Functional consequences of non-coding transcription – University of Copenhagen

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Functional consequences of non-coding transcription

Non-coding transcription by RNA polymerase II occurs frequently. Clarifying the functions of this process poses an important question for current biologists. There are at least two possibilities for how non-coding transcription can have biological consequences: 1.) Long non-coding RNA (lncRNA) species result from non-coding transcription and can function by multiple mechanisms, for example by recruiting chromatin remodeling activities to achieve long-term effects on gene expression. 2.) The act of non-coding transcription leaves marks associated with transcription on the underlying DNA regions, for example through chromatin remodeling and modifications. These marks established during non-coding transcription can affect gene expression.

We are particularly interested in how marks associated with non-coding transcription interfere with expression of nearby genes. The respective orientation of the gene and the non-coding transcript influences the mechanism by which interactions between the transcription units can occur. We have recently identified how alternative splicing and polyadenylation of an antisense transcript of the important Arabidopsis floral repressor gene FLOWERING LOCUS C (FLC) controls FLC expression and thus flowering time (2, 3). We are currently expanding our interest in this area and examine how the act of non-coding transcription affects nearby gene expression if the transcripts face away from each other (divergent non-coding transcription), or face towards each other (tandem) using yeast and Arabidopsis models. The plasticity of non-coding transcription motivates our investigation of the transcription kinetics in environmental interactions.

(2) Marquardt S, Raitskin O, Liu F, Wu Z, Sun Q, Dean C. "Functional consequences of splicing of the antisense transcript COOLAIR on FLC transcription”. Mol Cell. 2014 Apr 10;54(1):156-65.

(3) *Liu F, *Marquardt S, Lister C, Swiezewski S, Dean C. * Joint first authors. “Targeted 3' processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing”. Science. 2010 Jan 1;327(5961):94-7. 

FCNT

Figure: A.), B.) and C.) Schematic illustrations of different configurations of genes and non-coding transcription with respect to each other. D.) Summary illustrating the molecular and phenotypic consequences of Arabidopsis if non-coding FLC antisense transcript splicing and 3’end formation is disrupted (2,3).