-like stroma, with an estimated 10% risk of progression to invasive carcinoma. The origin of the ovarian-like stroma remains a subject of debate. In this study, we conducted immunohistochemical profiling, targeted DNA sequencing, and genome-wide DNA methylation analysis on a cohort of 15 pancreatic MCNs (MCN-P) and six hepatic MCNs (MCN-L). Using immunohistochemistry and targeted DNA sequencing, we unequivocally established the diagnosis of MCN. Unsupervised DNA methylation profile analysis of reference classes of pancreatic neoplasms (11 …

Rna-Binding Proteins Mediate The Maturation Of Chromatin Topology During Differentiation, Bondita Dehingia, Małgorzata Milewska-Puchała, Marcin Janowski, Mahmoud-Reza Rafiee, Misbah Abbas, Aleksandra Piotrowska, Jan Senge, Piotr Blaut, Dietrich Walsh, Jacqueline Severino, Debadeep Chaudhury, Sajjad Iqbal, Rogelio Montiel-Manriquez, Sylwia Jankowska, Peyman Zare, Wolfgang Huber, Jianliang Xu, Rafael Casellas, Timo Zimmermann, Paweł Dłotko, Jeroen Krijgsveld, Aleksandra Pękowska

Faculty, Staff and Student Publications

Topologically associating domains (TADs) and chromatin architectural loops impact promoter-enhancer interactions, with CCCTC-binding factor (CTCF) defining TAD borders and loop anchors. TAD boundaries and loops progressively strengthen upon embryonic stem (ES) cell differentiation, underscoring the importance of chromatin topology in ontogeny. However, the mechanisms driving this process remain unclear. Here we show a widespread increase in CTCF-RNA-binding protein (RBP) interactions upon ES to neural stem (NS) cell differentiation. While dispensable in ES cells, RBPs reinforce CTCF-anchored chromatin topology in NS cells. We identify Pantr1, a non-coding RNA, as a key facilitator of CTCF-RBP interactions, promoting chromatin maturation. Using acute CTCF …