Eukaryotic genomes are pervasively transcribed, producing large numbers of non-coding RNAs (ncRNAs), including tens of thousands of long ncRNAs (lncRNAs), defined as ncRNAs longer than 200 nucleotides. Recent studies have revealed the important roles lncRNAs play in the regulation of gene expression at various levels in all eukaryotes; moreover, emerging research in plants has identified roles for lncRNAs in key processes such as flowering time control, root organogenesis, reproduction, and adaptation to environmental changes. LncRNAs participate in regulating most steps of gene expression, including reshaping nuclear organization and chromatin structure; governing multiple steps of transcription, splicing, mRNA stability, and translation; and affecting post-translational protein modifications. In this review, I present the latest progress on the lncRNA-mediated regulatory mechanisms modulating transcription in Arabidopsis thaliana, focusing on their functions in regulation of gene expression via chromatin structure and interactions with the transcriptional machinery.

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