Biology subjects

Kindgren, P.

Publications and source records attributed to Kindgren, P..

7 recordsLinked to original sources

bioRxiv2026

H3K27me3 and H2A.Z prime cold regulated genes, and their remodelling governs plant cold response

To elucidate the contribution of chromatin modifications in plant cold response, we performed ChIP-seq for H3K27me3 and H2A.Z in Arabidopsis exposed to short-term cold. We combined our epigenetic data with NET-seq to investigate the direct transcriptional effects of histone marks. Prior to any stress cue, cold regulated genes share a similar chromatin environment with high H2A.Z and H3K27me3. H3K27me3 levels do not correlate with transcriptional activity or elongation speed. However, REF6-mediated reduction of H3K27me3 is essential for regulation of cold controlled genes. H2A.Z occupancy changes revealed a negative correlation between cold-induced changes to H2A.Z and RNAPII activity at differentially expressed genes. Importantly, changing H2A.Z levels preceded transcriptional changes, indicating that the variant functions as a critical cold-induced switch. Further, our data suggests that high H2A.Z levels slow down RNAPII. Thus, H2A.Z is essential for the transcriptional response and a decreased H3K27me3 level is important for the genomic adaptation to cold.

plant biology↗

bioRxiv2025

Two long non-coding RNAs, SVALKA and SVALNA, regulate CBF1 and CBF3 via multiple mechanisms

Long non-coding RNAs (lncRNAs) are emerging as key regulatory players of coding gene expression in eukaryotes. Here, we investigate the roles of the lncRNAs SVALKA (SVK) and SVALNA (SVN) in regulating CBF1 and CBF3 gene expression in Arabidopsis under cold stress conditions. We used Native Elongation Transcript Sequencing, CRISPR-Cas9 deletion strategies, and RT-qPCR to analyze the transcriptional dynamics and regulatory mechanisms of SVK and SVN. Our results demonstrate that SVK functions as a cis- and trans-acting lncRNA, regulating both CBF1 and CBF3 through RNAPII collision and chromatin remodeling, while SVN serves a cis role by negatively regulating CBF3 via a RNAPII collision mechanism. We identified isoforms of SVK, originating from distinct transcription start sites and undergo alternative splicing to adapt structural stability, crucial for their regulatory functions. This study elucidates the complex interplay of lncRNAs in gene regulation, highlighting their essential roles in modulating responses to environmental stresses. Our findings contribute to a deeper understanding of the mechanisms underlying lncRNA functionality and their significance in gene regulatory networks in eukaryotes.

plant biology↗

bioRxiv2023

MTA influences RNA Polymerase II transcription dynamics and regulates the cold response in Arabidopsis.

RNA methylation at the N6 position of adenosine residues (m6A) has been demonstrated to be a vital epigenetic mark in eukaryotes. In plants, it is involved in a myriad of developmental and stress responsive pathways, such as cold stress. However, the role of MTA (m6A writer) itself in such processes remains obscured. Here, we show that the cold induced changes in abundance of differentially methylated transcripts are at-least partly due to the differences in the rates of transcription of such transcripts. RNAPII stalling was observed only on RNA methylation motifs that were decorated with m6A, and those that had a specific nucleotide composition. We note that the downregulation of genes in a mta mutant is a result of lower transcription of these genes. Moreover, 5 ends of transcripts from a subset of genes are disproportionately more accumulated in mta as compared to wild type under cold stress. In the mta mutant, genes corresponding to these transcripts had significantly reduced RNAPII occupancy on their 3 ends but not on 5 ends indicating that mta serves as an important factor for RNAPII elongation in a subset of genes. Taken together, our data suggest a novel direct role for MTA as a gene specific influencer of RNAPII elongation dynamics and thus introduces a new path by which the m6A methylation machinery may affect differential gene expression during stress in plants.

plant biology↗

bioRxiv2020

Light-dependent translation change of Arabidopsis psbA correlates with RNA structure alterations at the translation initiation region

mRNA secondary structure influences translation. Proteins that modulate the mRNA secondary structure around the translation initiation region may regulate translation in plastids. To test this hypothesis, we exposed Arabidopsis thaliana to high light, which induces translation of psbA mRNA encoding the D1 subunit of photosystem II. We assayed translation by ribosome profiling and applied two complementary methods to analyze in vivo RNA secondary structure: DMS-MaPseq and SHAPE-seq. We detected increased accessibility of the translation initiation region of psbA after high light treatment, likely contributing to the observed increase in translation by facilitating translation initiation. Furthermore, we identified the footprint of a putative regulatory protein in the 5 UTR of psbA at a position where occlusion of the nucleotide sequence would cause the structure of the translation initiation region to open up, thereby facilitating ribosome access. Moreover, we show that other plastid genes with weak Shine-Dalgarno sequences (SD) are likely to exhibit psbA-like regulation, while those with strong SDs do not. This supports the idea that changes in mRNA secondary structure might represent a general mechanism for translational regulation of psbA and other plastid genes. SIGNIFICANCERNA structure changes in the translation initiation region, most likely as a result of protein binding, affect the translation of psbA and possibly other plastid genes with weak Shine-Dalgarno sequences.

plant biology↗

bioRxiv2019

Native Elongation Transcript sequencing reveals temperature dependent dynamics of nascent RNAPII transcription in Arabidopsis

Temperature profoundly affects the kinetics of biochemical reactions, yet how large molecular complexes such as the transcription machinery accommodate changing temperatures to maintain cellular function is poorly understood. Here, we developed plant native elongating transcripts sequencing (plaNET-seq) to profile genome-wide nascent RNA polymerase II (RNAPII) transcription during the cold-response of Arabidopsis thaliana with single-nucleotide resolution. Combined with temporal resolution, these data revealed transient genome-wide reprogramming of nascent RNAPII transcription during cold, including characteristics of RNAPII elongation and thousands of non-coding transcripts connected to gene expression. Our results suggest a role for promoter-proximal RNAPII stalling in predisposing genes for transcriptional activation during plant-environment interactions. At gene 3-ends, cold initially facilitated transcriptional termination by limiting the distance of read-through transcription. Within gene bodies, cold reduced the kinetics of co-transcriptional splicing leading to increased intragenic stalling. Our data resolved multiple distinct mechanisms by which temperature transiently altered the dynamics of nascent RNAPII transcription and associated RNA processing, illustrating potential biotechnological solutions and future focus areas to promote food security in the context of a changing climate.

genomics↗

bioRxiv2018

Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation

Most DNA in the genomes of higher organisms does not encode proteins, but is transcribed by RNA polymerase II (RNAPII) into long non-coding RNA (lncRNA). The biological significance of most lncRNA is largely unclear. Here, we identify a lncRNA (SVALKA) in a cold-sensitive region of the Arabidopsis genome. Mutations in SVALKA affect the timing of maximal CBF1 expression and freezing tolerance. RNAPII read-through transcription of SVALKA results in a cryptic lncRNA overlapping CBF1 on the antisense strand, termed asCBF1. asCBF1 transcription is anti-correlated with CBF1 expression. Our molecular dissection reveals that CBF1 is suppressed by RNAPII collision stemming from the SVALKA-asCBF1 lncRNA cascade. The SVK-asCBF1 cascade provides a mechanism to tightly control CBF1 expression and timing that could be exploited to maximize freezing tolerance with mitigated fitness costs. Inversion of the transcriptional direction of a lncRNA cascade relative to the genes in a co-regulated cluster provides an elegant inbuilt negative feedback for cluster expression. Our results provide a compelling example of local gene regulation by lncRNA transcription having a profound impact on the ability of plants to appropriately acclimate to suboptimal environmental conditions.

genomics↗

bioRxiv2018

Transcription-driven Chromatin Repression of Intragenic Promoters

Progression of RNA polymerase II (RNAPII) transcription relies on the appropriately positioned activities of elongation factors. The resulting profile of factors and chromatin signatures along transcription units provides a \"positional information system\" for transcribing RNAPII. Here, we investigate a chromatin-based mechanism that suppresses intragenic initiation of RNAPII transcription. We demonstrate that RNAPII transcription across gene promoters represses their function in plants. This repression is characterized by reduced promoter-specific molecular signatures and increased molecular signatures associated with RNAPII elongation. The FACT histone chaperone complex is required for this repression mechanism. Genome-wide mapping of Transcription Start Sites (TSSs) reveals thousands of discrete intragenic TSS positions in FACT mutants. Histone 3 lysine 4 mono-methylation poises exonic sites to initiate RNAPII transcription in FACT mutants. Uncovering the mechanism for intragenic TSS repression through the act of RNAPII elongation has important implications for understanding pervasive RNAPII transcription and the regulation of transcript isoform diversity.

genomics↗