Control of growth and gut maturation by
            <i>HoxD</i>
            genes and the associated lncRNA
            <i>Haglr</i>

Zákány, József; Darbellay, Fabrice; Mascrez, Bénédicte; Necşulea, Anamaria; Duboule, Denis

doi:10.1073/pnas.1712511114

Cited by 21 publications

(16 citation statements)

References 46 publications

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“…Read-through transcription of the lncRNA SVALKA may provide a mechanism to invade and break positive feedback mechanisms reinforcing CBF1 transcription. As lncRNA transcription in yeast and mammalian cells correlate with the boundaries of chromatin domains, roles of lncRNA in communicating regulation across domain boundaries may be common despite differences in genomic topologies 52 , 53 .…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2018

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Most DNA in the genomes of higher organisms does not encode proteins, yet much is transcribed by RNA polymerase II (RNAPII) into long non-coding RNAs (lncRNAs). The biological significance of most lncRNAs is largely unclear. Here, we identify a lncRNA (SVALKA) in a cold-sensitive region of the Arabidopsis genome. Mutations in SVALKA affect CBF1 expression and freezing tolerance. RNAPII read-through transcription of SVALKA results in a cryptic lncRNA overlapping CBF1 on the antisense strand, termed asCBF1. Our molecular dissection reveals that CBF1 is suppressed by RNAPII collision stemming from the SVALKA-asCBF1 lncRNA cascade. The SVALKA-asCBF1 cascade provides a mechanism to tightly control CBF1 expression and timing that could be exploited to maximize freezing tolerance with mitigated fitness costs. 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 challenging environmental conditions.

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Section: Discussionmentioning

confidence: 99%

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

et al. 2018

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Section: Discussionmentioning

confidence: 99%

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

Kindgren

Ard

Ivanov

2018

Preprint

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SummaryMost 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. not peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/287946 doi: bioRxiv preprint first posted online Mar. 23, 2018; Main RNA Polymerase II (RNAPII) transcription in genomes results in the production of many long noncoding RNAs (lncRNAs) 1 . The functional significance of resulting lncRNA molecules is actively debated even though biological roles are identified for an increasing number of examples [2][3][4] . Expression of lncRNAs is remarkably specific to the environmental condition, tissue or cell type, arguing for roles of lncRNA in regulation [5][6][7] . In addition to functions carried out by lncRNA molecules, the process of transcribing non-coding DNA sequences can by itself be regulatory in many systems 8,9 . Non-coding DNA regions in genomes can therefore affect gene expression by different mechanisms that need to be resolved experimentally.Sessile organisms respond to changing environmental conditions with regulation of gene expression. Early events in the Arabidopsis cold response include rapid transcriptional upregulation of the intron-less C-repeat/dehydration-responsive element binding factors (CBFs) 10,11 . The CBFs are highly conserved transcription factors that promote cold tolerance in many plant species and are often arranged in a single cluster 12. CBF expression during cold exposure activates downstream COLD REGULATED (COR) genes that promote freezing tolerance by adjusting the physiological and biochemical properties of plant cell interiors [13][14][15] . Intriguingly, constitutive CBF expression increases cold-tolerance but is also associated with fitness penalties [16][17][18][19] . antisense CBF1 lncRNA (...

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“…However, it remains to be verified if this Foxp1/lncRNA axis is also functionally important in a spinal cord context. An array of studies in various cell models has demonstrated regulation of Hox genes by lncRNAs such as Hotair, Hottip and Haglr [118,149,160]. However, to date, only one study has established a link between the roles of lncRNAs in MN development and Hox regulation.…”

Section: Lncrnas In the Regulation Of Postmitotic Neuronsmentioning

confidence: 99%

Functional Roles of Long Non-coding RNAs in Motor Neuron Development and Disease

Chen

2020

J Biomed Sci

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Long non-coding RNAs (lncRNAs) have gained increasing attention as they exhibit highly tissue-and cell-type specific expression patterns. LncRNAs are highly expressed in the central nervous system and their roles in the brain have been studied intensively in recent years, but their roles in the spinal motor neurons (MNs) are largely unexplored. Spinal MN development is controlled by precise expression of a gene regulatory network mediated spatiotemporally by transcription factors, representing an elegant paradigm for deciphering the roles of lncRNAs during development. Moreover, many MN-related neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA), are associated with RNA metabolism, yet the link between MN-related diseases and lncRNAs remains obscure. In this review, we summarize lncRNAs known to be involved in MN development and disease, and discuss their potential future therapeutic applications.

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Control of growth and gut maturation by HoxD genes and the associated lncRNA Haglr

Cited by 21 publications

References 46 publications

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

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

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

Functional Roles of Long Non-coding RNAs in Motor Neuron Development and Disease

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