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Velissari R, Ilieva M, Dao J, Miller HE, Madsen JH, Gorodkin J, Aikawa M, Ishii H, Uchida S. Systematic analysis and characterization of long non-coding RNA genes in inflammatory bowel disease. Brief Funct Genomics 2024; 23:395-405. [PMID: 37791426 PMCID: PMC11260263 DOI: 10.1093/bfgp/elad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/28/2023] [Accepted: 09/12/2023] [Indexed: 10/05/2023] Open
Abstract
The cases of inflammatory bowel disease (IBD) are increasing rapidly around the world. Due to the multifactorial causes of IBD, there is an urgent need to understand the pathogenesis of IBD. As such, the usage of high-throughput techniques to profile genetic mutations, microbiome environments, transcriptome and proteome (e.g. lipidome) is increasing to understand the molecular changes associated with IBD, including two major etiologies of IBD: Crohn disease (CD) and ulcerative colitis (UC). In the case of transcriptome data, RNA sequencing (RNA-seq) technique is used frequently. However, only protein-coding genes are analyzed, leaving behind all other RNAs, including non-coding RNAs (ncRNAs) to be unexplored. Among these ncRNAs, long non-coding RNAs (lncRNAs) may hold keys to understand the pathogenesis of IBD as lncRNAs are expressed in a cell/tissue-specific manner and dysregulated in a disease, such as IBD. However, it is rare that RNA-seq data are analyzed for lncRNAs. To fill this gap in knowledge, we re-analyzed RNA-seq data of CD and UC patients compared with the healthy donors to dissect the expression profiles of lncRNA genes. As inflammation plays key roles in the pathogenesis of IBD, we conducted loss-of-function experiments to provide functional data of IBD-specific lncRNA, lung cancer associated transcript 1 (LUCAT1), in an in vitro model of macrophage polarization. To further facilitate the lncRNA research in IBD, we built a web database, IBDB (https://ibd-db.shinyapps.io/IBDB/), to provide a one-stop-shop for expression profiling of protein-coding and lncRNA genes in IBD patients compared with healthy donors.
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Affiliation(s)
- Rania Velissari
- Faculty of Biology, Medicine and Health, University of Manchester, Oxford Rd, Manchester M13 9PL, UK
- Bioinformatics Research Network, Atlanta, GA 30317, USA
| | - Mirolyuba Ilieva
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen SV, Denmark
| | - James Dao
- Bioinformatics Research Network, Atlanta, GA 30317, USA
| | | | - Jens Hedelund Madsen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen SV, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Ridebanevej 9, DK-1870 Frederiksberg C, Denmark
| | - Masanori Aikawa
- Cardiovascular Division, Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Excellence in Vascular Biology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hideshi Ishii
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan
| | - Shizuka Uchida
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen SV, Denmark
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Abstract
The factors that trigger human puberty are among the central mysteries of reproductive biology. Several approaches, including mutational analysis of candidate genes, large-scale genome-wide association studies, whole exome sequencing, and whole genome sequencing have been performed in attempts to identify novel genetic factors that modulate the human hypothalamic-pituitary-gonadal axis to result in premature sexual development. Genetic abnormalities involving excitatory and inhibitory pathways regulating gonadotropin-releasing hormone secretion, represented by the kisspeptin (KISS1 and KISS1R) and makorin ring finger 3 (MKRN3) systems, respectively, have been associated with sporadic and familial cases of central precocious puberty (CPP). More recently, paternally inherited genetic defects of DLK1 were identified in four families with nonsyndromic CPP and a metabolic phenotype. DLK1 encodes a transmembrane protein that is important for adipose tissue homeostasis and neurogenesis and is located in the imprinted chromosome 14q32 region associated with Temple syndrome. In this review, we highlight the clinical and genetic features of patients with CPP caused by DLK1 mutations and explore the involvement of Notch signaling and DLK1 in the control of pubertal onset.
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Affiliation(s)
- Delanie B. Macedo
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ursula B. Kaiser
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
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Chery J, Larschan E. X-marks the spot: X-chromosome identification during dosage compensation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:234-40. [PMID: 24406325 DOI: 10.1016/j.bbagrm.2013.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Revised: 12/29/2013] [Accepted: 12/30/2013] [Indexed: 12/11/2022]
Abstract
Dosage compensation is the essential process that equalizes the dosage of X-linked genes between the sexes in heterogametic species. Because all of the genes along the length of a single chromosome are co-regulated, dosage compensation serves as a model system for understanding how domains of coordinate gene regulation are established. Dosage compensation has been best studied in mammals, flies and worms. Although dosage compensation systems are seemingly diverse across species, there are key shared principles of nucleation and spreading that are critical for accurate targeting of the dosage compensation complex to the X-chromosome(s). We will highlight the mechanisms by which long non-coding RNAs function together with DNA sequence elements to tether dosage compensation complexes to the X-chromosome. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.
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Affiliation(s)
- Jessica Chery
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA
| | - Erica Larschan
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA.
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