ArticleNucleic acids research2015
Depletion of REF/Aly alters gene expression and reduces RNA polymerase II occupancy.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
19 citing papers in PubMed, 38 citations in OpenAlex.
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- Nuclear speckles regulate functional programs in cancer.Nature cell biology · 2025Article
- RNA binding protein ALYREF regulates ferroptosis to facilitate LUAD growth and metastasis via promoting SLC7A11 mRNA stability.Scientific reports · 2025Article
- ALYREF/THOC4 expression and cell growth modulation in retinoblastoma.Pathology, research and practice · 2024Article
- ALYREF-mediated RNA 5-Methylcytosine modification Promotes Hepatocellular Carcinoma Progression Via Stabilizing EGFR mRNA and pSTAT3 activation.International journal of biological sciences · 2024Article
- Loss of aly/ALYREF suppresses toxicity in both tau and TDP-43 models of neurodegeneration.GeroScience · 2022Article
- The Mammalian Ecdysoneless Protein Interacts with RNA Helicase DDX39A To Regulate Nuclear mRNA Export.Molecular and cellular biology · 2021Article
- Article
- Co-transcriptional Loading of RNA Export Factors Shapes the Human Transcriptome.Molecular cell · 2019Article
- Drosophila Ref1/ALYREF regulates transcription and toxicity associated with ALS/FTD disease etiologies.Acta neuropathologica communications · 2019Article
- The mScientific reports · 2018Article
- Balance between MAT2A intron detention and splicing is determined cotranscriptionally.RNA (New York, N.Y.) · 2018Article
- Developmental dynamics of gene expression and alternative polyadenylation in the Caenorhabditis elegans germline.Genome biology · 2018Article
- Metabolic labeling and recovery of nascent RNA to accurately quantify mRNA stability.Methods (San Diego, Calif.) · 2017Article
- The role of TREX in gene expression and disease.The Biochemical journal · 2016Review
- TDP-43 aggregation mirrors TDP-43 knockdown, affecting the expression levels of a common set of proteins.Scientific reports · 2016Article
- Canonical Poly(A) Polymerase Activity Promotes the Decay of a Wide Variety of Mammalian Nuclear RNAs.PLoS genetics · 2015Article
- Control of mammalian gene expression by selective mRNA export.Nature reviews. Molecular cell biology · 2015Review
- Co-transcriptional mRNP formation is coordinated within a molecular mRNP packaging station in S. cerevisiae.BioEssays : news and reviews in molecular, cellular and developmental biology · 2015Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Pre-mRNA processing is mechanistically linked to transcription with RNA pol II serving as a platform to recruit RNA processing factors to nascent transcripts. The TREX complex member, REF/Aly, has been suggested to play roles in transcription and nuclear RNA stability in addition to its more broadly characterized role in mRNA export. We employed RNA-seq to identify a subset of transcripts with decreased expression in both nuclear and cytoplasmic fractions upon REF/Aly knockdown, which implies that REF/Aly affects their expression upstream of its role in mRNA export. Transcription inhibition experiments and metabolic labeling assays argue that REF/Aly does not affect stability of selected candidate transcripts. Instead, ChIP assays and nuclear run-on analysis reveal that REF/Aly depletion diminishes the transcription of these candidate genes. Furthermore, we determined that REF/Aly binds directly to candidate transcripts, supporting a direct effect of REF/Aly on candidate gene transcription. Taken together, our data suggest that the importance of REF/Aly is not limited to RNA export, but that REF/Aly is also critical for gene expression at the level of transcription. Our data are consistent with the model that REF/Aly is involved in linking splicing with transcription efficiency.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.