Results 71 to 80 of about 261,824 (309)

The newfound relationship between extrachromosomal DNAs and excised signal circles

FEBS Letters, EarlyView.
Extrachromosomal DNAs (ecDNAs) contribute to the progression of many human cancers. In addition, circular DNA by‐products of V(D)J recombination, excised signal circles (ESCs), have roles in cancer progression but have largely been overlooked. In this Review, we explore the roles of ecDNAs and ESCs in cancer development, and highlight why these ...
Dylan Casey, Zeqian Gao, Joan Boyes
wiley   +1 more source

Gene-Centered Regulatory Network Mapping [PDF]

, 2011
The Caenorhabditis elegans hermaphrodite is a complex multicellular animal that is composed of 959 somatic cells. The C. elegans genome contains ∼20,000 protein-coding genes, 940 of which encode regulatory transcription factors (TFs). In addition, the worm genome encodes more than 100 microRNAs and many other regulatory RNA and protein molecules.
openaire   +3 more sources

Estimating gene regulatory networks with pandaR [PDF]

Bioinformatics, 2017
Abstract PANDA (Passing Attributes between Networks for Data Assimilation) is a gene regulatory network inference method that begins with a model of transcription factor–target gene interactions and uses message passing to update the network model given available transcriptomic and protein–protein interaction data.
Schlauch, Daniel, Young, Albert, Paulson, Joseph, Glass, Kimberly, Quackenbush, John   +4 more
openaire   +3 more sources

An upstream open reading frame regulates expression of the mitochondrial protein Slm35 and mitophagy flux

FEBS Letters, EarlyView.
This study reveals how the mitochondrial protein Slm35 is regulated in Saccharomyces cerevisiae. The authors identify stress‐responsive DNA elements and two upstream open reading frames (uORFs) in the 5′ untranslated region of SLM35. One uORF restricts translation, and its mutation increases Slm35 protein levels and mitophagy.
Hernán Romo‐Casanueva, Ariann E. Mendoza‐Martínez, P. Abril Medina‐Flores, Carlos Campero‐Basaldua, Alexander DeLuna, Soledad Funes   +5 more
wiley   +1 more source

Methylation-directed regulatory networks determine enhancing and silencing of mutation disease driver genes and explain inter-patient expression variation

Genome Biology, 2023
Background Common diseases manifest differentially between patients, but the genetic origin of this variation remains unclear. To explore possible involvement of gene transcriptional-variation, we produce a DNA methylation-oriented, driver-gene-wide ...
Yifat Edrei, Revital Levy, Daniel Kaye, Anat Marom, Bernhard Radlwimmer, Asaf Hellman   +5 more
doaj   +1 more source

Probabilistic representation of gene regulatory networks [PDF]

Bioinformatics, 2004
Abstract Motivation: Recent experiments have established unambiguously that biological systems can have significant cell-to-cell variations in gene expression levels even in isogenic populations. Computational approaches to studying gene expression in cellular systems should capture such biological variations for a more realistic ...
Linyong, Mao, Haluk, Resat
openaire   +2 more sources

Sequence determinants of RNA G‐quadruplex unfolding by Arg‐rich regions

FEBS Letters, EarlyView.
We show that Arg‐rich peptides selectively unfold RNA G‐quadruplexes, but not RNA stem‐loops or DNA/RNA duplexes. This length‐dependent activity is inhibited by acidic residues and is conserved among SR and SR‐related proteins (SRSF1, SRSF3, SRSF9, U1‐70K, and U2AF1).
Naiduwadura Ivon Upekala De Silva, Puspa Kunwar, Md Ibnul Rifat Rahman, Joanna Koryo Kwao, Nathan Lehman, Zihan Zhang, Trenton Paul, Claire Cheng, Nicholas Truex, Hui‐Ting Lee, Jun Zhang   +10 more
wiley   +1 more source

Nicotinamide N‐methyltransferase promotes drug resistance in lung cancer, as revealed by nascent proteomic profiling

Molecular Oncology, EarlyView.
AZD9291 has shown promise in targeted cancer therapy but is limited by resistance. In this study, we employed metabolic labeling and LC–MS/MS to profile time‐resolved nascent protein perturbations, allowing dynamic tracking of drug‐responsive proteins. We demonstrated that increased NNMT expression is associated with drug resistance, highlighting NNMT ...
Zhanwu Hou, Zhen Wang, Fei Yang, Xiao Han, Lei Li, Huadong Liu   +5 more
wiley   +1 more source

Characterizing the salivary RNA landscape to identify potential diagnostic, prognostic, and follow‐up biomarkers for breast cancer

Molecular Oncology, EarlyView.
This study explores salivary RNA for breast cancer (BC) diagnosis, prognosis, and follow‐up. High‐throughput RNA sequencing identified distinct salivary RNA signatures, including novel transcripts, that differentiate BC from healthy controls, characterize histological and molecular subtypes, and indicate lymph node involvement.
Nicholas Rajan, Irina Primac, Emre Etlioglu, Laurens Debruyne, Ann Janssen, Magy Sallam, Kevin Tabury, Roel Quintens, Wiebren Tjalma, Mohammed Abderrafi Benotmane   +9 more
wiley   +1 more source

Genetic properties underlying transcriptional variability across different perturbations

Nature Communications
The rate and direction of phenotypic evolution depend on the availability of phenotypic variants induced genetically or environmentally. It is widely accepted that organisms do not display uniform phenotypic variation, with certain variants arising more ...
Saburo Tsuru, Chikara Furusawa
doaj   +1 more source