Carl Robert Rankin1, Zulfiqar Ali Lokhandwala1, Raymond Huang1, Joel Pekow2, Charalabos Pothoulakis1, David Padua3. 1. Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States of America. 2. Division of Gastroenterology, University of Chicago, Chicago, IL, United States of America. 3. Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States of America; Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, CA, United States of America. Electronic address: dpadua@mednet.ucla.edu.
Abstract
AIMS: The role of long non-coding RNA's (lncRNA) in the biology of ulcerative colitis (UC) is not well understood. We have previously detected changes in lncRNA's associated with UC. This study aims to characterize one specific lncRNA, CDKN2B-AS1 whose expression was downregulated in UC patients. MAIN METHODS: UC biopsies were used to determine the levels of linear and circular CDKN2B-AS1 relative to healthy controls. In situ hybridization was used to determine the localization of CKDN2B-AS1 in the colon. The intestinal epithelial cell line, Caco-2, was used to study the effects of shRNA mediated loss of CDKN2B-AS1. Transepithelial electrical resistance was used to measure barrier function. An RT-PCR array, immunoblots and immunohistochemistry were used to determine tight junction proteins that CDKN2B-AS1 regulates. KEY FINDINGS: CDKN2B-AS1 is transcribed into not only linear transcripts but also as circular RNA through back-splicing and both forms are decreased in IBD. CDKN2B-AS1 is expressed mainly in colonic epithelial cells. Cells with down-regulated CDKN2B-AS1 exhibited increased proliferation and no alterations in apoptosis. Targeting both the linear and circular transcripts of CDKN2B-AS1 with short hairpin RNAs enhanced barrier function. We subsequently determined that Claudin-2, a "leaky Claudin" known to decrease barrier function, was decreased in CDKN2B-AS1 knockdown cells. SIGNIFICANCE: This study identifies a novel lncRNA with both linear and circular transcripts affecting UC biology. Published by Elsevier Inc.
AIMS: The role of long non-coding RNA's (lncRNA) in the biology of ulcerative colitis (UC) is not well understood. We have previously detected changes in lncRNA's associated with UC. This study aims to characterize one specific lncRNA, CDKN2B-AS1 whose expression was downregulated in UC patients. MAIN METHODS: UC biopsies were used to determine the levels of linear and circular CDKN2B-AS1 relative to healthy controls. In situ hybridization was used to determine the localization of CKDN2B-AS1 in the colon. The intestinal epithelial cell line, Caco-2, was used to study the effects of shRNA mediated loss of CDKN2B-AS1. Transepithelial electrical resistance was used to measure barrier function. An RT-PCR array, immunoblots and immunohistochemistry were used to determine tight junction proteins that CDKN2B-AS1 regulates. KEY FINDINGS:CDKN2B-AS1 is transcribed into not only linear transcripts but also as circular RNA through back-splicing and both forms are decreased in IBD. CDKN2B-AS1 is expressed mainly in colonic epithelial cells. Cells with down-regulated CDKN2B-AS1 exhibited increased proliferation and no alterations in apoptosis. Targeting both the linear and circular transcripts of CDKN2B-AS1 with short hairpin RNAs enhanced barrier function. We subsequently determined that Claudin-2, a "leaky Claudin" known to decrease barrier function, was decreased in CDKN2B-AS1 knockdown cells. SIGNIFICANCE: This study identifies a novel lncRNA with both linear and circular transcripts affecting UC biology. Published by Elsevier Inc.
Authors: Kathryn P Burdon; Stuart Macgregor; Alex W Hewitt; Shiwani Sharma; Glyn Chidlow; Richard A Mills; Patrick Danoy; Robert Casson; Ananth C Viswanathan; Jimmy Z Liu; John Landers; Anjali K Henders; John Wood; Emmanuelle Souzeau; April Crawford; Paul Leo; Jie Jin Wang; Elena Rochtchina; Dale R Nyholt; Nicholas G Martin; Grant W Montgomery; Paul Mitchell; Matthew A Brown; David A Mackey; Jamie E Craig Journal: Nat Genet Date: 2011-05-01 Impact factor: 38.330
Authors: Jessica Shea; Vineeta Agarwala; Anthony A Philippakis; Jared Maguire; Eric Banks; Mark Depristo; Brian Thomson; Candace Guiducci; Robert C Onofrio; Sekar Kathiresan; Stacey Gabriel; Noël P Burtt; Mark J Daly; Leif Groop; David Altshuler Journal: Nat Genet Date: 2011-07-24 Impact factor: 38.330
Authors: Christin E Burd; William R Jeck; Yan Liu; Hanna K Sanoff; Zefeng Wang; Norman E Sharpless Journal: PLoS Genet Date: 2010-12-02 Impact factor: 5.917
Authors: Wenqiang Yu; David Gius; Patrick Onyango; Kristi Muldoon-Jacobs; Judith Karp; Andrew P Feinberg; Hengmi Cui Journal: Nature Date: 2008-01-10 Impact factor: 49.962
Authors: J Antonio Gomez; Orly L Wapinski; Yul W Yang; Jean-François Bureau; Smita Gopinath; Denise M Monack; Howard Y Chang; Michel Brahic; Karla Kirkegaard Journal: Cell Date: 2013-02-14 Impact factor: 41.582
Authors: Aashiq H Mirza; Claus Hb Berthelsen; Stefan E Seemann; Xiaoyong Pan; Klaus S Frederiksen; Mogens Vilien; Jan Gorodkin; Flemming Pociot Journal: Genome Med Date: 2015-05-13 Impact factor: 11.117
Authors: Margaret Wrensch; Robert B Jenkins; Jeffrey S Chang; Ru-Fang Yeh; Yuanyuan Xiao; Paul A Decker; Karla V Ballman; Mitchel Berger; Jan C Buckner; Susan Chang; Caterina Giannini; Chandralekha Halder; Thomas M Kollmeyer; Matthew L Kosel; Daniel H LaChance; Lucie McCoy; Brian P O'Neill; Joe Patoka; Alexander R Pico; Michael Prados; Charles Quesenberry; Terri Rice; Amanda L Rynearson; Ivan Smirnov; Tarik Tihan; Joe Wiemels; Ping Yang; John K Wiencke Journal: Nat Genet Date: 2009-07-05 Impact factor: 38.330