Encoding memory of winter by noncoding RNAs

Heo, Jae Bok; Sung, Sibum

doi:10.4161/epi.6.5.15235

Cited by 29 publications

(16 citation statements)

References 34 publications

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“…Our data are consistent with the COLDAIR lncRNA acting to maintain repression of FLC by recruiting the PRC2 machinery [23]. None of the T-DNA insertions tested interrupt the COLDAIR transcript and all show maintenance of repression after vernalization.…”

Section: Resultssupporting

confidence: 85%

Vernalization-Repression of Arabidopsis FLC Requires Promoter Sequences but Not Antisense Transcripts

et al. 2011

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The repression of Arabidopsis FLC expression by vernalization (extended cold) has become a model for understanding polycomb-associated epigenetic regulation in plants. Antisense and sense non-coding RNAs have been respectively implicated in initiation and maintenance of FLC repression by vernalization. We show that the promoter and first exon of the FLC gene are sufficient to initiate repression during vernalization; this initial repression of FLC does not require antisense transcription. Long-term maintenance of FLC repression requires additional regions of the gene body, including those encoding sense non-coding transcripts.

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Section: Resultssupporting

confidence: 85%

Vernalization-Repression of Arabidopsis FLC Requires Promoter Sequences but Not Antisense Transcripts

et al. 2011

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“…A potential alternative epigenetic mechanism involves an ECR that can regulate gene expression within a greater than 2 Mb region together with, for example, lncRNAs and chromatin structure. An example of such a mechanism has been previously described as an ICR, where an imprinted DNA methylation site (for example, H19 and IGF2 ) influences a lncRNA to regulate gene expression for over a megabase in either direction [17,22,23,27]. The imprinted H19 and IGF2 loci together with a lncRNA have been shown to distally regulate the expression of multiple different genes [17,25,26,28].…”

Section: Discussionmentioning

confidence: 99%

“…The ICR for IGF2 and H19 [17,25] has been shown to act through long non-coding RNA (lncRNA) and distally for over a megabase in either direction to regulate the expression of multiple genes [26,27]. Therefore, an epigenetic DNA methylation region can regulate the expression of a number of distal genes [17,28].…”

Section: Introductionmentioning

confidence: 99%

Epigenetic transgenerational inheritance of somatic transcriptomes and epigenetic control regions

et al. 2012

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BackgroundEnvironmentally induced epigenetic transgenerational inheritance of adult onset disease involves a variety of phenotypic changes, suggesting a general alteration in genome activity.ResultsInvestigation of different tissue transcriptomes in male and female F3 generation vinclozolin versus control lineage rats demonstrated all tissues examined had transgenerational transcriptomes. The microarrays from 11 different tissues were compared with a gene bionetwork analysis. Although each tissue transgenerational transcriptome was unique, common cellular pathways and processes were identified between the tissues. A cluster analysis identified gene modules with coordinated gene expression and each had unique gene networks regulating tissue-specific gene expression and function. A large number of statistically significant over-represented clusters of genes were identified in the genome for both males and females. These gene clusters ranged from 2-5 megabases in size, and a number of them corresponded to the epimutations previously identified in sperm that transmit the epigenetic transgenerational inheritance of disease phenotypes.ConclusionsCombined observations demonstrate that all tissues derived from the epigenetically altered germ line develop transgenerational transcriptomes unique to the tissue, but common epigenetic control regions in the genome may coordinately regulate these tissue-specific transcriptomes. This systems biology approach provides insight into the molecular mechanisms involved in the epigenetic transgenerational inheritance of a variety of adult onset disease phenotypes.

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“…In Arabidopsis , two transcripts , COOLAIR and COLDAIR , are related with FLOWERING LOCUS C ( FLC ), which encodes a floral repressor in vernalization. 25,26 …”

Section: Introductionmentioning

confidence: 99%

Genome-wide view of natural antisense transcripts in Arabidopsis thaliana

et al. 2015

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Natural antisense transcripts (NATs) are endogenous transcripts that can form double-stranded RNA structures. Many protein-coding genes (PCs) and non-protein-coding genes (NPCs) tend to form cis-NATs and trans-NATs, respectively. In this work, we identified 4,080 cis-NATs and 2,491 trans-NATs genome-widely in Arabidopsis. Of these, 5,385 NAT-siRNAs were detected from the small RNA sequencing data. NAT-siRNAs are typically 21nt, and are processed by Dicer-like 1 (DCL1)/DCL2 and RDR6 and function in epigenetically activated situations, or 24nt, suggesting these are processed by DCL3 and RDR2 and function in environment stress. NAT-siRNAs are significantly derived from PC/PC pairs of trans-NATs and NPC/NPC pairs of cis-NATs. Furthermore, NAT pair genes typically have similar pattern of epigenetic status. Cis-NATs tend to be marked by euchromatic modifications, whereas trans-NATs tend to be marked by heterochromatic modifications.

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Encoding memory of winter by noncoding RNAs

Cited by 29 publications

References 34 publications

Vernalization-Repression of Arabidopsis FLC Requires Promoter Sequences but Not Antisense Transcripts

Vernalization-Repression of Arabidopsis FLC Requires Promoter Sequences but Not Antisense Transcripts

Epigenetic transgenerational inheritance of somatic transcriptomes and epigenetic control regions

Genome-wide view of natural antisense transcripts in Arabidopsis thaliana

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