Chromatin structure, epigenetic mechanisms and long‐range interactions in the human insulin locus

Regulation of gene expression in eukaryotes is largely dependent on variations in chromatin structure. More recently, it has become clear that this may involve not only local chromatin organization but also distant regulatory elements that participate in large‐scale chromatin architecture within the nucleus. We describe recent methods that make possible the detection of such structures and apply them to analysis of the human insulin (INS) locus in pancreatic islets. We show that the INS gene is part of an extended ‘open’ chromatin domain that includes adjacent genes as well. We also find that in islets, the INS promoter is in physical contact with distant sites on the same human chromosome and notably, with the SYT8 gene, located nearly 300 kb away. The strength of the contact between INS and SYT8 is increased by glucose, and this results in stimulation of SYT8 expression. Inhibition of INS transcription decreases SYT8 expression. Furthermore, downregulation of SYT8 results in decreased secretion of insulin. Our results thus establish the existence of a regulatory network between the INS gene and other distant genes through long‐range physical interactions, and suggest that such networks may have general importance for insulin biology and diabetes.

[1]  J. Rinn,et al.  Modular regulatory principles of large non-coding RNAs , 2012, Nature.

[2]  Raymond K. Auerbach,et al.  Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation , 2012, Cell.

[3]  R. Shiekhattar,et al.  Noncoding RNAs and enhancers: complications of a long-distance relationship. , 2011, Trends in genetics : TIG.

[4]  Howard Y. Chang,et al.  Molecular mechanisms of long noncoding RNAs. , 2011, Molecular cell.

[5]  Ty C. Voss,et al.  Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism , 2011, Cell.

[6]  H. Tsukamura,et al.  Single-stranded Noncoding RNAs Mediate Local Epigenetic Alterations at Gene Promoters in Rat Cell Lines* , 2011, The Journal of Biological Chemistry.

[7]  Howard Y. Chang,et al.  Long noncoding RNAs and human disease. , 2011, Trends in cell biology.

[8]  C. Kanduri.  Kcnq1ot1: a chromatin regulatory RNA. , 2011, Seminars in cell & developmental biology.

[9]  L. Lefebvre,et al.  An Extended Domain of Kcnq1ot1 Silencing Revealed by an Imprinted Fluorescent Reporter , 2011, Molecular and Cellular Biology.

[10]  K. Zhao,et al.  Mapping of INS promoter interactions reveals its role in long-range regulation of SYT8 transcription , 2011, Nature Structural &Molecular Biology.

[11]  Stephen C. J. Parker,et al.  Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci. , 2010, Cell metabolism.

[12]  I. Temple,et al.  6q24 transient neonatal diabetes , 2010, Reviews in Endocrine and Metabolic Disorders.

[13]  C. Kanduri,et al.  Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1 , 2010, Development.

[14]  A. Hoffman,et al.  Loss of IGF2 imprinting is associated with abrogation of long-range intrachromosomal interactions in human cancer cells. , 2010, Human molecular genetics.

[15]  Jonathan C. Cohen,et al.  Targeted Deletion of the 9p21 Noncoding Coronary Artery Disease Risk Interval in Mice , 2010, Nature.

[16]  Daniel F. Gudbjartsson,et al.  Parental origin of sequence variants associated with complex diseases , 2009, Nature.

[17]  S. O’Rahilly,et al.  Human genetics illuminates the paths to metabolic disease , 2009, Nature.

[18]  G. Felsenfeld,et al.  The human insulin gene is part of a large open chromatin domain specific for human islets , 2009, Proceedings of the National Academy of Sciences.

[19]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[20]  K. Docherty,et al.  An engineered zinc finger protein reveals a role for the insulin VNTR in the regulation of the insulin and adjacent IGF2 genes , 2009, FEBS letters.

[21]  E. Liu,et al.  An Oestrogen Receptor α-bound Human Chromatin Interactome , 2009, Nature.

[22]  V. Corces,et al.  CTCF: Master Weaver of the Genome , 2009, Cell.

[23]  A. Hattersley,et al.  Severe intrauterine growth retardation and atypical diabetes associated with a translocation breakpoint disrupting regulation of the insulin-like growth factor 2 gene. , 2008, The Journal of clinical endocrinology and metabolism.

[24]  J. Komorowski,et al.  Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. , 2008, Molecular cell.

[25]  L. Groop,et al.  Variants in KCNQ1 are associated with susceptibility to type 2 diabetes mellitus , 2008, Nature Genetics.

[26]  R. Mirmira,et al.  Pdx1 and BETA2/NeuroD1 Participate in a Transcriptional Complex That Mediates Short-range DNA Looping at the Insulin Gene* , 2008, Journal of Biological Chemistry.

[27]  T. Südhof,et al.  Impaired insulin secretion and glucose intolerance in synaptotagmin-7 null mutant mice , 2008, Proceedings of the National Academy of Sciences.

[28]  G. Abecasis,et al.  A Genome-Wide Association Study of Type 2 Diabetes in Finns Detects Multiple Susceptibility Variants , 2007, Science.

[29]  Nathaniel D. Heintzman,et al.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome , 2007, Nature Genetics.

[30]  S. Kitanaka,et al.  Regulation of human insulin, IGF-I, and multidrug resistance protein 2 promoter activity by hepatocyte nuclear factor (HNF)-1β and HNF-1α and the abnormality of HNF-1β mutants , 2007 .

[31]  S. Kitanaka,et al.  Regulation of human insulin, IGF-I, and multidrug resistance protein 2 promoter activity by hepatocyte nuclear factor (HNF)-1beta and HNF-1alpha and the abnormality of HNF-1beta mutants. , 2007, The Journal of endocrinology.

[32]  M. Karaca,et al.  Transgenic expression of human INS gene in Ins1/Ins2 double knockout mice leads to insulin underproduction and diabetes in some male mice. , 2007, Frontiers in bioscience : a journal and virtual library.

[33]  B. Steensel,et al.  Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C) , 2006, Nature Genetics.

[34]  K. Sandhu,et al.  Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions , 2006, Nature Genetics.

[35]  C. Nusbaum,et al.  Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. , 2006, Genome research.

[36]  Rolf Ohlsson,et al.  CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[37]  R. Siebert,et al.  A maternal hypomethylation syndrome presenting as transient neonatal diabetes mellitus , 2006, Human Genetics.

[38]  P. Gounon,et al.  RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse , 2006, Nature.

[39]  S Apostolidou,et al.  Imprinting of IGF2 P0 transcript and novel alternatively spliced INS-IGF2 isoforms show differences between mouse and human. , 2006, Human molecular genetics.

[40]  J. Clayton-Smith,et al.  Epimutation of the TNDM locus and the Beckwith–Wiedemann syndrome centromeric locus in individuals with transient neonatal diabetes mellitus , 2006, Human Genetics.

[41]  L. Eliasson,et al.  Adenovirus‐mediated silencing of Synaptotagmin 9 inhibits Ca2+‐dependent insulin secretion in islets , 2005, FEBS letters.

[42]  M. Oshimura,et al.  ZAC, LIT1 (KCNQ1OT1) and p57KIP2 (CDKN1C) are in an imprinted gene network that may play a role in Beckwith–Wiedemann syndrome , 2005, Nucleic acids research.

[43]  Jan-Fang Cheng,et al.  Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome , 2005, Nature Genetics.

[44]  G. Felsenfeld,et al.  CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species. , 2004, Molecular cell.

[45]  R. Ghirlando,et al.  Chromatin boundaries and chromatin domains. , 2004, Cold Spring Harbor symposia on quantitative biology.

[46]  C. Junien,et al.  The focal form of persistent hyperinsulinemic hypoglycemia of infancy: morphological and molecular studies show structural and functional differences with insulinoma. , 2003, Diabetes.

[47]  C. Wollheim,et al.  Activation of the Insulin Gene Promoter through a Direct Effect of Hepatocyte Nuclear Factor 4α* , 2002, The Journal of Biological Chemistry.

[48]  J. Dekker,et al.  Capturing Chromosome Conformation , 2002, Science.

[49]  A. Pugliese,et al.  The insulin gene in diabetes , 2002, Diabetes/metabolism research and reviews.

[50]  E. Cerasi,et al.  Regulation of insulin gene transcription , 2002, Diabetologia.

[51]  B. Glaser,et al.  p57(KIP2) expression in normal islet cells and in hyperinsulinism of infancy. , 2001, Diabetes.

[52]  W Miller,et al.  Sequence and comparative analysis of the mouse 1-megabase region orthologous to the human 11p15 imprinted domain. , 2000, Genome research.

[53]  Victor V Lobanenkov,et al.  Functional association of CTCF with the insulator upstream of the H19 gene is parent of origin-specific and methylation-sensitive , 2000, Current Biology.

[54]  G. Felsenfeld,et al.  Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene , 2000, Nature.

[55]  A. West,et al.  The Protein CTCF Is Required for the Enhancer Blocking Activity of Vertebrate Insulators , 1999, Cell.

[56]  D. Bucchini,et al.  Imprinting at the mouse Ins2 locus: evidence for cis- and trans-allelic interactions. , 1998, Genomics.

[57]  J. Strouboulis,et al.  The effect of distance on long-range chromatin interactions. , 1997, Molecular cell.

[58]  Amanda J. Wilson,et al.  Insulin VNTR allele-specific effect in type 1 diabetes depends on identity of untransmitted paternal allele , 1997, Nature Genetics.

[59]  M. Pazin,et al.  An enhancer deletion affects both H19 and Igf2 expression. , 1995, Genes & development.

[60]  S. Tilghman,et al.  Disruption of imprinting caused by deletion of the H19 gene region in mice , 1995, Nature.

[61]  G. Felsenfeld,et al.  A 5′ element of the chicken β-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila , 1993, Cell.

[62]  L. G. Moss,et al.  Hepatocyte nuclear factor 1 alpha is expressed in a hamster insulinoma line and transactivates the rat insulin I gene. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[63]  J. Gearhart,et al.  Hyperinsulinemia in transgenic mice carrying multiple copies of the human insulin gene. , 1989, Developmental genetics.

[64]  M. Vidal,et al.  A dominant control region from the human β-globin locus conferring integration site-independent gene expression , 1989, Nature.

[65]  W. C. Forrester,et al.  Evidence for a locus activation region: the formation of developmentally stable hypersensitive sites in globin-expressing hybrids. , 1987, Nucleic acids research.