A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis.
Zhang, Runxuan; Kuo, Richard; Coulter, Max; Calixto, Cristiane P G; Entizne, Juan Carlos; Guo, Wenbin; Marquez, Yamile; Milne, Linda; Riegler, Stefan; Matsui, Akihiro; Tanaka, Maho; Harvey, Sarah; Gao, Yubang; Wießner-Kroh, Theresa; Paniagua, Alejandro; Crespi, Martin; Denby, Katherine; Hur, Asa Ben; Huq, Enamul; Jantsch, Michael; Jarmolowski, Artur; Koester, Tino; Laubinger, Sascha; Li, Qingshun Quinn; Gu, Lianfeng; Seki, Motoaki; Staiger, Dorothee; Sunkar, Ramanjulu; Szweykowska-Kulinska, Zofia; Tu, Shih-Long; Wachter, Andreas; Waugh, Robbie; Xiong, Liming; Zhang, Xiao-Ning; Conesa, Ana; Reddy, Anireddy S N; Barta, Andrea; Kalyna, Maria; Brown, John W S
Light regulates alternative splicing outcomes via the TOR kinase pathway.
Riegler, Stefan; Servi, Lucas; Scarpin, M Regina; Godoy Herz, Micaela A; Kubaczka, María G; Venhuizen, Peter; Meyer, Christian; Brunkard, Jacob O; Kalyna, Maria; Barta, Andrea; Petrillo, Ezequiel
Targeting alternative splicing by RNAi: from the differential impact on splice variants to triggering artificial pre-mRNA splicing.
Fuchs, Armin; Riegler, Stefan; Ayatollahi, Zahra; Cavallari, Nicola; Giono, Luciana E; Nimeth, Barbara A; Mutanwad, Krishna V; Schweighofer, Alois; Lucyshyn, Doris; Barta, Andrea; Petrillo, Ezequiel; Kalyna, Maria
The Cyclin Dependent Kinase G group defines a thermo-sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU2AF65A.
Cavallari, Nicola; Nibau, Candida; Fuchs, Armin; Dadarou, Despoina; Barta, Andrea; Doonan, John H
RNA in Disease and development
Barta, Andrea; Jantsch, Michael F
A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing.
Zhang, Runxuan; Calixto, Cristiane P G; Marquez, Yamile; Venhuizen, Peter; Tzioutziou, Nikoleta A; Guo, Wenbin; Spensley, Mark; Entizne, Juan Carlos; Lewandowska, Dominika; Ten Have, Sara; Frei Dit Frey, Nicolas; Hirt, Heribert; James, Allan B; Nimmo, Hugh G; Barta, Andrea; Kalyna, Maria; Brown, John W S
The spliceosome-associated protein Nrl1 suppresses homologous recombination-dependent R-loop formation in fission yeast.
Aronica, Lucia; Kasparek, Torben; Ruchman, David; Marquez, Yamile; Cipak, Lubos; Cipakova, Ingrid; Anrather, Dorothea; Mikolaskova, Barbora; Radtke, Maximilian; Sarkar, Sovan; Pai, Chen-Chun; Blaikley, Elizabeth; Walker, Carol; Shen, Kuo-Fang; Schroeder, Renee; Barta, Andrea; Forsburg, Susan L; Humphrey, Timothy C
Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity.
Marquez, Yamile; Höpfler, Markus; Ayatollahi, Zahra; Barta, Andrea; Kalyna, Maria
AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.
Zhang, Runxuan; Calixto, Cristiane P G; Tzioutziou, Nikoleta A; James, Allan B; Simpson, Craig G; Guo, Wenbin; Marquez, Yamile; Kalyna, Maria; Patro, Rob; Eyras, Eduardo; Barta, Andrea; Nimmo, Hugh G; Brown, John W S
Lost in Translation: Pitfalls in Deciphering Plant Alternative Splicing Transcripts.
Brown, John W S; Simpson, Craig G; Marquez, Yamile; Gadd, Geoffrey M; Barta, Andrea; Kalyna, Maria
Shedding light on the chloroplast as a remote control of nuclear gene expression.
Godoy Herz, Micaela A; Kornblihtt, Alberto R; Barta, Andrea; Kalyna, Maria; Petrillo, Ezequiel
Let there be light: Regulation of gene expression in plants.
Petrillo, Ezequiel; Godoy Herz, Micaela A; Barta, Andrea; Kalyna, Maria; Kornblihtt, Alberto R
Imaging of endogenous messenger RNA splice variants in living cells reveals nuclear retention of transcripts inaccessible to nonsense-mediated decay in Arabidopsis.
Göhring, Janett; Jacak, Jaroslaw; Barta, Andrea
Suitable transfection methods for single particle tracing in plant suspension cells.
Göhring, Janett; Fulcher, Nick; Schilcher, Kurt; Barta, Andrea; Jacak, Jaroslaw
A chloroplast retrograde signal regulates nuclear alternative splicing.
Petrillo, Ezequiel; Herz, Micaela A Godoy; Fuchs, Armin; Reifer, Dominik; Fuller, John; Yanovsky, Marcelo J; Simpson, Craig; Brown, John W S; Barta, Andrea; Kalyna, Maria; Kornblihtt, Alberto R
Complexity of the alternative splicing landscape in plants.
Reddy, Anireddy S N; Marquez, Yamile; Kalyna, Maria; Barta, Andrea
Introns of plant pri-miRNAs enhance miRNA biogenesis.
Bielewicz, Dawid; Kalak, Malgorzata; Kalyna, Maria; Windels, David; Barta, Andrea; Vazquez, Franck; Szweykowska-Kulinska, Zofia; Jarmolowski, Artur
Identification of RNA targets for the nuclear multidomain cyclophilin atCyp59 and their effect on PPIase activity.
Bannikova, Olga; Zywicki, Marek; Marquez, Yamile; Skrahina, Tatsiana; Kalyna, Maria; Barta, Andrea
Alternative splicing in plants - coming of age.
Syed, Naeem H; Kalyna, Maria; Marquez, Yamile; Barta, Andrea; Brown, John W S
Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis.
Yamile Marquez, John W.S. Brown, Craig Simpson, Andrea Barta, Maria Kalyna
Phage therapy for treating bacterial infections: a double-edged sword
Suckers and segments of the octopus arm
Using the house mouse radiation to study the rapid evolution of genes and genetic processes
CRISPR jumps ahead: mechanistic insights into CRISPR-associated transposons
SLiMs and SHelMs: Decoding how short linear and helical motifs direct PPP specificity to direct signaling
Title to be announced
Enigmatic evolutionary origin and multipotency of the neural crest cells - major drivers of vertebrate evolution
Visualising mitotic chromosomes and nuclear dynamics by correlative light and electron microscopy
Engineered nanocarriers for imaging of small proteins by CryoEM
Bacterial cell envelope homeostasis at the (post)transcriptional level
Title to be announced
Hydrologic extremes alter mechanisms and pathways of carbon export from mountainous floodplain soils
Dissecting post-transcriptional gene expression regulation in humans and viruses
Polyploidy and rediploidisation in stressful times
Prdm9 control of meiotic synapsis of homologs in intersubspecific hybrids
Title to be announced
RNA virus from museum specimens
Programmed DNA double-strand breaks during meiosis: Mechanism and evolution
Title to be announced