Unlinking an lncRNA from Its Associated cis Element

Vikram R. Paralkar, Cristian C. Taborda, Peng Huang, Yu Yao, Andrew V. Kossenkov, Rishi Prasad, Jing Luan, James O.J. Davies, Jim R. Hughes, Ross Cameron Hardison, Gerd A. Blobel, Mitchell J. Weiss

Research output: Contribution to journalArticle

79 Citations (Scopus)

Abstract

Long non-coding (lnc) RNAs can regulate gene expression and protein functions. However, the proportion of lncRNAs with biological activities among the thousands expressed in mammalian cells is controversial. We studied Lockd (lncRNA downstream of Cdkn1b), a 434-nt polyadenylated lncRNA originating 4 kb 3' to the Cdkn1b gene. Deletion of the 25-kb Lockd locus reduced Cdkn1b transcription by approximately 70% in an erythroid cell line. In contrast, homozygous insertion of a polyadenylation cassette 80 bp downstream of the Lockd transcription start site reduced the entire lncRNA transcript level by >90% with no effect on Cdkn1b transcription. The Lockd promoter contains a DNase-hypersensitive site, binds numerous transcription factors, and physically associates with the Cdkn1b promoter in chromosomal conformation capture studies. Therefore, the Lockd gene positively regulates Cdkn1b transcription through an enhancer-like cis element, whereas the lncRNA itself is dispensable, which may be the case for other lncRNAs.

Original languageEnglish (US)
Pages (from-to)104-110
Number of pages7
JournalMolecular cell
Volume62
Issue number1
DOIs
StatePublished - Apr 7 2016

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Long Noncoding RNA
Erythroid Cells
Polyadenylation
Deoxyribonucleases
Transcription Initiation Site
Genes
Transcription Factors
Gene Expression
Cell Line

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Cell Biology

Cite this

Paralkar, V. R., Taborda, C. C., Huang, P., Yao, Y., Kossenkov, A. V., Prasad, R., ... Weiss, M. J. (2016). Unlinking an lncRNA from Its Associated cis Element. Molecular cell, 62(1), 104-110. https://doi.org/10.1016/j.molcel.2016.02.029
Paralkar, Vikram R. ; Taborda, Cristian C. ; Huang, Peng ; Yao, Yu ; Kossenkov, Andrew V. ; Prasad, Rishi ; Luan, Jing ; Davies, James O.J. ; Hughes, Jim R. ; Hardison, Ross Cameron ; Blobel, Gerd A. ; Weiss, Mitchell J. / Unlinking an lncRNA from Its Associated cis Element. In: Molecular cell. 2016 ; Vol. 62, No. 1. pp. 104-110.
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Paralkar, VR, Taborda, CC, Huang, P, Yao, Y, Kossenkov, AV, Prasad, R, Luan, J, Davies, JOJ, Hughes, JR, Hardison, RC, Blobel, GA & Weiss, MJ 2016, 'Unlinking an lncRNA from Its Associated cis Element', Molecular cell, vol. 62, no. 1, pp. 104-110. https://doi.org/10.1016/j.molcel.2016.02.029

Unlinking an lncRNA from Its Associated cis Element. / Paralkar, Vikram R.; Taborda, Cristian C.; Huang, Peng; Yao, Yu; Kossenkov, Andrew V.; Prasad, Rishi; Luan, Jing; Davies, James O.J.; Hughes, Jim R.; Hardison, Ross Cameron; Blobel, Gerd A.; Weiss, Mitchell J.

In: Molecular cell, Vol. 62, No. 1, 07.04.2016, p. 104-110.

Research output: Contribution to journalArticle

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Paralkar VR, Taborda CC, Huang P, Yao Y, Kossenkov AV, Prasad R et al. Unlinking an lncRNA from Its Associated cis Element. Molecular cell. 2016 Apr 7;62(1):104-110. https://doi.org/10.1016/j.molcel.2016.02.029