Analysis of Poly(A) Site Choice Using a Java-Based Clustering Algorithm

Thomas, Patrick E.

doi:10.1007/978-1-4939-2175-1_5

Cited by 2 publications

(2 citation statements)

References 8 publications

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“…Several quality control measures were used to evaluate the qualities of the PATseq libraries. These included determinations of the consistencies of poly(A) site choice between replicates using the ‘PATAPP’ tool (Thomas, ), confirmation of individual 3´‐ends using a different 3´‐end sequencing strategy, and comparison of gene expressions using PATseq reads. Details concerning the library preparation, mappings, and quality control analyses are described in Appendix S1.…”

Section: Methodsmentioning

confidence: 99%

Wide‐ranging transcriptome remodelling mediated by alternative polyadenylation in response to abiotic stresses in Sorghum

et al. 2020

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Alternative polyadenylation (APA) regulates diverse developmental and physiological processes through its effects on gene expression, mRNA stability, translatability, and transport. Sorghum is a major cereal crop in the world and, despite its importance, not much is known about the role of post-transcriptional regulation in mediating responses to abiotic stresses in Sorghum. A genome-wide APA analysis unveiled widespread occurrence of APA in Sorghum in response to drought, heat, and salt stress. Abiotic stress treatments incited changes in poly(A) site choice in a large number of genes. Interestingly, abiotic stresses led to the re-directing of transcriptional output into non-productive pathways defined by the class of poly(A) site utilized. This result revealed APA to be part of a larger global response of Sorghum to abiotic stresses that involves the re-direction of transcriptional output into non-productive transcriptional and translational pathways. Large numbers of stress-inducible poly(A) sites could not be linked with known, annotated genes, suggestive of the existence of numerous unidentified genes whose expression is strongly regulated by abiotic stresses. Furthermore, we uncovered a novel stress-specific cis-element in intronic poly(A) sites used in drought-and heat-stressed plants that might play an important role in non-canonical poly(A) site choice in response to abiotic stresses.

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Section: Methodsmentioning

confidence: 99%

Wide‐ranging transcriptome remodelling mediated by alternative polyadenylation in response to abiotic stresses in Sorghum

et al. 2020

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“…This final library was quantified using a Qubit and submitted for sequencing on an Illumina HiSeq2500 instrument at the University of Kentucky HealthCare Genomics Core Laboratory. PATSeq reads were analyzed using the pipeline described in the preceding paragraph and elsewhere ( Thomas et al., 2012 ; Thomas, 2015 ; de Lorenzo et al., 2017 ). These sequencing data are available under Bioproject PRJNA1023006.…”

Section: Methodsmentioning

confidence: 99%

Natural variation in the plant polyadenylation complex

Zhou,

Li,

Hunt

2024

Front. Plant Sci.

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Messenger RNA polyadenylation, the process wherein the primary RNA polymerase II transcript is cleaved and a poly(A) tract added, is a key step in the expression of genes in plants. Moreover, it is a point at which gene expression may be regulated by determining the functionality of the mature mRNA. Polyadenylation is mediated by a complex (the polyadenylation complex, or PAC) that consists of between 15 and 20 subunits. While the general functioning of these subunits may be inferred by extending paradigms established in well-developed eukaryotic models, much remains to be learned about the roles of individual subunits in the regulation of polyadenylation in plants. To gain further insight into this, we conducted a survey of variability in the plant PAC. For this, we drew upon a database of naturally-occurring variation in numerous geographic isolates of Arabidopsis thaliana. For a subset of genes encoding PAC subunits, the patterns of variability included the occurrence of premature stop codons in some Arabidopsis accessions. These and other observations lead us to conclude that some genes purported to encode PAC subunits in Arabidopsis are actually pseudogenes, and that others may encode proteins with dispensable functions in the plant. Many subunits of the PAC showed patterns of variability that were consistent with their roles as essential proteins in the cell. Several other PAC subunits exhibit patterns of variability consistent with selection for new or altered function. We propose that these latter subunits participate in regulatory interactions important for differential usage of poly(A) sites.

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Analysis of Poly(A) Site Choice Using a Java-Based Clustering Algorithm

Cited by 2 publications

References 8 publications

Wide‐ranging transcriptome remodelling mediated by alternative polyadenylation in response to abiotic stresses in Sorghum

Wide‐ranging transcriptome remodelling mediated by alternative polyadenylation in response to abiotic stresses in Sorghum

Natural variation in the plant polyadenylation complex

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