Cargando…

LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival

BACKGROUND: The sequence content of the 3′ UTRs of many mRNA transcripts is regulated through alternative polyadenylation (APA). The study of this process using RNAseq data, though, has been historically challenging. RESULTS: To combat this problem, we developed LABRAT, an APA isoform quantification...

Descripción completa

Detalles Bibliográficos
Autores principales:	Goering, Raeann, Engel, Krysta L., Gillen, Austin E., Fong, Nova, Bentley, David L., Taliaferro, J. Matthew
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2021
Materias:	Methodology Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8234626/ https://www.ncbi.nlm.nih.gov/pubmed/34174817 http://dx.doi.org/10.1186/s12864-021-07781-1

Ejemplares similares

The Role of Alternative Polyadenylation in the Regulation of Subcellular RNA Localization
por: Arora, Ankita, et al.
Publicado: (2022)

Nucleotide-level linkage of transcriptional elongation and polyadenylation
por: Geisberg, Joseph V, et al.
Publicado: (2022)

Diverse cell-specific patterns of alternative polyadenylation in Drosophila
por: Lee, Seungjae, et al.
Publicado: (2022)

Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq
por: Engel, Krysta L, et al.
Publicado: (2021)

ELAV/Hu RNA binding proteins determine multiple programs of neural alternative splicing
por: Lee, Seungjae, et al.
Publicado: (2021)

Transcriptional activity regulates alternative cleavage and polyadenylation
por: Ji, Zhe, et al.
Publicado: (2011)

Dysfunctional transcripts are formed by alternative polyadenylation in OPMD
por: Raz, Vered, et al.
Publicado: (2017)

RNA localization mechanisms transcend cell morphology
por: Goering, Raeann, et al.
Publicado: (2023)

The role of alternative Polyadenylation in regulation of rhythmic gene expression
por: Ptitsyna, Natalia, et al.
Publicado: (2017)

The transcriptional elongation rate regulates alternative polyadenylation in yeast
por: Geisberg, Joseph V, et al.
Publicado: (2020)

Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression
por: Lianoglou, Steve, et al.
Publicado: (2013)

Identification and Characterization of Transcripts Regulated by Circadian Alternative Polyadenylation in Mouse Liver
por: Gendreau, Kerry L., et al.
Publicado: (2018)

Alternative Polyadenylation: a new frontier in post transcriptional regulation
por: Ren, Fanggang, et al.
Publicado: (2020)

Widespread transcript shortening through alternative polyadenylation in secretory cell differentiation
por: Cheng, Larry C., et al.
Publicado: (2020)

Cluster analysis of replicated alternative polyadenylation data using canonical correlation analysis
por: Ye, Wenbin, et al.
Publicado: (2019)

Antisense transcription regulates the expression of sense gene via alternative polyadenylation
por: Shen, Ting, et al.
Publicado: (2017)

Post-Transcriptional Dysregulation of microRNA and Alternative Polyadenylation in Colorectal Cancer
por: Mao, Zhanrui, et al.
Publicado: (2020)

AltTrans: Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation
por: Le Texier, Vincent, et al.
Publicado: (2006)

HTLV-I antisense transcripts initiating in the 3'LTR are alternatively spliced and polyadenylated
por: Cavanagh, Marie-Hélène, et al.
Publicado: (2006)

Alternative polyadenylation diversifies post‐transcriptional regulation by selective RNA–protein interactions
por: Gupta, Ishaan, et al.
Publicado: (2014)

Alternative cleavage and polyadenylation in spermatogenesis connects chromatin regulation with post-transcriptional control
por: Li, Wencheng, et al.
Publicado: (2016)

Alternative Polyadenylation Results in mRNA Transcript Instability in Gestational Diabetes Mellitus
por: He, Yujing, et al.
Publicado: (2023)

Fast ribozyme cleavage releases transcripts from RNA polymerase II and aborts co-transcriptional pre-mRNA processing
por: Fong, Nova, et al.
Publicado: (2009)

The RNA-binding protein FPA regulates flg22-triggered defense responses and transcription factor activity by alternative polyadenylation
por: Lyons, Rebecca, et al.
Publicado: (2013)

Endothelin-Converting Enzyme-1 (ECE-1) Is Post-Transcriptionally Regulated by Alternative Polyadenylation
por: Whyteside, Alison R., et al.
Publicado: (2014)

Transcript shortening via alternative polyadenylation promotes gene expression during fracture healing
por: Khajuria, Deepak Kumar, et al.
Publicado: (2023)

Mapping genome-wide transcription factor binding sites in frozen tissues
por: Savic, Daniel, et al.
Publicado: (2013)

Premature transcription termination at the expanded GAA repeats and aberrant alternative polyadenylation contributes to the Frataxin transcriptional deficit in Friedreich’s ataxia
por: Li, Yanjie, et al.
Publicado: (2022)

Evaluation of alternative RNA labeling protocols for transcript profiling with Arabidopsis AGRONOMICS1 tiling arrays
por: Müller, Marlen, et al.
Publicado: (2012)

Interplay between splicing and transcriptional pausing exerts genome-wide control over alternative polyadenylation
por: Mora Gallardo, Carmen, et al.
Publicado: (2021)

Recognition of Transcription Termination Signal by the Nuclear Polyadenylated RNA-binding (NAB) 3 Protein
por: Hobor, Fruzsina, et al.
Publicado: (2011)

Dam mutants provide improved sensitivity and spatial resolution for profiling transcription factor binding
por: Szczesnik, Tomasz, et al.
Publicado: (2019)

Genome-wide Mapping of 5′-monophosphorylated Ends of Mammalian Nascent RNA Transcripts
por: Cortázar, Michael A., et al.
Publicado: (2023)

Genome-wide transcription factor binding site/promoter databases for the analysis of gene sets and co-occurrence of transcription factor binding motifs
por: Veerla, Srinivas, et al.
Publicado: (2010)

Predicting tissue specific transcription factor binding sites
por: Zhong, Shan, et al.
Publicado: (2013)

Searching for transcription factor binding sites in vector spaces
por: Lee, Chih, et al.
Publicado: (2012)

A screening system to identify transcription factors that induce binding site-directed DNA demethylation
por: Suzuki, Takahiro, et al.
Publicado: (2017)

Transcription elongation rate affects nascent histone pre-mRNA folding and 3′ end processing
por: Saldi, Tassa, et al.
Publicado: (2018)

RNA Binding Protein CELF2 Regulates Signal-Induced Alternative Polyadenylation by Competing with Enhancers of the Polyadenylation Machinery
por: Chatrikhi, Rakesh, et al.
Publicado: (2019)

The RNA-Binding Protein HuD Regulates Alternative Splicing and Alternative Polyadenylation in the Mouse Neocortex
por: Sena, Rebecca M., et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_5mdes4mjotu7mu1fcqvj6hgbqr