Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation

Sherstnev, Alexander; Duc, Céline; Cole, Christian; Zacharaki, Vasiliki; Hornyik, Csaba; Ozsolak, Fatih; Milos, Patrice M; Barton, Geoffrey J; Simpson, Gordon G
July 2012
Nature Structural & Molecular Biology;Jul2012, Vol. 19 Issue 8, p845
Academic Journal
It has recently been shown that RNA 3′-end formation plays a more widespread role in controlling gene expression than previously thought. To examine the impact of regulated 3′-end formation genome-wide, we applied direct RNA sequencing to A. thaliana. Here we show the authentic transcriptome in unprecedented detail and describe the effects of 3′-end formation on genome organization. We reveal extreme heterogeneity in RNA 3′ ends, discover previously unrecognized noncoding RNAs and propose widespread reannotation of the genome. We explain the origin of most poly(A)+ antisense RNAs and identify cis elements that control 3′-end formation in different registers. These findings are essential to understanding what the genome actually encodes, how it is organized and how regulated 3′-end formation affects these processes.


Related Articles

  • Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach. Jiandong Ding; Danqing Li; Ohler, Uwe; Jihong Guan; Shuigeng Zhou // BMC Genomics;2012, Vol. 13 Issue Suppl 3, p1 

    Background: MiRNA are about 22nt long small noncoding RNAs that post transcriptionally regulate gene expression in animals, plants and protozoa. Confident identification of MiRNA-Target Interactions (MTI) is vital to understand their function. Currently, several integrated computational programs...

  • Genome-wide profiling of Populus small RNAs. Klevebring, Daniel; Street, Nathaniel R.; Fahlgren, Noah; Kasschau, Kristin D.; Carrington, James C.; Lundeberg, Joakim; Jansson, Stefan // BMC Genomics;2009, Vol. 10, p620 

    Background: Short RNAs, and in particular microRNAs, are important regulators of gene expression both within defined regulatory pathways and at the epigenetic scale. We investigated the short RNA (sRNA) population (18-24 nt) of the transcriptome of green leaves from the sequenced Populus...

  • Genomic analysis reveals novel connections between alternative splicing and circadian regulatory networks. Perez-Santángelo, Soledad; Schlaen, Rubén Gustavo; Yanovsky, Marcelo J. // Briefings in Functional Genomics;Jan2013, Vol. 12 Issue 1, p13 

    Circadian clocks, the molecular devices present in almost all eukaryotic and some prokaryotic organisms, phase biological activities to the most appropriate time of day. These devices are synchronized by the daily cycles of light and temperature, and control hundreds of processes, ranging from...

  • Protocol: high throughput silica-based purification of RNA from Arabidopsis seedlings in a 96-well format.  // Plant Methods;2011, Vol. 7 Issue 1, p40 

    The article reports on the development of high throughput (HTP) method of RNA extraction from Arabidopsis thaliana (A. thaliana) to facilitate for gene expression studies in this widely used plant model. It reports on the use of silica membrane-based methodology for extraction of total RNA from...

  • MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana. Grant-Downton, Robert; Le Trionnaire, Gael; Schmid, Ralf; Rodriguez-Enriquez, Josefina; Hafidh, Said; Mehdi, Saher; Twell, David; Dickinson, Hugh // BMC Genomics;2009, Vol. 10, p643 

    Background: New generation sequencing technology has allowed investigation of the small RNA populations of flowering plants at great depth. However, little is known about small RNAs in their reproductive cells, especially in post-meiotic cells of the gametophyte generation. Pollen - the male...

  • Selection for the compactness of highly expressed genes in Gallus gallus. Rao, You S.; Wang, Zhang F.; Chai, Xue W.; Wu, Guo Z.; Ming Zhou; Nie, Qing H.; Zhang, Xi Q. // Biology Direct;2010, Vol. 5, p35 

    Background: Coding sequence (CDS) length, gene size, and intron length vary within a genome and among genomes. Previous studies in diverse organisms, including human, D. Melanogaster, C. elegans, S. cerevisiae, and Arabidopsis thaliana, indicated that there are negative relationships between...

  • Gardening the genome: DNA methylation in Arabidopsis thaliana. Chan, Simon W. -L.; Henderson, Ian R.; Jacobsen, Steven E. // Nature Reviews Genetics;May2005, Vol. 6 Issue 5, p351 

    DNA methylation has two essential roles in plants and animals-defending the genome against transposons and regulating gene expression. Recent experiments in Arabidopsis thaliana have begun to address crucial questions about how DNA methylation is established and maintained. One cardinal insight...

  • Differential activity of clustered genes in Arabidopsis thaliana. Minakova, N.; Shirshikova, G.; Kreslavski, V.; Boutanaev, A. // Doklady Biochemistry & Biophysics;Aug2011, Vol. 439 Issue 1, p185 

    The article presents a study which examines the expression of clustered genes in Arabidopsis thaliana. The study made use of the computer processing of profiles to performed a genome-wide identification of gene clusters in Arabidopsis. The result of the study indicates the coactivation of the...

  • TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation. Bernard, Virginie; Brunaud, Véronique; Lecharny, Alain // BMC Genomics;2010, Vol. 11, p166 

    Background: The TATA-box and TATA-variants are regulatory elements involved in the formation of a transcription initiation complex. Both have been conserved throughout evolution in a restricted region close to the Transcription Start Site (TSS). However, less than half of the genes in model...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics