title: Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light.
abstract: Seedling photomorphogenesis is a sophisticated developmental process that is controlled by both the transcriptional and posttranscriptional regulation of gene expression. Here, we identify an Arabidopsis noncoding RNA, designated hidden treasure 1 (HID1), as a factor promoting photomorphogenesis in continuous red light (cR). We show that HID1 acts through phytochrome-interacting factor 3 (PIF3), which encodes a basic helix-loop-helix transcription factor known to be a key repressor of photomorphogenesis. Knockdown of HID1 in hid1 mutants leads to a significant increase in the expression of PIF3, which in turn drives the development of elongated hypocotyls in cR. We identified two major stem-loops in HID1 that are essential for its modulation of hypocotyl growth in cR-grown seedlings. Furthermore, our data reveal that HID1 is assembled into large nuclear protein-RNA complex(es) and that it associates with the chromatin of the first intron of PIF3 to repress its transcription. Strikingly, phylogenetic analysis reveals that many land plants have conserved homologs of HID1 and that its rice homolog can rescue the mutant phenotype when expressed in Arabidopsis hid1 mutants. We thus concluded that HID1 is a previously uncharacterized noncoding RNA whose function represents another layer of regulation in the precise control of seedling photomorphogenesis.
authors: State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China;
authors: Yuqiu
authors: Y
authors: Wang
authors: State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China;
authors: Xiuduo
authors: X
authors: Fan
authors: State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China;
authors: Fang
authors: F
authors: Lin
authors: State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China;
authors: Guangming
authors: G
authors: He
authors: Department of Biology, Wilkes University, Wilkes-Barre, PA 18766; andDepartment of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520.
authors: William
authors: W
authors: Terzaghi
authors: State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China; xingwang.deng@yale.edu zhudanmeng@pku.edu.cn.
authors: Danmeng
authors: D
authors: Zhu
authors: State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China;Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520 xingwang.deng@yale.edu zhudanmeng@pku.edu.cn.
authors: Xing Wang
authors: XW
authors: Deng
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000096:biosynthesis* / Q000235:genetics; D001483:Base Sequence; D051792:Basic Helix-Loop-Helix Proteins / Q000096:biosynthesis* / Q000235:genetics; D055785:Gene Knockdown Techniques; D018546:Hypocotyl / Q000235:genetics / Q000378:metabolism*; D008969:Molecular Sequence Data; D022022:Nuclear Pore / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism*; D022661:RNA, Untranslated / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic / Q000502:physiology*
chemical_list: D029681:Arabidopsis Proteins; D051792:Basic Helix-Loop-Helix Proteins; D018749:RNA, Plant; D022661:RNA, Untranslated; C116162:PIF3 protein, Arabidopsis
keywords: light signaling; transcriptional regulation