---
_id: '13214'
abstract:
- lang: eng
  text: Nitrogen is an important macronutrient required for plant growth and development,
    thus directly impacting agricultural productivity. In recent years, numerous studies
    have shown that nitrogen-driven growth depends on pathways that control nitrate/nitrogen
    homeostasis and hormonal networks that act both locally and systemically to coordinate
    growth and development of plant organs. In this review, we will focus on recent
    advances in understanding the role of the plant hormones auxin and cytokinin and
    their crosstalk in nitrate-regulated growth and discuss the significance of novel
    findings and possible missing links.
acknowledgement: 'This work was supported by the Austrian Academy of Sciences ÖAW:
  Doc fellowship (26130) to Stefan Riegler.'
article_number: '1613'
article_processing_charge: Yes
article_type: review
author:
- first_name: R
  full_name: Abualia, R
  last_name: Abualia
- first_name: Stefan
  full_name: Riegler, Stefan
  id: FF6018E0-D806-11E9-8E43-0B14E6697425
  last_name: Riegler
  orcid: 0000-0003-3413-1343
- first_name: Eva
  full_name: Benková, Eva
  id: 38F4F166-F248-11E8-B48F-1D18A9856A87
  last_name: Benková
  orcid: 0000-0002-8510-9739
citation:
  ama: Abualia R, Riegler S, Benková E. Nitrate, auxin and cytokinin - a trio to tango.
    <i>Cells</i>. 2023;12(12). doi:<a href="https://doi.org/10.3390/cells12121613">10.3390/cells12121613</a>
  apa: Abualia, R., Riegler, S., &#38; Benková, E. (2023). Nitrate, auxin and cytokinin
    - a trio to tango. <i>Cells</i>. MDPI. <a href="https://doi.org/10.3390/cells12121613">https://doi.org/10.3390/cells12121613</a>
  chicago: Abualia, R, Stefan Riegler, and Eva Benková. “Nitrate, Auxin and Cytokinin
    - a Trio to Tango.” <i>Cells</i>. MDPI, 2023. <a href="https://doi.org/10.3390/cells12121613">https://doi.org/10.3390/cells12121613</a>.
  ieee: R. Abualia, S. Riegler, and E. Benková, “Nitrate, auxin and cytokinin - a
    trio to tango,” <i>Cells</i>, vol. 12, no. 12. MDPI, 2023.
  ista: Abualia R, Riegler S, Benková E. 2023. Nitrate, auxin and cytokinin - a trio
    to tango. Cells. 12(12), 1613.
  mla: Abualia, R., et al. “Nitrate, Auxin and Cytokinin - a Trio to Tango.” <i>Cells</i>,
    vol. 12, no. 12, 1613, MDPI, 2023, doi:<a href="https://doi.org/10.3390/cells12121613">10.3390/cells12121613</a>.
  short: R. Abualia, S. Riegler, E. Benková, Cells 12 (2023).
date_created: 2023-07-12T07:41:25Z
date_published: 2023-06-13T00:00:00Z
date_updated: 2024-03-06T14:00:33Z
day: '13'
ddc:
- '570'
department:
- _id: EvBe
doi: 10.3390/cells12121613
external_id:
  isi:
  - '001017033600001'
  pmid:
  - '37371083'
file:
- access_level: open_access
  checksum: 6dc9df5f4f59fc27c509c275060354a5
  content_type: application/pdf
  creator: alisjak
  date_created: 2023-07-12T10:01:54Z
  date_updated: 2023-07-12T10:01:54Z
  file_id: '13218'
  file_name: 2023_cells_Abualia.pdf
  file_size: 1066802
  relation: main_file
  success: 1
file_date_updated: 2023-07-12T10:01:54Z
has_accepted_license: '1'
intvolume: '        12'
isi: 1
issue: '12'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 62883ed7-2b32-11ec-9570-93580204e56b
  grant_number: '26130'
  name: Functional asymmetry of medial habenula outputs in mice
publication: Cells
publication_identifier:
  issn:
  - 2073-4409
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: Nitrate, auxin and cytokinin - a trio to tango
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2023'
...
---
_id: '11587'
abstract:
- lang: eng
  text: "Background: Accurate and comprehensive annotation of transcript sequences
    is essential for transcript quantification and differential gene and transcript
    expression analysis. Single-molecule long-read sequencing technologies provide
    improved integrity of transcript structures including alternative splicing, and
    transcription start and polyadenylation sites. However, accuracy is significantly
    affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis.\r\nResults:
    We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset
    3 (AtRTD3). AtRTD3 contains over 169,000 transcripts—twice that of the best current
    Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent
    of transcripts are from Iso-seq with accurately defined splice junctions and transcription
    start and end sites. We develop novel methods to determine splice junctions and
    transcription start and end sites accurately. Mismatch profiles around splice
    junctions provide a powerful feature to distinguish correct splice junctions and
    remove false splice junctions. Stratified approaches identify high-confidence
    transcription start and end sites and remove fragmentary transcripts due to degradation.
    AtRTD3 is a major improvement over existing transcriptomes as demonstrated by
    analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides
    higher resolution of transcript expression profiling and identifies cold-induced
    differential transcription start and polyadenylation site usage.\r\nConclusions:
    AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves
    the precision of differential gene and transcript expression, differential alternative
    splicing, and transcription start/end site usage analysis from RNA-seq data. The
    novel methods for identifying accurate splice junctions and transcription start/end
    sites are widely applicable and will improve single-molecule sequencing analysis
    from any species."
acknowledgement: "This work was jointly supported by funding from the Biotechnology
  and Biological Sciences Research Council (BBSRC) BB/P009751/1 to JB; BB/R014582/1
  to RW and RZ; BB/S020160/1 to RZ; BB/S004610/1 (16 ERA-CAPS BARN) to RW; the Scottish
  Government Rural and Environment Science and Analytical Services division (RESAS)
  [to RZ, RW, and JB]; the\r\nNational Science Foundation (MCB-2014408) and the National
  Institute of Health (NIH) (GM-114297) to E.H.; S. H. was supported by funding to
  K.D. from the University of York; the Austrian Science Fund (FWF) SFB F43 to AB
  and MJ and [P26333] to MK; The French Agence Nationale de la Recherche grant ANR-16-CE12-0032
  to MC; the Japan Science and\r\nTechnology Agency (JST), the Core Research for Evolutionary
  Science and Technology (CREST; Grant Number JPMJCR13B4) to M.S.; the National Science
  Foundation (Grant No. DBI1949036 to A.b.H and A.S.N.R, and Grant No. MCB 2014542
  to E.H. and A.S.N.R.); and the DOE Office of Science, Office of Biological and Environmental
  Research (Grant\r\nNo. DE-SC0010733) to A.S.N.R and A.b.H.; the Deutsche Forschungsgemeinschaft
  (DFG) STA653/14-1 and STA653/15-1 to DS; the National Science Foundation grant (IOS-154173)
  to Q.Q.L.; the German Research Foundation (DFG) WA2167/8-1 to AW and SFB1101/C03
  to AW and TWK; the Research Grants Council (RGC) of Hong Kong (GRF 12103020) to
  LX. NSF grant IOS-1849708 and NSF EPSCoR grant 1826836 to RS; the Academia Sinica
  to S.-L. T."
article_number: '149'
article_processing_charge: No
article_type: original
author:
- first_name: Runxuan
  full_name: Zhang, Runxuan
  last_name: Zhang
- first_name: Richard
  full_name: Kuo, Richard
  last_name: Kuo
- first_name: Max
  full_name: Coulter, Max
  last_name: Coulter
- first_name: Cristiane P.G.
  full_name: Calixto, Cristiane P.G.
  last_name: Calixto
- first_name: Juan Carlos
  full_name: Entizne, Juan Carlos
  last_name: Entizne
- first_name: Wenbin
  full_name: Guo, Wenbin
  last_name: Guo
- first_name: Yamile
  full_name: Marquez, Yamile
  last_name: Marquez
- first_name: Linda
  full_name: Milne, Linda
  last_name: Milne
- first_name: Stefan
  full_name: Riegler, Stefan
  id: FF6018E0-D806-11E9-8E43-0B14E6697425
  last_name: Riegler
  orcid: 0000-0003-3413-1343
- first_name: Akihiro
  full_name: Matsui, Akihiro
  last_name: Matsui
- first_name: Maho
  full_name: Tanaka, Maho
  last_name: Tanaka
- first_name: Sarah
  full_name: Harvey, Sarah
  last_name: Harvey
- first_name: Yubang
  full_name: Gao, Yubang
  last_name: Gao
- first_name: Theresa
  full_name: Wießner-Kroh, Theresa
  last_name: Wießner-Kroh
- first_name: Alejandro
  full_name: Paniagua, Alejandro
  last_name: Paniagua
- first_name: Martin
  full_name: Crespi, Martin
  last_name: Crespi
- first_name: Katherine
  full_name: Denby, Katherine
  last_name: Denby
- first_name: Asa Ben
  full_name: Hur, Asa Ben
  last_name: Hur
- first_name: Enamul
  full_name: Huq, Enamul
  last_name: Huq
- first_name: Michael
  full_name: Jantsch, Michael
  last_name: Jantsch
- first_name: Artur
  full_name: Jarmolowski, Artur
  last_name: Jarmolowski
- first_name: Tino
  full_name: Koester, Tino
  last_name: Koester
- first_name: Sascha
  full_name: Laubinger, Sascha
  last_name: Laubinger
- first_name: Qingshun Quinn
  full_name: Li, Qingshun Quinn
  last_name: Li
- first_name: Lianfeng
  full_name: Gu, Lianfeng
  last_name: Gu
- first_name: Motoaki
  full_name: Seki, Motoaki
  last_name: Seki
- first_name: Dorothee
  full_name: Staiger, Dorothee
  last_name: Staiger
- first_name: Ramanjulu
  full_name: Sunkar, Ramanjulu
  last_name: Sunkar
- first_name: Zofia
  full_name: Szweykowska-Kulinska, Zofia
  last_name: Szweykowska-Kulinska
- first_name: Shih Long
  full_name: Tu, Shih Long
  last_name: Tu
- first_name: Andreas
  full_name: Wachter, Andreas
  last_name: Wachter
- first_name: Robbie
  full_name: Waugh, Robbie
  last_name: Waugh
- first_name: Liming
  full_name: Xiong, Liming
  last_name: Xiong
- first_name: Xiao Ning
  full_name: Zhang, Xiao Ning
  last_name: Zhang
- first_name: Ana
  full_name: Conesa, Ana
  last_name: Conesa
- first_name: Anireddy S.N.
  full_name: Reddy, Anireddy S.N.
  last_name: Reddy
- first_name: Andrea
  full_name: Barta, Andrea
  last_name: Barta
- first_name: Maria
  full_name: Kalyna, Maria
  last_name: Kalyna
- first_name: John W.S.
  full_name: Brown, John W.S.
  last_name: Brown
citation:
  ama: Zhang R, Kuo R, Coulter M, et al. A high-resolution single-molecule sequencing-based
    Arabidopsis transcriptome using novel methods of Iso-seq analysis. <i>Genome Biology</i>.
    2022;23. doi:<a href="https://doi.org/10.1186/s13059-022-02711-0">10.1186/s13059-022-02711-0</a>
  apa: Zhang, R., Kuo, R., Coulter, M., Calixto, C. P. G., Entizne, J. C., Guo, W.,
    … Brown, J. W. S. (2022). A high-resolution single-molecule sequencing-based Arabidopsis
    transcriptome using novel methods of Iso-seq analysis. <i>Genome Biology</i>.
    BioMed Central. <a href="https://doi.org/10.1186/s13059-022-02711-0">https://doi.org/10.1186/s13059-022-02711-0</a>
  chicago: Zhang, Runxuan, Richard Kuo, Max Coulter, Cristiane P.G. Calixto, Juan
    Carlos Entizne, Wenbin Guo, Yamile Marquez, et al. “A High-Resolution Single-Molecule
    Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.”
    <i>Genome Biology</i>. BioMed Central, 2022. <a href="https://doi.org/10.1186/s13059-022-02711-0">https://doi.org/10.1186/s13059-022-02711-0</a>.
  ieee: R. Zhang <i>et al.</i>, “A high-resolution single-molecule sequencing-based
    Arabidopsis transcriptome using novel methods of Iso-seq analysis,” <i>Genome
    Biology</i>, vol. 23. BioMed Central, 2022.
  ista: Zhang R, Kuo R, Coulter M, Calixto CPG, Entizne JC, Guo W, Marquez Y, Milne
    L, Riegler S, Matsui A, Tanaka M, Harvey S, Gao Y, Wießner-Kroh T, Paniagua A,
    Crespi M, Denby K, Hur AB, Huq E, Jantsch M, Jarmolowski A, Koester T, Laubinger
    S, Li QQ, Gu L, Seki M, Staiger D, Sunkar R, Szweykowska-Kulinska Z, Tu SL, Wachter
    A, Waugh R, Xiong L, Zhang XN, Conesa A, Reddy ASN, Barta A, Kalyna M, Brown JWS.
    2022. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome
    using novel methods of Iso-seq analysis. Genome Biology. 23, 149.
  mla: Zhang, Runxuan, et al. “A High-Resolution Single-Molecule Sequencing-Based
    Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” <i>Genome
    Biology</i>, vol. 23, 149, BioMed Central, 2022, doi:<a href="https://doi.org/10.1186/s13059-022-02711-0">10.1186/s13059-022-02711-0</a>.
  short: R. Zhang, R. Kuo, M. Coulter, C.P.G. Calixto, J.C. Entizne, W. Guo, Y. Marquez,
    L. Milne, S. Riegler, A. Matsui, M. Tanaka, S. Harvey, Y. Gao, T. Wießner-Kroh,
    A. Paniagua, M. Crespi, K. Denby, A.B. Hur, E. Huq, M. Jantsch, A. Jarmolowski,
    T. Koester, S. Laubinger, Q.Q. Li, L. Gu, M. Seki, D. Staiger, R. Sunkar, Z. Szweykowska-Kulinska,
    S.L. Tu, A. Wachter, R. Waugh, L. Xiong, X.N. Zhang, A. Conesa, A.S.N. Reddy,
    A. Barta, M. Kalyna, J.W.S. Brown, Genome Biology 23 (2022).
date_created: 2022-07-17T22:01:53Z
date_published: 2022-07-07T00:00:00Z
date_updated: 2023-08-03T12:04:18Z
day: '07'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1186/s13059-022-02711-0
external_id:
  isi:
  - '000821915500002'
file:
- access_level: open_access
  checksum: 2c30ef84151d257a6b835b4e069b70ac
  content_type: application/pdf
  creator: dernst
  date_created: 2022-07-18T08:15:24Z
  date_updated: 2022-07-18T08:15:24Z
  file_id: '11597'
  file_name: 2022_GenomeBiology_Zhang.pdf
  file_size: 3146207
  relation: main_file
  success: 1
file_date_updated: 2022-07-18T08:15:24Z
has_accepted_license: '1'
intvolume: '        23'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Genome Biology
publication_identifier:
  eissn:
  - 1474-760X
publication_status: published
publisher: BioMed Central
quality_controlled: '1'
scopus_import: '1'
status: public
title: A high-resolution single-molecule sequencing-based Arabidopsis transcriptome
  using novel methods of Iso-seq analysis
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 23
year: '2022'
...
---
_id: '7603'
abstract:
- lang: eng
  text: Plants are exposed to a variety of abiotic and biotic stresses that may result
    in DNA damage. Endogenous processes - such as DNA replication, DNA recombination,
    respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore
    essential to understand the strategies plants have developed for DNA damage detection,
    signaling, and repair. Alternative splicing (AS) is a key post-transcriptional
    process with a role in regulation of gene expression. Recent studies demonstrate
    that the majority of intron-containing genes in plants are alternatively spliced,
    highlighting the importance of AS in plant development and stress response. Not
    only does AS ensure a versatile proteome and influence the abundance and availability
    of proteins greatly, it has also emerged as an important player in the DNA damage
    response (DDR) in animals. Despite extensive studies of DDR carried out in plants,
    its regulation at the level of AS has not been comprehensively addressed. Here,
    we provide some insights into the interplay between AS and DDR in plants.
article_number: '91'
article_processing_charge: No
article_type: original
author:
- first_name: Barbara Anna
  full_name: Nimeth, Barbara Anna
  last_name: Nimeth
- first_name: Stefan
  full_name: Riegler, Stefan
  id: FF6018E0-D806-11E9-8E43-0B14E6697425
  last_name: Riegler
  orcid: 0000-0003-3413-1343
- first_name: Maria
  full_name: Kalyna, Maria
  last_name: Kalyna
citation:
  ama: Nimeth BA, Riegler S, Kalyna M. Alternative splicing and DNA damage response
    in plants. <i>Frontiers in Plant Science</i>. 2020;11. doi:<a href="https://doi.org/10.3389/fpls.2020.00091">10.3389/fpls.2020.00091</a>
  apa: Nimeth, B. A., Riegler, S., &#38; Kalyna, M. (2020). Alternative splicing and
    DNA damage response in plants. <i>Frontiers in Plant Science</i>. Frontiers. <a
    href="https://doi.org/10.3389/fpls.2020.00091">https://doi.org/10.3389/fpls.2020.00091</a>
  chicago: Nimeth, Barbara Anna, Stefan Riegler, and Maria Kalyna. “Alternative Splicing
    and DNA Damage Response in Plants.” <i>Frontiers in Plant Science</i>. Frontiers,
    2020. <a href="https://doi.org/10.3389/fpls.2020.00091">https://doi.org/10.3389/fpls.2020.00091</a>.
  ieee: B. A. Nimeth, S. Riegler, and M. Kalyna, “Alternative splicing and DNA damage
    response in plants,” <i>Frontiers in Plant Science</i>, vol. 11. Frontiers, 2020.
  ista: Nimeth BA, Riegler S, Kalyna M. 2020. Alternative splicing and DNA damage
    response in plants. Frontiers in Plant Science. 11, 91.
  mla: Nimeth, Barbara Anna, et al. “Alternative Splicing and DNA Damage Response
    in Plants.” <i>Frontiers in Plant Science</i>, vol. 11, 91, Frontiers, 2020, doi:<a
    href="https://doi.org/10.3389/fpls.2020.00091">10.3389/fpls.2020.00091</a>.
  short: B.A. Nimeth, S. Riegler, M. Kalyna, Frontiers in Plant Science 11 (2020).
date_created: 2020-03-22T23:00:46Z
date_published: 2020-02-19T00:00:00Z
date_updated: 2023-08-18T07:05:18Z
day: '19'
ddc:
- '580'
department:
- _id: FyKo
doi: 10.3389/fpls.2020.00091
external_id:
  isi:
  - '000518903600001'
file:
- access_level: open_access
  checksum: 57c37209f7b6712ced86c0f11b2be74e
  content_type: application/pdf
  creator: dernst
  date_created: 2020-03-23T09:03:40Z
  date_updated: 2020-07-14T12:48:01Z
  file_id: '7607'
  file_name: 2020_FrontiersPlants_Nimeth.pdf
  file_size: 507414
  relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
intvolume: '        11'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Frontiers in Plant Science
publication_identifier:
  eissn:
  - 1664462X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Alternative splicing and DNA damage response in plants
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2020'
...