{tab=Research}

Peter Kindgren with aspen trees in the UPSC greenhousePhoto: Fredrik LarssonThe DNA is the blue-print for how a living organism should develop and respond to different environmental cues. It does so by activating and repressing coding regions of the genome. Surprisingly, most of the DNA in genomes do not encode for proteins but is non-coding. With the development of new sequencing technologies, it is apparent that much of this non-coding DNA is transcribed into RNA. A key question in modern biology is therefore why organisms spend so much energy to transcribe something that is not used as template for protein synthesis.

Increasing evidence shows that transcription of non-coding regions are important players in the response to stress situations and control of organismal development. The challenge is often to detect these non-coding transcripts due to their rapid degradation. Therefore, we are only scratching the surface of the functional role of this hidden layer of transcription. Thus, we need to develop new techniques to fully appreciate the roles and rules of non-coding transcription.

A consequence of wide-spread or pervasive transcription of the genome is that many coding regions have non-coding transcription occurring in proximity. This may lead to transcriptional conflicts when two RNA polymerases meet on the DNA template but also regulate the dynamics of coding transcription.

My research group is interested in the dynamics of active transcription and how conflicts between non-coding and coding transcription regulate and dictate decisions made by the plant for optimal stress response and development. We primarily work with the model plant Arabidopsis thaliana but develop new techniques to study non-coding transcription in trees.

The figure illustrates the research in the Kindgren group.

{tab=Team}
  • Personnel Image
    Asgari, Mishaneh
    PostDoc
    E-mail
    Room: C4-29-40
  • Personnel Image
    Chanwala, Jeky
    PostDoc
    E-mail
    Room: B5-42-45
  • Personnel Image
    Kindgren, Peter
    Assistant Professor
    E-mail
    Room: KB5C5
    Website
  • Personnel Image
    Lühmann, Kim
    PostDoc
    E-mail
    Room: B5-16-45
  • Personnel Image
    Mermet, Sarah
    PostDoc
    E-mail
    Room: B5-44-45
  • Personnel Image
    Rosenkranz, Isabell
    PhD Student
    E-mail
    Room: B5-44-45

{tab=Publications}
  2024 (2)
Antisense transcription from stress-responsive transcription factors fine-tunes the cold response in Arabidopsis. Meena, S. K., Quevedo, M., Nardeli, S. M., Verez, C., Bhat, S. S., Zacharaki, V., & Kindgren, P. The Plant Cell, 36(9): 3467–3482. September 2024.
doi   link   bibtex   abstract  
The nuclear exosome subunit HEN2 acts independently of the core exosome to assist transcription in Arabidopsis. Bhat, S. S., Asgari, M., Mermet, S., Mishra, P., & Kindgren, P. Plant Physiology,kiae503. September 2024.
The nuclear exosome subunit HEN2 acts independently of the core exosome to assist transcription in Arabidopsis [link]Paper   doi   link   bibtex   abstract  
  2023 (1)
The non-coding RNA SVALKA locus produces a cis-natural antisense transcript that negatively regulates the expression of CBF1 and biomass production at normal temperatures. Zacharaki, V., Meena, S. K., & Kindgren, P. Plant Communications, 4(4): 100551. July 2023.
The non-coding RNA SVALKA locus produces a cis-natural antisense transcript that negatively regulates the expression of CBF1 and biomass production at normal temperatures [link]Paper   doi   link   bibtex   abstract  
  2020 (2)
Native elongation transcript sequencing reveals temperature dependent dynamics of nascent RNAPII transcription in Arabidopsis. Kindgren, P., Ivanov, M., & Marquardt, S. Nucleic Acids Research, 48(5): 2332–2347. March 2020.
Native elongation transcript sequencing reveals temperature dependent dynamics of nascent RNAPII transcription in Arabidopsis [link]Paper   doi   link   bibtex   abstract   11 downloads  
Organismal benefits of transcription speed control at gene boundaries. Leng, X., Ivanov, M., Kindgren, P., Malik, I., Thieffry, A., Brodersen, P., Sandelin, A., Kaplan, C. D, & Marquardt, S. EMBO reports, 21(4). April 2020.
Organismal benefits of transcription speed control at gene boundaries [link]Paper   doi   link   bibtex   3 downloads  
  2019 (2)
The E domain of CRR2 participates in sequence‐specific recognition of RNA in plastids. Ruwe, H., Gutmann, B., Schmitz‐Linneweber, C., Small, I., & Kindgren, P. New Phytologist, 222(1): 218–229. April 2019.
The E domain of CRR2 participates in sequence‐specific recognition of RNA in plastids [link]Paper   doi   link   bibtex   11 downloads  
Transcription-driven chromatin repression of Intragenic transcription start sites. Nielsen, M., Ard, R., Leng, X., Ivanov, M., Kindgren, P., Pelechano, V., & Marquardt, S. PLOS Genetics, 15(2): e1007969. February 2019.
Transcription-driven chromatin repression of Intragenic transcription start sites [link]Paper   doi   link   bibtex   1 download  
  2018 (2)
Editing of Chloroplast rps14 by PPR Editing Factor EMB2261 Is Essential for Arabidopsis Development. Sun, Y. K., Gutmann, B., Yap, A., Kindgren, P., & Small, I. Frontiers in Plant Science, 9: 841. June 2018.
Editing of Chloroplast rps14 by PPR Editing Factor EMB2261 Is Essential for Arabidopsis Development [link]Paper   doi   link   bibtex   1 download  
Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation. Kindgren, P., Ard, R., Ivanov, M., & Marquardt, S. Nature Communications, 9(1): 4561. November 2018. Number: 1 Publisher: Nature Publishing Group
Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation [link]Paper   doi   link   bibtex   abstract   1 download  
  2016 (1)
Circadian and Plastid Signaling Pathways Are Integrated to Ensure Correct Expression of the CBF and COR Genes during Photoperiodic Growth. Norén, L., Kindgren, P., Stachula, P., Rühl, M., Eriksson, M. E., Hurry, V., & Strand, Å. Plant Physiology, 171(2): 1392–1406. June 2016.
Circadian and Plastid Signaling Pathways Are Integrated to Ensure Correct Expression of the CBF and COR Genes during Photoperiodic Growth [link]Paper   doi   link   bibtex   abstract   6 downloads  
  2015 (4)
AEF1/MPR25 is implicated in RNA editing of plastid atpF and mitochondrial nad5, and also promotes atpF splicing in Arabidopsis and rice. Yap, A., Kindgren, P., Colas des Francs-Small, C., Kazama, T., Tanz, S. K., Toriyama, K., & Small, I. Plant J, 81(5): 661–9. March 2015. Edition: 2015/01/15
AEF1/MPR25 is implicated in RNA editing of plastid atpF and mitochondrial nad5, and also promotes atpF splicing in Arabidopsis and rice [link]Paper   doi   link   bibtex   abstract  
Chloroplast transcription, untangling the Gordian Knot. Kindgren, P., & Strand, A. New Phytol, 206(3): 889–891. May 2015. Edition: 2015/04/14
Chloroplast transcription, untangling the Gordian Knot [link]Paper   doi   link   bibtex   1 download  
Predictable alteration of sequence recognition by RNA editing factors from Arabidopsis. Kindgren, P., Yap, A., Bond, C. S., & Small, I. Plant Cell, 27(2): 403–16. February 2015. Edition: 2015/02/05
Predictable alteration of sequence recognition by RNA editing factors from Arabidopsis [link]Paper   doi   link   bibtex   abstract  
The Recovery of Plastid Function Is Required for Optimal Response to Low Temperatures in Arabidopsis. Kindgren, P., Dubreuil, C., & Strand, A. PLoS One, 10(9): e0138010. September 2015. Edition: 2015/09/15
The Recovery of Plastid Function Is Required for Optimal Response to Low Temperatures in Arabidopsis [link]Paper   doi   link   bibtex   abstract  
  2014 (1)
The cytidine deaminase signature HxE(x)nCxxC of DYW1 binds zinc and is necessary for RNA editing of ndhD-1. Boussardon, C., Avon, A., Kindgren, P., Bond, C. S., Challenor, M., Lurin, C., & Small, I. New Phytologist, 203(4): 1090–1095. 2014. _eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.12928
The cytidine deaminase signature HxE(x)nCxxC of DYW1 binds zinc and is necessary for RNA editing of ndhD-1 [link]Paper   doi   link   bibtex   abstract  
  2013 (1)
A DYW-protein knockout in Physcomitrella affects two closely spaced mitochondrial editing sites and causes a severe developmental phenotype. Schallenberg-Rüdinger, M., Kindgren, P., Zehrmann, A., Small, I., & Knoop, V. The Plant Journal, 76(3): 420–432. 2013. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.12304
A DYW-protein knockout in Physcomitrella affects two closely spaced mitochondrial editing sites and causes a severe developmental phenotype [link]Paper   doi   link   bibtex   abstract  
  2012 (2)
Interplay between HEAT SHOCK PROTEIN 90 and HY5 Controls PhANG Expression in Response to the GUN5 Plastid Signal. Kindgren, P., Norén, L., Barajas López, J. d. D., Shaikhali, J., & Strand, Å. Molecular Plant, 5(4): 901–913. July 2012.
Interplay between HEAT SHOCK PROTEIN 90 and HY5 Controls PhANG Expression in Response to the GUN5 Plastid Signal [link]Paper   doi   link   bibtex   abstract   1 download  
The plastid redox insensitive 2 mutant of Arabidopsis is impaired in PEP activity and high light-dependent plastid redox signalling to the nucleus. Kindgren, P., Kremnev, D., Blanco, N. E., López, J. d. D. B., Fernández, A. P., Tellgren-Roth, C., Small, I., & Strand, Å. The Plant Journal, 70(2): 279–291. 2012. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2011.04865.x
The plastid redox insensitive 2 mutant of Arabidopsis is impaired in PEP activity and high light-dependent plastid redox signalling to the nucleus [link]Paper   doi   link   bibtex   abstract   1 download  
  2011 (1)
A novel proteomic approach reveals a role for Mg-protoporphyrin IX in response to oxidative stress. Kindgren, P., Eriksson, M., Benedict, C., Mohapatra, A., Gough, S. P., Hansson, M., Kieselbach, T., & Strand, Å. Physiologia Plantarum, 141(4): 310–320. 2011. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1399-3054.2010.01440.x
A novel proteomic approach reveals a role for Mg-protoporphyrin IX in response to oxidative stress [link]Paper   doi   link   bibtex   abstract  
  2007 (2)
Genome-Wide Gene Expression Analysis Reveals a Critical Role for CRYPTOCHROME1 in the Response of Arabidopsis to High Irradiance. Kleine, T., Kindgren, P., Benedict, C., Hendrickson, L., & Strand, Å. Plant Physiology, 144(3): 1391–1406. July 2007.
Genome-Wide Gene Expression Analysis Reveals a Critical Role for CRYPTOCHROME1 in the Response of Arabidopsis to High Irradiance [link]Paper   doi   link   bibtex   abstract   2 downloads  
In Vivo Visualization of Mg-ProtoporphyrinIX, a Coordinator of Photosynthetic Gene Expression in the Nucleus and the Chloroplast. Ankele, E., Kindgren, P., Pesquet, E., & Strand, Å. The Plant Cell, 19(6): 1964–1979. June 2007.
In Vivo Visualization of Mg-ProtoporphyrinIX, a Coordinator of Photosynthetic Gene Expression in the Nucleus and the Chloroplast [link]Paper   doi   link   bibtex   abstract   1 download  
{tab=Svenska} Peter Kindgren med aspträd i UPSC växthus Foto: Fredrik Larsson

Alla organismer på Jorden måste interagera med sin omgivning på ett bra sätt för att växa och fortplanta sig. Planritningen för hur det ska gå till finns i deras arvsmassa, deras DNA. Vi förstår relativt väl hur DNA som kodar för proteiner fungerar men ny utveckling i genomiska metoder har identifierat att det till största del är DNA som inte kodar för protein som skrivs av, eller transkriberas, till RNA när en organism utsätts för ändringar i omgivningen. Vad som tidigare kallats för ”skräp-DNA” har nu omvärderats och vi förstår nu att så kallade icke-kodande delar av genomet är essentiella för organismer. Hur transkription av icke-kodande DNA regleras och vad det har för funktion är en nyckelfråga inom modern biologi.

Växter är experter på att snabbt reglera sin transkription och representerar därför viktiga modellsystem i denna typ av forskning. Vikten av icke-kodande transkription undersöks också i asp. Träd företräder andra viktiga biologiska frågor som är omöjliga att svara på i backtrav (Arabidopsis). Hur svarar ett träd när vinter blir till vår och när sommar blir till vinter? Hur regleras transkriptionen genom livscykeln i ett träd?

Min forskargrupp använder de senaste genomiska metoderna för att försöka förstå funktionen av icke-kodande transkription och hur detta reglerar den kodande transkriptionen.