Cargando…

Long-range RNA structures in the human transcriptome beyond evolutionarily conserved regions

RNA structure has been increasingly recognized as a critical player in the biogenesis and turnover of many transcripts classes. In eukaryotes, the prediction of RNA structure by thermodynamic modeling meets fundamental limitations due to the large sizes and complex, discontinuous organization of euk...

Descripción completa

Detalles Bibliográficos
Autores principales:	Margasyuk, Sergey, Zavileyskiy, Lev, Cao, Changchang, Pervouchine, Dmitri
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	PeerJ Inc. 2023
Materias:	Bioinformatics
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10691357/ https://www.ncbi.nlm.nih.gov/pubmed/38047033 http://dx.doi.org/10.7717/peerj.16414

Ejemplares similares

RNA in situ conformation sequencing reveals novel long-range RNA structures with impact on splicing
por: Margasyuk, Sergey, et al.
Publicado: (2023)

IRBIS: a systematic search for conserved complementarity
por: Pervouchine, Dmitri D.
Publicado: (2014)

Transcriptome sequencing suggests that pre-mRNA splicing counteracts widespread intronic cleavage and polyadenylation
por: Vlasenok, Maria, et al.
Publicado: (2023)

Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved
por: Nitsche, Anne, et al.
Publicado: (2015)

Conserved RNA secondary structures and long-range interactions in hepatitis C viruses
por: Fricke, Markus, et al.
Publicado: (2015)

Towards Long-Range RNA Structure Prediction in Eukaryotic Genes
por: Pervouchine, Dmitri D.
Publicado: (2018)

Conserved long-range base pairings are associated with pre-mRNA processing of human genes
por: Kalmykova, Svetlana, et al.
Publicado: (2021)

Splicing conservation signals in plant long noncoding RNAs
por: Corona-Gomez, Jose Antonio, et al.
Publicado: (2020)

Comparative genomics in the search for conserved long noncoding RNAs
por: Szcześniak, Michał Wojciech, et al.
Publicado: (2021)

Computational detection of abundant long-range nucleotide covariation in Drosophila genomes
por: Bindewald, Eckart, et al.
Publicado: (2013)

Modulation of alternative splicing by long-range RNA structures in Drosophila
por: Raker, Veronica A., et al.
Publicado: (2009)

HiCEnterprise: identifying long range chromosomal contacts in Hi-C data
por: Kranas, Hanna, et al.
Publicado: (2021)

Human adenovirus DNA polymerase is evolutionarily and functionally associated with human telomerase reverse transcriptase based on in silico molecular characterization that implicate abacavir and zidovudine
por: Fatoki, Toluwase Hezekiah
Publicado: (2023)

Changes in long non-coding RNA transcriptomic profiles after ischemia-reperfusion injury in rat spinal cord
por: Zhou, Zhibin, et al.
Publicado: (2020)

RNAcontacts: A Pipeline for Predicting Contacts from RNA Proximity Ligation Assays
por: Margasyuk, S. D., et al.
Publicado: (2023)

Diverse modes of evolutionary emergence and flux of conserved microRNA clusters
por: Mohammed, Jaaved, et al.
Publicado: (2014)

Going beyond base-pairs: topology-based characterization of base-multiplets in RNA
por: Bhattacharya, Sohini, et al.
Publicado: (2019)

CAPRI enables comparison of evolutionarily conserved RNA interacting regions
por: Panhale, Amol, et al.
Publicado: (2019)

Conserved developmental transcriptomes in evolutionarily divergent species
por: Parikh, Anup, et al.
Publicado: (2010)

Tissue-specific regulation of gene expression via unproductive splicing
por: Mironov, Alexei, et al.
Publicado: (2023)

cRegions—a tool for detecting conserved cis-elements in multiple sequence alignment of diverged coding sequences
por: Puustusmaa, Mikk, et al.
Publicado: (2019)

DRUID: a pipeline for transcriptome-wide measurements of mRNA stability
por: Lugowski, Andrew, et al.
Publicado: (2018)

RNA sequencing analysis of FGF2-responsive transcriptome in skin fibroblasts
por: Wu, Baojin, et al.
Publicado: (2021)

A prognostic long non-coding RNA-associated competing endogenous RNA network in head and neck squamous cell carcinoma
por: Zhang, Chengyao, et al.
Publicado: (2020)

The role of RNA structure at 5′ untranslated region in microRNA-mediated gene regulation
por: Gu, Wanjun, et al.
Publicado: (2014)

Fungal communities represent the majority of root-specific transcripts in the transcriptomes of Agave plants grown in semiarid regions
por: Marone, Marina Püpke, et al.
Publicado: (2022)

Long non-coding RNA polymorphisms on 8q24 are associated with the prognosis of gastric cancer in a Chinese population
por: Zhang, Yangyu, et al.
Publicado: (2020)

RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look
por: Rangan, Ramya, et al.
Publicado: (2020)

An epithelial–mesenchymal transition-related long noncoding RNA signature correlates with the prognosis and progression in patients with bladder cancer
por: Tong, Hang, et al.
Publicado: (2021)

The transcriptomic response to a short day to long day shift in leaves of the reference legume Medicago truncatula
por: Thomson, Geoffrey, et al.
Publicado: (2019)

RNA sequencing (RNA-Seq) of lymph node, spleen, and thymus transcriptome from wild Peninsular Malaysian cynomolgus macaque (Macaca fascicularis)
por: Ee Uli, Joey, et al.
Publicado: (2017)

Highly conserved RNA pseudoknots at the gag-pol junction of HIV-1 suggest a novel mechanism of −1 ribosomal frameshifting
por: Huang, Xiaolan, et al.
Publicado: (2014)

Nanoblot: an R-package for visualization of RNA isoforms from long-read RNA-sequencing data
por: DeMario, Samuel, et al.
Publicado: (2023)

Analysis of the in planta transcriptome expressed by the corn pathogen Pantoea stewartii subsp. stewartii via RNA-Seq
por: Packard, Holly, et al.
Publicado: (2017)

Transcriptome profiling of lncRNA and co-expression network in the vaginal epithelial tissue of women with lubrication disorders
por: Zhang, Jingjing, et al.
Publicado: (2021)

bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling
por: Vock, Isaac W., et al.
Publicado: (2023)

HbA1c may contribute to the development of non-alcoholic fatty liver disease even at normal-range levels
por: Chen, Changxi, et al.
Publicado: (2020)

Identification of key genes and long non-coding RNA associated ceRNA networks in hepatocellular carcinoma
por: Liu, Jun, et al.
Publicado: (2019)

Linkage disequilibrium of evolutionarily conserved regions in the human genome
por: Kato, Mamoru, et al.
Publicado: (2006)

Competing endogenous RNA (ceRNA) hypothetic model based on comprehensive analysis of long non-coding RNA expression in lung adenocarcinoma
por: Wang, Xiwen, et al.
Publicado: (2019)

Cannot write session to /tmp/vufind_sessions/sess_e4tqeg677bvn2fktqaj4fviqpn