Unraveling cell type–specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs

DNA replication is highly regulated, ensuring faithful inheritance of genetic information through each cell cycle. In metazoans, this process is initiated at many thousands of DNA replication origins whose cell type–specific distribution and usage are poorly understood. We exhaustively mapped the genome-wide location of replication origins in human cells using deep sequencing of short nascent strands and identified ten times more origin positions than we expected; most of these positions were conserved in four different human cell lines. Furthermore, we identified a consensus G-quadruplex–forming DNA motif that can predict the position of DNA replication origins in human cells, accounting for their distribution, usage efficiency and timing. Finally, we discovered a cell type–specific reprogrammable signature of cell identity that was revealed by specific efficiencies of conserved origin positions and not by the selection of cell type–specific subsets of origins.

[1]  M. Méchali,et al.  Eukaryotic DNA replication origins: many choices for appropriate answers , 2010, Nature Reviews Molecular Cell Biology.

[2]  F. Antequera.  Genomic specification and epigenetic regulation of eukaryotic DNA replication origins , 2004, The EMBO journal.

[3]  P. Dijkwel,et al.  The Chinese hamster dihydrofolate reductase origin consists of multiple potential nascent-strand start sites , 1995, Molecular and cellular biology.

[4]  Ann E. Loraine,et al.  The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets , 2009, Bioinform..

[5]  M. Méchali,et al.  Transition in Specification of Embryonic Metazoan DNA Replication Origins , 1995, Science.

[6]  Rashi Halder,et al.  Genome-wide analysis predicts DNA structural motifs as nucleosome exclusion signals. , 2009, Molecular bioSystems.

[7]  David M. Gilbert,et al.  Evaluating genome-scale approaches to eukaryotic DNA replication , 2010, Nature Reviews Genetics.

[8]  M. Botchan,et al.  DNA topology, not DNA sequence, is a critical determinant for Drosophila ORC–DNA binding , 2004, The EMBO journal.

[9]  Neerja Karnani,et al.  Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas. , 2007, Genome research.

[10]  M. DePamphilis.  Eukaryotic DNA replication: anatomy of an origin. , 1993, Annual review of biochemistry.

[11]  G. Wahl,et al.  Replication Initiation Patterns in the β-Globin Loci of Totipotent and Differentiated Murine Cells: Evidence for Multiple Initiation Regions , 2002, Molecular and Cellular Biology.

[12]  Mirit I. Aladjem,et al.  Replication in context: dynamic regulation of DNA replication patterns in metazoans , 2007, Nature Reviews Genetics.

[13]  David J Young,et al.  High‐throughput mapping of origins of replication in human cells , 2007, EMBO reports.

[14]  M. Giacca,et al.  Mapping replication origins by quantifying relative abundance of nascent DNA strands using competitive polymerase chain reaction. , 1997, Methods.

[15]  O. Gandrillon,et al.  Broadening of DNA replication origin usage during metazoan cell differentiation , 2006, EMBO reports.

[16]  G. Garg,et al.  Guanine quadruplex DNA structure restricts methylation of CpG dinucleotides genome-wide. , 2010, Molecular bioSystems.

[17]  Laurent Duret,et al.  Genome-wide studies highlight indirect links between human replication origins and gene regulation , 2008, Proceedings of the National Academy of Sciences.

[18]  Alain Arneodo,et al.  Replication-associated strand asymmetries in mammalian genomes: toward detection of replication origins. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[19]  D. Gilbert,et al.  Replication timing and transcriptional control: beyond cause and effect--part II. , 2002, Current Opinion in Genetics and Development.

[20]  G. Wahl,et al.  Genetic dissection of a mammalian replicator in the human beta-globin locus. , 1998, Science.

[21]  G. Bernardi,et al.  Representing GC variation along eukaryotic chromosomes. , 2004, Gene.

[22]  M. Méchali,et al.  Mitotic Remodeling of the Replicon and Chromosome Structure , 2005, Cell.

[23]  Roy Riblet,et al.  Progressive activation of DNA replication initiation in large domains of the immunoglobulin heavy chain locus during B cell development. , 2005, Molecular cell.

[24]  Eric Rivals,et al.  Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features. , 2011, Genome research.

[25]  Stefan Bekiranov,et al.  Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription. , 2011, Genome research.

[26]  Owen T McCann,et al.  Replication timing of the human genome. , 2004, Human molecular genetics.

[27]  P. Dijkwel,et al.  Distal sequences, but not ori-beta/OBR-1, are essential for initiation of DNA replication in the Chinese hamster DHFR origin. , 1998, Molecular cell.

[28]  Ana Pombo,et al.  Replicon Clusters Are Stable Units of Chromosome Structure: Evidence That Nuclear Organization Contributes to the Efficient Activation and Propagation of S Phase in Human Cells , 1998, The Journal of cell biology.

[29]  G. Bernardi,et al.  Replication timing, chromosomal bands, and isochores , 2008, Proceedings of the National Academy of Sciences.

[30]  A. Riggs,et al.  On the mechanism of DNA replication in mammalian chromosomes. , 1968, Journal of molecular biology.

[31]  Shankar Balasubramanian,et al.  Prevalence of quadruplexes in the human genome , 2005, Nucleic acids research.

[32]  David M MacAlpine,et al.  Coordination of replication and transcription along a Drosophila chromosome. , 2004, Genes & development.

[33]  Dirk Schübeler,et al.  Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation , 2008, PLoS biology.

[34]  S. Vashee,et al.  Sequence-independent DNA binding and replication initiation by the human origin recognition complex. , 2003, Genes & development.

[35]  Claude Sardet,et al.  The histone H4 Lys 20 methyltransferase PR-Set7 regulates replication origins in mammalian cells , 2010, Nature Cell Biology.

[36]  N. Maizels,et al.  Selection for the G4 DNA motif at the 5′ end of human genes , 2009, Molecular carcinogenesis.

[37]  M. Méchali,et al.  HoxB domain induction silences DNA replication origins in the locus and specifies a single origin at its boundary , 2006, EMBO reports.

[38]  Ramón Díaz-Uriarte,et al.  Transcription Initiation Activity Sets Replication Origin Efficiency in Mammalian Cells , 2009, PLoS genetics.

[39]  Mirit I. Aladjem,et al.  Preferential Localization of Human Origins of DNA Replication at the 5′-Ends of Expressed Genes and at Evolutionarily Conserved DNA Sequences , 2011, PloS one.

[40]  Mark Gerstein,et al.  DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[41]  S. Dalton,et al.  Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. , 2010, Genome research.

[42]  Neerja Karnani,et al.  Genomic Study of Replication Initiation in Human Chromosomes Reveals the Influence of Transcription Regulation and Chromatin Structure on Origin Selection , 2010, Molecular biology of the cell.

[43]  Bertram Ludäscher,et al.  Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data , 2009, Nucleic acids research.

[44]  G. Wahl,et al.  Participation of the Human β-Globin Locus Control Region in Initiation of DNA Replication , 1995, Science.

[45]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[46]  Mitchell D. Probasco,et al.  Feeder-independent culture of human embryonic stem cells , 2006, Nature Methods.

[47]  Shulan Tian,et al.  Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells , 2007, Science.

[48]  John Herrick,et al.  Replication fork velocities at adjacent replication origins are coordinately modified during DNA replication in human cells. , 2007, Molecular biology of the cell.

[49]  P. Dijkwel,et al.  Promiscuous initiation on mammalian chromosomal DNA templates and its possible suppression by transcription. , 2005, Experimental cell research.

[50]  L. Hurley,et al.  The importance of negative superhelicity in inducing the formation of G-quadruplex and i-motif structures in the c-Myc promoter: implications for drug targeting and control of gene expression. , 2009, Journal of medicinal chemistry.

[51]  J. Hamlin,et al.  A revisionist replicon model for higher eukaryotic genomes , 2008, Journal of cellular biochemistry.