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The long noncoding RNA ROCKI regulates inflammatory gene expression.

  • Author(s): Zhang, Qiong
  • Chao, Ti-Chun
  • Patil, Veena S
  • Qin, Yue
  • Tiwari, Shashi Kant
  • Chiou, Joshua
  • Dobin, Alexander
  • Tsai, Chih-Ming
  • Li, Zhonghan
  • Dang, Jason
  • Gupta, Shagun
  • Urdahl, Kevin
  • Nizet, Victor
  • Gingeras, Thomas R
  • Gaulton, Kyle J
  • Rana, Tariq M
  • et al.
Abstract

Long noncoding RNAs (lncRNAs) can regulate target gene expression by acting in cis (locally) or in trans (non-locally). Here, we performed genome-wide expression analysis of Toll-like receptor (TLR)-stimulated human macrophages to identify pairs of cis-acting lncRNAs and protein-coding genes involved in innate immunity. A total of 229 gene pairs were identified, many of which were commonly regulated by signaling through multiple TLRs and were involved in the cytokine responses to infection by group B Streptococcus We focused on elucidating the function of one lncRNA, named lnc-MARCKS or ROCKI (Regulator of Cytokines and Inflammation), which was induced by multiple TLR stimuli and acted as a master regulator of inflammatory responses. ROCKI interacted with APEX1 (apurinic/apyrimidinic endodeoxyribonuclease 1) to form a ribonucleoprotein complex at the MARCKS promoter. In turn, ROCKI-APEX1 recruited the histone deacetylase HDAC1, which removed the H3K27ac modification from the promoter, thus reducing MARCKS transcription and subsequent Ca2+ signaling and inflammatory gene expression. Finally, genetic variants affecting ROCKI expression were linked to a reduced risk of certain inflammatory and infectious disease in humans, including inflammatory bowel disease and tuberculosis. Collectively, these data highlight the importance of cis-acting lncRNAs in TLR signaling, innate immunity, and pathophysiological inflammation.

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