The 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.

PeterKindgren Snow 1150x766Photo: Alexandra Rouillard

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.

PeterKindgren iceberg 1920


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Publication list

  1. Native elongation transcript sequencing reveals temperature dependent dynamics of nascent RNAPII transcription in Arabidopsis
    Nucleic Acids Research 2019, gkz1189
  2. Transcription-driven chromatin repression of Intragenic transcription start sites
    PLoS Genet 2018 15(2): e1007969
  3. Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation
    Nat. Commun, 2018 9, 4561
  4. The E domain of CRR2 participates in sequence‐specific recognition of RNA in plastids
    New Phytologist 2018 1: 218-229
  5. Editing of Chloroplast rps14 by PPR Editing Factor EMB2261 Is Essential for Arabidopsis Development
    Front. Plant Sci. 2018 9: 841
  6. Circadian and Plastid Signaling Pathways Are Integrated to Ensure Correct Expression of the CBF and COR Genes during Photoperiodic Growth
    Plant Physiol. 2016, 171(2):1392-1406
  7. The Recovery of Plastid Function Is Required for Optimal Response to Low Temperatures in Arabidopsis
    PLoS One. 2015 Sep 14;10(9):e0138010
  8. Chloroplast transcription, untangling the Gordian Knot
    New Phytol. 2015 May;206(3):889-91
  9. Predictable Alteration of Sequence Recognition by RNA Editing Factors from Arabidopsis
    Plant Cell 2015 27(2): 403-416
  10. AEF1/MPR25 is implicated in RNA editing of plastid atpF and mitochondrial nad5, and also promotes atpF splicing in Arabidopsis and rice
    Plant J 2015 81(5): 661-669
  11. The cytidine deaminase signature HxE(x)nCxxC of DYW1 binds zinc and is necessary for RNA editing of ndhD‐1
    Plant J 2013 7(3): 420-432
  12. A DYW‐protein knockout in Physcomitrella affects two closely spaced mitochondrial editing sites and causes a severe developmental phenotype
    Plant J 2013 7(3): 420-432
  13. The plastid redox insensitive 2 mutant of Arabidopsis is impaired in PEP activity and high light-dependent plastid redox signalling to the nucleus
    Plant J. 2012, 70(2):279-91
    Kindgren P, Kremnev D, Blanco NE, de Dios Barajas López J, Fernández AP, Tellgren-Roth C, Small I, Strand A
  14. Interplay between HEAT SHOCK PROTEIN 90 and HY5 Controls PhANG Expression in Response to the GUN5 Plastid Signal
    Mol Plant. 2012 5(4):901-913
  15. A novel proteomic approach reveals a role for Mg-protoporphyrin IX in response to oxidative stress
    Physiologia Plantarum: 2011 141:310-320
  16. In Vivo visualization of Mg-ProtoporphyrinIX, a coordinator of photosynthetic gene expression in the nucleus and the chloroplast
    The Plant Cell: 2007 19:1964-1979
  17. Genome-wide gene expression analysis reveals a critical role for CRYPTOCHROME1 in response of Arabidopsis to high irradiance
    Plant Physiology: 2007 144:1391-1406