Results 81 to 90 of about 10,207 (224)

Pervasive RNA-binding protein enrichment on TAD boundaries regulates TAD organization

Nucleic Acids Research
Abstract Mammalian genome is hierarchically organized by CTCF and cohesin through loop extrusion mechanism to facilitate the organization of topologically associating domains (TADs). Mounting evidence suggests additional factors/mechanisms exist to orchestrate TAD formation and maintenance.
Qiang Sun, Qin Zhou, Yulong Qiao, Xiaona Chen, Hao Sun, Huating Wang   +5 more
openaire   +2 more sources

Quantitative analysis of DNA‐GATA1 binding alterations linked to hematopoietic disorders

The FEBS Journal, EarlyView.
Native holdup allows the quantitative determination of affinities between full‐length transcription factors and DNA. Mutations in either the protein or the DNA can modulate binding strength, which can be precisely quantified using this approach. Applied to GATA1, it revealed mutations that alter DNA binding.
Boglarka Zambo, Bastien Morlet, Luc Negroni, Orsolya Mózner, Balázs Sarkadi, Gilles Travé, Gergo Gogl   +6 more
wiley   +1 more source

RAB4A acts as a negative feedback regulator of extracellular vesicle secretion during TGF‐β signaling

The FEBS Journal, EarlyView.
TGF‐β signaling regulates extracellular vesicle (EV) release in cancer cells by modulating the expression and activity of genes associated with EV biogenesis. The TGF‐β‐induced upregulation of RAB4A expression facilitates fast endosomal recycling, a process that limits the fusion of multivesicular bodies with the plasma membrane and EV secretion. Hence,
Dorival Mendes Rodrigues‐Junior, Maria Anastasia Doumani, Hao Fu, Jelle van den Bor, Olof Idevall‐Hagren, Aristidis Moustakas   +5 more
wiley   +1 more source

The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit flies

Epigenetics & Chromatin
Background Multiple studies have demonstrated a negative correlation between gene expression and positioning of genes at the nuclear envelope (NE) lined by nuclear lamina, but the exact relationship remains unclear, especially in light of the highly ...
Alexander Y. Afanasyev, Yoonjin Kim, Igor S. Tolokh, Igor V. Sharakhov, Alexey V. Onufriev   +4 more
doaj   +1 more source

A quantitative dissection of the DNA‐binding properties of pathogenic GATA1 mutants

The FEBS Journal, EarlyView.
Transcription factor activity is influenced by cell context, accessibility of target sequences, and co‐factor recruitment. Quantitatively characterizing the consequences of individual mutations in the transcription factors or their target sequences remains technically challenging. Zambo et al. use mutant GATA1‐ATP2B4 binding to illustrate an innovation
Kaoru Takasaki
wiley   +1 more source

Persistent homology-based multiscale Hi-C analysis uncovers TADs-mediated gene regulation

Scientific Reports
Topologically associating domains (TADs), computationally defined 3D chromatin structures, play pivotal roles in gene expression regulation and genome organization. However, their structural basis and functional implications remain contentious.
Zhen Chiang, Yue Wu
doaj   +1 more source

TOP1MT rs2293925 is an enhancer‐active regulatory SNP that shapes mitochondrial R‐loop dynamics

The FEBS Journal, EarlyView.
This study shows how a common genetic variant of mitochondrial topoisomerase 1 (TOP1MT rs2293925) can influence mitochondrial gene regulation, DNA topology, and formation of noncanonical nucleic acid structures such as R‐loops. By linking this enhancer‐active variant to mitochondrial nucleic acid stress in cellular contexts relevant to amyotrophic ...
Dóra Varga, Zsolt Ráduly, Beáta Boros‐Oláh, Éva Nagy, Zsolt Karányi, László Halász, Bálint László Bálint, György Vámosi, Emese Tóth, Péter Bai, Serena Santangelo, Patrizia Bossolasco, Antonia Ratti, Vincent Géli, Yves Pommier, Lóránt Székvölgyi   +15 more
wiley   +1 more source

Identifying topologically associating domains using differential kernels.

PLoS Computational Biology
Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional (3D) structure and organization of chromatin controls DNA transcription and replication.
Luka Maisuradze, Megan C King, Ivan V Surovtsev, Simon G J Mochrie, Mark D Shattuck, Corey S O'Hern   +5 more
doaj   +1 more source

Dolutegravir population pharmacokinetics in racially, sex‐ and age‐diverse and antiretroviral therapy‐experienced adults with HIV in the United States

HIV Medicine, EarlyView.
Abstract Objectives Dolutegravir (DTG) has been associated with weight gain in women with HIV, Black people with HIV and people with HIV60 years. This study aimed to characterise DTG population pharmacokinetics (PopPK) in a diverse population including these sub‐populations.
Adrian Khoei, Andrew Edmonds, Yen Chang, Catalina Ramirez, Mackenzie Vogan, Amanda Poliseno, Steven Wolinsky, Ken Ho, Todd T. Brown, Joseph B. Margolick, Jacquett Batson, Jennifer Hoffmann, Mark A. Marzinke, Mirjam‐Colette Kempf, Maria L. Alcaide, Joffi Effoe, Cecile D. Lahiri, Igho Ofotokun, Anandi N. Sheth, Stephen Gange, Audrey L. French, Bani Tamraz, Bradley E. Aouizerat, Phyllis C. Tien, Seble G. Kassaye, Jack DeHovitz, Kathryn Anastos, Kara W. Chew, Michelle Floris‐Moore, Julie B. Dumond   +29 more
wiley   +1 more source

Determining the functional relationship between epigenetic and physical chromatin domains in Drosophila

Genome Biology
The tight correlation between topologically associating domains (TADs) and epigenetic domains in Drosophila suggests that the epigenome contributes to define TADs. However, it is still unknown whether histone modifications are essential for TAD formation
Sandrine Denaud, Gonzalo Sabarís, Marco Di Stefano, Giorgio-Lucio Papadopoulos, Bernd Schuettengruber, Giacomo Cavalli   +5 more
doaj   +1 more source