title: High-resolution RNA allelotyping along the inactive X chromosome: evidence of RNA polymerase III in regulating chromatin configuration.
abstract: We carried out padlock capture, a high-resolution RNA allelotyping method, to study X chromosome inactivation (XCI). We examined the gene reactivation pattern along the inactive X (Xi), after Xist (X-inactive specific transcript), a prototype long non-coding RNA essential for establishing X chromosome inactivation (XCI) in early embryos, is conditionally deleted from Xi in somatic cells (Xi∆Xist). We also monitored the behaviors of X-linked non-coding transcripts before and after XCI. In each mutant cell line, gene reactivation occurs to ~6% genes along Xi∆Xistin a recognizable pattern. Genes with upstream regions enriched for SINEs are prone to be reactivated. SINE is a class of retrotransposon transcribed by RNA polymerase III (Pol III). Intriguingly, a significant fraction of Pol III transcription from non-coding regions is not subjected to Xist-mediated transcriptional silencing. Pol III inhibition affects gene reactivation status along Xi∆Xist, alters chromatin configuration and interferes with the establishment XCI during in vitro differentiation of ES cells. These results suggest that Pol III transcription is involved in chromatin structure re-organization during the onset of XCI and functions as a general mechanism regulating chromatin configuration in mammalian cells.
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore.
authors.forename: Ru
authors.initials: R
authors.lastname: Hong
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore.
authors.forename: Bingqing
authors.initials: B
authors.lastname: Lin
authors.affiliation: Genome Institute of Singapore, 138672, Singapore.
authors.forename: Xinyi
authors.initials: X
authors.lastname: Lu
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore.
authors.forename: Lan-Tian
authors.initials: LT
authors.lastname: Lai
authors.affiliation: Division of Mathematical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link 637371, Singapore.
authors.forename: Xin
authors.initials: X
authors.lastname: Chen
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore.
authors.forename: Amartya
authors.initials: A
authors.lastname: Sanyal
authors.affiliation: Genome Institute of Singapore, 138672, Singapore.
authors.forename: Huck-Hui
authors.initials: HH
authors.lastname: Ng
authors.affiliation: Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093, USA.
authors.forename: Kun
authors.initials: K
authors.lastname: Zhang
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore.
authors.forename: Li-Feng
authors.initials: LF
authors.lastname: Zhang
mesh_terms: D000483:Alleles; D000818:Animals; D002460:Cell Line; D002843:Chromatin / Q000378:metabolism*; D030541:Databases, Genetic; D050172:Genes, X-Linked; D051379:Mice; D020641:Polymorphism, Single Nucleotide; D034622:RNA Interference; D012320:RNA Polymerase III / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism*; D062085:RNA, Long Noncoding / Q000235:genetics / Q000378:metabolism; D034741:RNA, Small Interfering / Q000378:metabolism; D019474:Transcription Factors, TFIII / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism; D014960:X Chromosome / Q000235:genetics* / Q000378:metabolism; D000098832:Transcription Factor TFIIIC
chemical_list: D002843:Chromatin; D062085:RNA, Long Noncoding; D034741:RNA, Small Interfering; D019474:Transcription Factors, TFIII; C077885:XIST non-coding RNA; D000098832:Transcription Factor TFIIIC; D012320:RNA Polymerase III