ArticleGenome research2019
Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing.
Erratum issuedOpen access · bronzeAbstract read
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Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 23 papers.
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23citing papers in PubMed
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23 citing papers in PubMed, 35 citations in OpenAlex.
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- Profiling mitochondria-polyribosome lncRNAs associated with pluripotency.Scientific data · 2023Article
- Chromatin-RNA in situ Reverse Transcription Sequencing (CRIST-seq) Approach to Profile the Non-coding RNA Interaction Network.Bio-protocol · 2023Article
- LncRNA Osilr9 coordinates promoter DNA demethylation and the intrachromosomal loop structure required for maintaining stem cell pluripotency.Molecular therapy : the journal of the American Society of Gene Therapy · 2023Article
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- Epigenetic reprogramming during prostate cancer progression: A perspective from development.Seminars in cancer biology · 2022Review
- LncRNAs and CircRNAs in cancer.MedComm · 2022Review
- Pluripotency exit is guided by the Peln1-mediated disruption of intrachromosomal architecture.The Journal of cell biology · 2022Article
- The landscape of promoter-centred RNA-DNA interactions in rice.Nature plants · 2022Article
- Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network.Genome biology · 2021Article
- Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data.Genome research · 2021Article
- Non-coding RNA Expression Patterns of Two Different Teleost Gonad Maturation Stages.Marine biotechnology (New York, N.Y.) · 2020Article
- Long non-coding RNA ADAMTS9-AS1 suppresses colorectal cancer by inhibiting the Wnt/β-catenin signalling pathway and is a potential diagnostic biomarker.Journal of cellular and molecular medicine · 2020Article
- Systematic characterization of non-coding RNAs in triple-negative breast cancer.Cell proliferation · 2020Review
- Oplr16 serves as a novel chromatin factor to control stem cell fate by modulating pluripotency-specific chromosomal looping and TET2-mediated DNA demethylation.Nucleic acids research · 2020Article
- Role of Long Non-coding RNAs in Reprogramming to Induced Pluripotency.Genomics, proteomics & bioinformatics · 2020Review
- Genome-wide interaction target profiling reveals a novelTheranostics · 2020Article
- LncRNA Functions as a New Emerging Epigenetic Factor in Determining the Fate of Stem Cells.Frontiers in genetics · 2020Review
Corrections and comments
- Erratum issued
Authors and funding
28 authors at 6 institutions in 2 countries.
Shilin Zhang *Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China.
Yichen Wang *Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China.
Lin Jia *Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China.
Xue Wen *Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China.
Zhonghua Du *Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China.
Cong WangKey Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China.
Yajing HaoCAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China.
Dehai YuKey Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China.
Lei ZhouKey Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China.
Naifei ChenKey Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China.
Jingcheng ChenKey Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China.
Huiling ChenDepartment of Endocrinology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China.
Hui ZhangGuangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, P.R. China.
Ilkay CelikStanford University Medical School, VA Palo Alto Health Care System, Palo Alto, California 94304, USA.
Günhan GülsoyGoogle Incorporated, Mountain View, California 94043, USA.
Jianjun LuoCAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China.
Baoming QinGuangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, P.R. China.
Xueling CuiDepartment of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, P.R. China.
Zhonghui LiuDepartment of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, P.R. China.
Songling ZhangKey Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China.
Miguel A EstebanGuangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, P.R. China.
Ferhat AyLa Jolla Institute for Allergy and Immunology, La Jolla, California 92037, USA.
Wei XuKey Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China.
Runsheng ChenCAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China.
Wei LiKey Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China.
Andrew R HoffmanStanford University Medical School, VA Palo Alto Health Care System, Palo Alto, California 94304, USA.
Ji-Fan HuKey Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China.ORCID 0000-0002-2174-0361
Jiuwei CuiKey Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China.
Jilin University · CNChinese Academy of Sciences · CNVA Palo Alto Health Care System · USCentral South University · CNLa Jolla Institute for Immunology · USMoog (United States) · US
Funding
The Role of Long Noncoding RNAs in CancerI01BX002905 · VA · VETERANS ADMIN PALO ALTO HEALTH CARE SYS · PI HOFFMAN, ANDREW R · 2016 to 2023
–BLRD VA I01 BX002905
Abstract
Long noncoding RNAs (lncRNAs) can regulate the activity of target genes by participating in the organization of chromatin architecture. We have devised a "chromatin-RNA in situ reverse transcription sequencing" (CRIST-seq) approach to profile the lncRNA interaction network in gene regulatory elements by combining the simplicity of RNA biotin labeling with the specificity of the CRISPR/Cas9 system. Using gene-specific gRNAs, we describe a pluripotency-specific lncRNA interacting network in the promoters of
Indexed as
AnimalsCell LineCellular ReprogrammingChromatinCRISPR-Cas SystemsFibroblastsMiceOctamer Transcription Factor-3Pluripotent Stem CellsPromoter Regions, GeneticRegulatory Sequences, Nucleic AcidRNA, Long NoncodingSequence Analysis, RNASOXB1 Transcription FactorsChromatinOctamer Transcription Factor-3Pou5f1 protein, mouseRNA, Long NoncodingSox2 protein, mouseSOXB1 Transcription Factors
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