Results 141 to 150 of about 2,133,969 (419)

Hardness of RNA Folding Problem with Four Symbols [PDF]

arXiv, 2015
An RNA sequence is a string composed of four types of nucleotides, $A, C, G$, and $U$. The goal of the RNA folding problem is to find a maximum cardinality set of crossing-free pairs of the form $\{A,U\}$ or $\{C,G\}$ in a given RNA sequence. The problem is central in bioinformatics and has received much attention over the years.
arxiv  

A-to-I RNA Editing: Current Knowledge Sources and Computational Approaches with Special Emphasis on Non-Coding RNA Molecules [PDF]

, 2015
RNA editing is a dynamic mechanism for gene regulation attained through the alteration of the sequence of primary RNA transcripts. A-to-I (Adenosine-to-Inosine) RNA editing, which is catalyzed by members of the Adenosine Deaminase Acting on RNA (ADAR ...
Alfredo Ferro, Dario Veneziano, Giovanni Nigita   +2 more
core   +2 more sources

Regulation of RNA editing by RNA-binding proteins in human cells

Communications Biology, 2019
Adenosine-to-inosine (A-to-I) editing, mediated by the ADAR enzymes, diversifies the transcriptome by altering RNA sequences. Recent studies reported global changes in RNA editing in disease and development. Such widespread editing variations necessitate
Giovanni Quinones-Valdez, Stephen S. Tran, Hyun-Ik Jun, J. Bahn, Ei-Wen Yang, L. Zhan, Anneke Brümmer, Xintao Wei, Eric L. Van Nostrand, G. Pratt, Gene W. Yeo, B. Graveley, Xinshu Xiao   +12 more
semanticscholar   +1 more source

Chemoresistome mapping in individual breast cancer patients unravels diversity in dynamic transcriptional adaptation

Molecular Oncology, EarlyView.
This study used longitudinal transcriptomics and gene‐pattern classification to uncover patient‐specific mechanisms of chemotherapy resistance in breast cancer. Findings reveal preexisting drug‐tolerant states in primary tumors and diverse gene rewiring patterns across patients, converging on a few dysregulated functional modules. Despite receiving the
Maya Dadiani, Gilgi Friedlander, Gili Perry, Nora Balint‐Lahat, Shlomit Gilad, Dana Morzaev‐Sulzbach, Anjana Shenoy, Noa Bossel Ben‐Moshe, Anya Pavlovsky, Rinat Bernstein‐Molho, Eytan Domany, Iris Barshack, Tamar Geiger, Bella Kaufman, Einav Nili Gal‐Yam   +14 more
wiley   +1 more source

Extensive adenosine-to-inosine editing detected in Alu repeats of antisense RNAs reveals scarcity of sense–antisense duplex formation [PDF]

, 2006
One type of RNA editing converts adenosine residues to inosine in double-stranded regions. Recent transcriptome analysis has revealed that numerous Alu repeats, present within introns and untranslated regions of human transcripts, are subject to this A→I
Kawahara, Yukio, Nishikura, Kazuko
core   +1 more source

Tonic signaling of the B‐cell antigen‐specific receptor is a common functional hallmark in chronic lymphocytic leukemia cell phosphoproteomes at early disease stages

Molecular Oncology, EarlyView.
B‐cell chronic lymphocytic leukemia (B‐CLL) and monoclonal B‐cell lymphocytosis (MBL) show altered proteomes and phosphoproteomes, analyzed using mass spectrometry, protein microarrays, and western blotting. Identifying 2970 proteins and 316 phosphoproteins, including 55 novel phosphopeptides, we reveal BCR and NF‐kβ/STAT3 signaling in disease ...
Paula Díez, Pablo Juanes‐Velasco, Marina L. García‐Vaquero, Conrad Droste, Alicia Landeira‐Viñuela, Miguel Alcoceba, Helena Fidalgo‐Gómez, Sara Misiego‐Herrero, Almudena Navarro‐Bailón, Mónica Baile, José M. Bastida, Jose Manuel Sanchez‐Santos, Rafael Góngora, Julia Almeida, Marcos Gonzalez‐Diaz, Alberto Orfao, Javier De Las Rivas, Manuel Fuentes   +17 more
wiley   +1 more source

Developmental stage-specific A-to-I editing pattern in the postnatal pineal gland of pigs (Sus scrofa)

Journal of Animal Science and Biotechnology, 2020
Background RNA editing is a widespread post-transcriptional modification mechanism in mammalian genomes. Although many editing sites have been identified in domestic pigs (Sus scrofa), little is known about the characteristics and dynamic regulation of ...
Rong Zhou, Wenye Yao, Chundi Xie, Leixia Zhang, Yangli Pei, Hua Li, Zheng Feng, Yalan Yang, Kui Li   +8 more
doaj   +1 more source

REDIportal: a comprehensive database of A-to-I RNA editing events in humans

Nucleic Acids Res., 2016
RNA editing by A-to-I deamination is the prominent co-/post-transcriptional modification in humans. It is carried out by ADAR enzymes and contributes to both transcriptomic and proteomic expansion.
E. Picardi, A. D’Erchia, Claudio Lo Giudice, G. Pesole   +3 more
semanticscholar   +1 more source

Determination of ADP/ATP translocase isoform ratios in malignancy and cellular senescence

Molecular Oncology, EarlyView.
The individual functions of three isoforms exchanging ADP and ATP (ADP/ATP translocases; ANTs) on the mitochondrial membrane remain unclear. We developed a method for quantitatively differentiating highly similar human ANT1, ANT2, and ANT3 using parallel reaction monitoring. This method allowed us to assess changes in translocase levels during cellular
Zuzana Liblova, Dominika Maurencova, Barbora Salovska, Marek Kratky, Tomas Mracek, Zuzana Korandova, Alena Pecinova, Pavla Vasicova, David Rysanek, Ladislav Andera, Ivo Fabrik, Rudolf Kupcik, Pavel Kashmel, Pinky Sultana, Vojtech Tambor, Jiri Bartek, Josef Novak, Marie Vajrychova, Zdenek Hodny   +18 more
wiley   +1 more source

In vivo RNA editing of point mutations via RNA-guided adenosine deaminases. [PDF]

, 2019
We present in vivo sequence-specific RNA base editing via adenosine deaminases acting on RNA (ADAR) enzymes with associated ADAR guide RNAs (adRNAs). To achieve this, we systematically engineered adRNAs to harness ADARs, and comprehensively evaluated the
Chen, Genghao, Ganesh, Ashwin, Katrekar, Dhruva, Mali, Prashant, Meluzzi, Dario, Shih, Yu-Ru, Varghese, Shyni, Worlikar, Atharv   +7 more
core   +1 more source