In many developing organisms, early rounds of DNA replication occur in the absence of zygotic gene transcription: in both Drosophila and Xenopus embryos, the rapid genome duplication in early cycles is facilitated by the use of many, closely spaced, replication initiation sites (Blumenthal et al., 1974; Callan, 1974). Within Drosophila and Xenopus, the onset of zygotic transcription is accompanied by a marked increase in S phase length, caused by a reduction in the number of replication initiation events, rather than changes in the rate of replication fork progression (Blumenthal et al., 1974). Numerous studies in metazoa have found particular chromatin signatures that typify transcriptionally active chromatin are enriched at replication initiation sites and also influence the relative time in S phase that origins are active (MacAlpine and Almouzni, 2013). Yet a specific signature within chromatin that marks distinct sites in a genome where replication initiates has not been identified (Urban et al., 2015).

We chose to investigate DNA replication within developing C. elegans embryos, with the goal of characterizing signatures of replication origins and understanding replication patterns through early development. Our approach relies on transient depletion of DNA ligase I, which results in the accumulation of Okazaki fragments on the lagging strand (Smith and Whitehouse, 2012; McGuffee et al., 2013). By sequencing Okazaki fragments we, and others, have provided high-resolution maps of DNA replication across budding yeast (McGuffee et al., 2013) and human genomes (Petryk et al., 2016). One advantage of sequencing Okazaki fragments is that replication signatures can be deduced from a population of cells growing at steady state. Thus, providing that Okazaki fragments can be harvested in sufficient quantity, DNA replication can be mapped in cells, tissues or organisms without need for synchronization (Smith and Whitehouse, 2012).

Okazaki fragments were purified from mixed early embryos (ME) following RNAi depletion of lig-1, which is the sole C. elegans DNA ligase responsible for ligating Okazaki fragments. To minimize genome instability and prevent embryonic lethality associated with complete lig-1 depletion, we determined an optimal level of depletion to maintain normal development, while enriching for fragments by dilution of the lig-1 RNAi bacteria (Figure 1A, Figure 1—figure supplement 1). Resolution of labeled DNA harvested from lig-1 depleted embryos on a denaturing agarose gel, revealed a highly periodic pattern of Okazaki fragment size, similar to that of the nucleosome repeat uncovered by MNase digestion (Figure 1A). While the periodicity is far more pronounced in C. elegans, the size distribution of Okazaki fragments matches those observed in budding yeast, indicating that the coupling of lagging strand synthesis and nucleosome assembly is likely conserved (Smith and Whitehouse, 2012; Yadav and Whitehouse, 2016).

Figure 1. Purification and sequencing of Okazaki fragments from C. elegans with 4 supplements see all

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Next, we analyzed the Okazaki fragments by deep sequencing using a protocol that preserves strand identity (Smith and Whitehouse, 2012). Mapping to the worm WS220 reference genome, we find a clear strand bias, which matches the expected distribution of Okazaki fragments synthesized on the lagging strand: replication origins are at sites of transition from Watson to Crick strand reads (Figure 1B) (McGuffee et al., 2013). While the data is noisier than budding yeast – in part due to the high A:T content of the genome, residual DNA ligase activity and the complexity of the sample preparation – we identified >2000 replication origins using a modified mapping protocol (McGuffee et al., 2013). Median spacing between origins is 40 kb, and 96% of origins are within 100 kb of another origin; the median efficiency – that is, the likelihood that a given origin is utilized during S phase, is ~50%, although we note that numerous origins are fired in most cells in the population (Figure 1—figure supplement 2A and B). In contrast to budding yeast, in which initiation is confined to a narrow range (McGuffee et al., 2013), replication in C. elegans apparently initiates within broad zones at most origins, similar to human cells (Figure 1—figure supplement 3) (Petryk et al., 2016; Dijkwel et al., 1991). Replication origins potentially influence gene organization: genes near origins tend to be shorter and genes flanking origins show a pronounced bias to ensure that replication fork progression and transcription are co-directional (Figure 1—figure supplement 4A and B) (Petryk et al., 2016).

Having generated a high-resolution map of replication origins, we next considered whether particular chromatin signatures are enriched near origins. Thus, we analyzed the abundance of several histone modifications that were mapped in embryos at similar stages (Gerstein et al., 2010). As Figure 2 shows, there is a remarkable concordance between the location of replication origins and acetylation of histone H3 and methylation of H3 at lysine 4 (K4). Analyzing H3 K27ac (H3 K4me2 is near identical), we find that 75% of efficient origins (>30% efficiency) are within 1 kb of the histone mark and most H3 K27ac peaks overlap origins (Figure 2B). Further, the most efficient replication origins are associated with sites with the most H3K27 acetylation (Figure 2C, Figure 2—figure supplement 1). By surveying the abundance of various modifications present at replication origins, we tested whether other modifications behaved similarly to H3K27ac (Figure 2D); this revealed that acetylation of H3 at K18, K23, K27 and dimethylation of H3 at K4 are not only present at origins, but the level of modification increases according to origin efficiency. Significantly the histone modifications, we find most strongly associated with origins are those that define gene enhancers in metazoan genomes (Ho et al., 2014).

Figure 2 with 1 supplement see all

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Given that ME embryos are transcriptionally active, our finding that replication initiates near histone marks linked with enhancers indicates that origins are localized to ‘accessible’ transcriptionally active regions. In this scenario, replication origins become defined once zygotic transcription has initiated; DNA replication in pre-gastrula embryos (PG), where transcription is limited and non essential (Robertson and Lin, 2015), would presumably initiate from many, seemingly random sites – much like the apparent situation in Drosophila and Xenopus embryos prior to the Mid Blastula Transition (MBT). To investigate this, we harvested pre-gastrula embryos from a hyperactive egg laying strain (PG: median 9, mean 13 cells/embryo, n = 50; Figure 3A) and late embryos from wild-type worms (L: ~200–558 cells/embryo), which represent different levels and extent of gene expression (Figure 3B). We compared origin location and efficiency for each population and found that the patterns of replication were highly similar (Figure 3C) – especially for the most efficient origins (Figure 3D). Evidently, even though gene transcription is fundamentally altered through this time course, replication origin usage is globally similar through early development. Thus, the establishment of specific replication origins in C. elegans occurs prior to the broad onset of zygotic transcription – meaning that the replication origins we define are unlikely to be dependent upon transcription. This finding is in keeping with data showing that isolated embryonic cells treated with α-amanitin divide normally up to approximately 100 cells (Edgar et al., 1994). Indeed, S phase length, lineage-specific cell cycle timing, asymmetric cell division and cleavage patterns all proceed normally in the absence of transcription in pre-gastrula early embryos (Robertson and Lin, 2015; Edgar and McGhee, 1988; Edgar et al., 1994).

Figure 3

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Coupling of DNA replication with gene enhancers within rapidly dividing embryonic cells likely imposes particular constraints upon genome duplication. S phase in pre-gastrula embryonic cells ranges from ~10 to 25 min, depending on the lineage (Edgar and McGhee, 1988). In an ideal system, where all origins fire in each S phase (100% efficiency), complete genome duplication could be achieved in ~15 min if origins are uniformly spaced every ~75 kb and replication forks progress at 2.5 kb/min. We find that the median origin spacing is ~40 kb (Figure 1—figure supplement 1), which reflects that not all origins are fired within each S phase. Given that DNA replication appears to initiate at enhancers, the requirement for closely spaced origins to achieve timely genome duplication would seemingly constrain the positions of enhancers across the genome. Thus, enhancers, and the genes they regulate, may be organized to facilitate the execution of the DNA replication and transcription programs in rapidly dividing embryonic cells. To investigate this, we first performed a gene ontology analysis of genes at varying distances from replication origins: this revealed that genes whose products are involved growth, embryonic development, cell cycle, gene expression, and chromatin are clustered near replication origins (Figure 4A and Figure 4—figure supplement 1). Next, we compared origins with the whole embryo transcriptome time series derived from individual embryos from the one-cell stage through hatching (Hashimshony et al., 2015). For each of the 50 time points, we removed maternally derived transcripts and plotted the sum of normalized transcript levels for each gene relative to the midpoint of replication origins. As shown in Figure 4B and Figure 4—figure supplement 2, transcript abundance accumulates through the early time points with no apparent trends in the data; but, beginning at time point ~9 and coincident with gastrulation, there is an apparent clustering of actively transcribed genes near replication origins. The association of transcription with origins spans to time point ~25 and broadly scales according with origin efficiency (Figure 4—figure supplement 2). Beyond time point 25, the association breaks down; yet, as gene expression changes, the pattern evolves such that from time point 40 onwards, sites of active transcription now appear anti-correlated with replication origins. As we have shown in Figure 3, replication origins are defined prior to the onset of global zygotic gene activation, yet Figure 4B reveals that when the genome becomes broadly transcriptionally active, transcription generally occurs in close proximity to the pre-defined origins. At time point 25, which is ~300 min into embryogenesis, transcription begins to shift away from the origins, and by 500 min, peak transcription occurs some 15–25 kb from the origin. Since the median spacing between origins is 40 kb, the shift in transcription late in embryogenesis ensures that gene transcription is as far removed as possible from sites of replication initiation. The alteration in transcription that occurs after ~300 min is coincident with ventral enclosure and has been shown previously to underlie a developmental milestone wherein the ‘morphogenesis’ transcriptome is activated (Levin et al., 2012). Given the close association between replication origins and expressed genes, we considered whether global alterations in the transcriptome may be related to origin activity. Thus, we compared the origin/transcript profiles with a time course that measured living nuclei per embryo during embryogenesis from Sulston et al (Sulston et al., 1983) (Figure 4C). Significantly, the shift of transcription from origins that begins at ~300 min is coincident with the completion of the last wave of cell division that occurs within the embryo – indicating that the inactivation of replication origins may be coupled with the restructuring of the transcriptome to facilitate post replicative development.

Figure 4 with 2 supplements see all

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Our finding that replication initiates at specific sites in PG embryos is in marked contrast to the seemingly random patterns observed in the rapid and synchronous cycles in both Drosophila and Xenopus embryos (Blumenthal et al., 1974; Callan, 1974). However, early development in C. elegans differs from these organisms: initial cell divisions are asynchronous, and the cell cycle does not slow abruptly near gastrulation (Bao et al., 2008). Thus, the rapid establishment of the defined replication landscape in C. elegans may be related to the very early stage at which cell lineages are specified. Indeed, several histone modifications, including H3K27ac and H3K4me2, are potentially passaged with the maternal genome and are known to be present in two cell embryos (Arico et al., 2011; Samson et al., 2014). Replication origins appear to be tied with gene expression: in general terms, origin proximal genes experience the first wave of zygotic transcription and are expressed in replicating cells; origin distal regions encode genes whose transcription is delayed until later in development when DNA replication has ceased. Our results indicate that the C. elegans genome has evolved to couple embryonic transcription with replication; yet, such coupling would appear to impose constraints on a system that needs not only to transcribe a diverse array of genes, but also replicate the ~100 mb genome in ~15 min. C. elegans seemingly resolves this issue as follows: first, replication origins appear to be co-localized with gene enhancers which can activate transcription of genes at a distance; second, genes required for cell division and early development are clustered near replication origins (Figure 4—figure supplement 1). Such association is likely to be functionally important in rapidly cycling cells with limited gap phases: most obviously, genes near to origins such as histones, will be replicated at the start of S phase and have a higher effective copy number than those further away. Relatedly, the passage of the replication fork may trigger genes to be reactivated that were presumably repressed during mitosis; thus ensuring replication-transcription conflicts do not occur. Finally, the inactivation of replication origins may serve as a trigger to relieve the gene expression program from replication origin-associated spatial constraints – allowing the expression of genes whose products are required for the many aspects of development that occur in the absence of cell division. The spatiotemporal coupling and uncoupling of gene expression with replication may be a general principal underlying the profound transcriptional and morphological changes that occur during embryogenesis across species: genes expressed early are characterized by proteins involved in proliferation, while those expressed late are typically involved in differentiation (Levin et al., 2016). Separating early and late genes is a comparatively short phase termed the ‘mid-developmental transition’ (Levin et al., 2016); in C. elegans, we find that this transition is coincident with the uncoupling of transcription from replication origins (Figure 4B,C). It will be of great interest to learn whether this is a ubiquitous feature of the mid-developmental transition across species.

1. 1. Ehsan Pourkarimi
   2. James M Bellush
   3. Iestyn Whitehouse

   (2016) Replication maps of developing C. elegans embryos.

   Publicly available at the NCBI Gene Expression Omnibus (accession no. GSE90939).

   https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE90939

1. 1. Arico JK
   2. Katz DJ
   3. van der Vlag J
   4. Kelly WG

   (2011) Epigenetic patterns maintained in early Caenorhabditis elegans embryos can be established by gene activity in the parental germ cells

   PLoS Genetics 7:e1001391.

   https://doi.org/10.1371/journal.pgen.1001391

   • PubMed
   • Google Scholar
2. 1. Bao Z
   2. Zhao Z
   3. Boyle TJ
   4. Murray JI
   5. Waterston RH

   (2008) Control of cell cycle timing during C. elegans embryogenesis

   Developmental Biology 318:65–72.

   https://doi.org/10.1016/j.ydbio.2008.02.054

   • PubMed
   • Google Scholar
3. 1. Blumenthal AB
   2. Kriegstein HJ
   3. Hogness DS

   (1974) The units of DNA replication in Drosophila melanogaster chromosomes

   Cold Spring Harbor Symposia on Quantitative Biology 38:205–223.

   https://doi.org/10.1101/SQB.1974.038.01.024

   • PubMed
   • Google Scholar
4. 1. Brenner S

   (1974)

   The genetics of caenorhabditis elegans

   Genetics 77:71–94.

   • PubMed
   • Google Scholar
5. 1. Callan HG

   (1974) DNA replication in the chromosomes of eukaryotes

   Cold Spring Harbor Symposia on Quantitative Biology 38:195–203.

   https://doi.org/10.1101/SQB.1974.038.01.023

   • PubMed
   • Google Scholar
6. 1. Chikina MD
   2. Troyanskaya OG

   (2012) An effective statistical evaluation of ChIPseq dataset similarity

   Bioinformatics 28:607–613.

   https://doi.org/10.1093/bioinformatics/bts009

   • PubMed
   • Google Scholar
7. 1. Dijkwel PA
   2. Vaughn JP
   3. Hamlin JL

   (1991) Mapping of replication initiation sites in mammalian genomes by two-dimensional gel analysis: stabilization and enrichment of replication intermediates by isolation on the nuclear matrix

   Molecular and Cellular Biology 11:3850–3859.

   https://doi.org/10.1128/MCB.11.8.3850

   • PubMed
   • Google Scholar
8. 1. Edgar LG
   2. McGhee JD

   (1988) DNA synthesis and the control of embryonic gene expression in C. elegans

   Cell 53:589–599.

   https://doi.org/10.1016/0092-8674(88)90575-2

   • PubMed
   • Google Scholar
9. 1. Edgar LG
   2. Wolf N
   3. Wood WB

   (1994)

   Early transcription in caenorhabditis elegans embryos

   Development 120:443–451.

   • PubMed
   • Google Scholar
10. 1. Edgar LG
    2. Goldstein B

    (2012) Culture and manipulation of embryonic cells

    Methods in Cell Biology 107:151–175.

    https://doi.org/10.1016/B978-0-12-394620-1.00005-9

    • PubMed
    • Google Scholar
11. 1. Fraser AG
    2. Kamath RS
    3. Zipperlen P
    4. Martinez-Campos M
    5. Sohrmann M
    6. Ahringer J

    (2000) Functional genomic analysis of C. elegans chromosome I by systematic RNA interference

    Nature 408:325–330.

    https://doi.org/10.1038/35042517

    • PubMed
    • Google Scholar
12. 1. Gerstein MB
    2. Lu ZJ
    3. Van Nostrand EL
    4. Cheng C
    5. Arshinoff BI
    6. Liu T
    7. Yip KY
    8. Robilotto R
    9. Rechtsteiner A
    10. Ikegami K
    11. Alves P
    12. Chateigner A
    13. Perry M
    14. Morris M
    15. Auerbach RK
    16. Feng X
    17. Leng J
    18. Vielle A
    19. Niu W
    20. Rhrissorrakrai K
    21. Agarwal A
    22. Alexander RP
    23. Barber G
    24. Brdlik CM
    25. Brennan J
    26. Brouillet JJ
    27. Carr A
    28. Cheung MS
    29. Clawson H
    30. Contrino S
    31. Dannenberg LO
    32. Dernburg AF
    33. Desai A
    34. Dick L
    35. Dosé AC
    36. Du J
    37. Egelhofer T
    38. Ercan S
    39. Euskirchen G
    40. Ewing B
    41. Feingold EA
    42. Gassmann R
    43. Good PJ
    44. Green P
    45. Gullier F
    46. Gutwein M
    47. Guyer MS
    48. Habegger L
    49. Han T
    50. Henikoff JG
    51. Henz SR
    52. Hinrichs A
    53. Holster H
    54. Hyman T
    55. Iniguez AL
    56. Janette J
    57. Jensen M
    58. Kato M
    59. Kent WJ
    60. Kephart E
    61. Khivansara V
    62. Khurana E
    63. Kim JK
    64. Kolasinska-Zwierz P
    65. Lai EC
    66. Latorre I
    67. Leahey A
    68. Lewis S
    69. Lloyd P
    70. Lochovsky L
    71. Lowdon RF
    72. Lubling Y
    73. Lyne R
    74. MacCoss M
    75. Mackowiak SD
    76. Mangone M
    77. McKay S
    78. Mecenas D
    79. Merrihew G
    80. Miller DM
    81. Muroyama A
    82. Murray JI
    83. Ooi SL
    84. Pham H
    85. Phippen T
    86. Preston EA
    87. Rajewsky N
    88. Rätsch G
    89. Rosenbaum H
    90. Rozowsky J
    91. Rutherford K
    92. Ruzanov P
    93. Sarov M
    94. Sasidharan R
    95. Sboner A
    96. Scheid P
    97. Segal E
    98. Shin H
    99. Shou C
    100. Slack FJ
    101. Slightam C
    102. Smith R
    103. Spencer WC
    104. Stinson EO
    105. Taing S
    106. Takasaki T
    107. Vafeados D
    108. Voronina K
    109. Wang G
    110. Washington NL
    111. Whittle CM
    112. Wu B
    113. Yan KK
    114. Zeller G
    115. Zha Z
    116. Zhong M
    117. Zhou X
    118. Ahringer J
    119. Strome S
    120. Gunsalus KC
    121. Micklem G
    122. Liu XS
    123. Reinke V
    124. Kim SK
    125. Hillier LW
    126. Henikoff S
    127. Piano F
    128. Snyder M
    129. Stein L
    130. Lieb JD
    131. Waterston RH
    132. modENCODE Consortium

    (2010) Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

    Science 330:1775–1787.

    https://doi.org/10.1126/science.1196914

    • PubMed
    • Google Scholar
13. 1. Hashimshony T
    2. Feder M
    3. Levin M
    4. Hall BK
    5. Yanai I

    (2015) Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer

    Nature 519:219–222.

    https://doi.org/10.1038/nature13996

    • PubMed
    • Google Scholar
14. 1. Ho JW
    2. Jung YL
    3. Liu T
    4. Alver BH
    5. Lee S
    6. Ikegami K
    7. Sohn KA
    8. Minoda A
    9. Tolstorukov MY
    10. Appert A
    11. Parker SC
    12. Gu T
    13. Kundaje A
    14. Riddle NC
    15. Bishop E
    16. Egelhofer TA
    17. Hu SS
    18. Alekseyenko AA
    19. Rechtsteiner A
    20. Asker D
    21. Belsky JA
    22. Bowman SK
    23. Chen QB
    24. Chen RA
    25. Day DS
    26. Dong Y
    27. Dose AC
    28. Duan X
    29. Epstein CB
    30. Ercan S
    31. Feingold EA
    32. Ferrari F
    33. Garrigues JM
    34. Gehlenborg N
    35. Good PJ
    36. Haseley P
    37. He D
    38. Herrmann M
    39. Hoffman MM
    40. Jeffers TE
    41. Kharchenko PV
    42. Kolasinska-Zwierz P
    43. Kotwaliwale CV
    44. Kumar N
    45. Langley SA
    46. Larschan EN
    47. Latorre I
    48. Libbrecht MW
    49. Lin X
    50. Park R
    51. Pazin MJ
    52. Pham HN
    53. Plachetka A
    54. Qin B
    55. Schwartz YB
    56. Shoresh N
    57. Stempor P
    58. Vielle A
    59. Wang C
    60. Whittle CM
    61. Xue H
    62. Kingston RE
    63. Kim JH
    64. Bernstein BE
    65. Dernburg AF
    66. Pirrotta V
    67. Kuroda MI
    68. Noble WS
    69. Tullius TD
    70. Kellis M
    71. MacAlpine DM
    72. Strome S
    73. Elgin SC
    74. Liu XS
    75. Lieb JD
    76. Ahringer J
    77. Karpen GH
    78. Park PJ

    (2014) Comparative analysis of metazoan chromatin organization

    Nature 512:449–452.

    https://doi.org/10.1038/nature13415

    • PubMed
    • Google Scholar
15. 1. Levin M
    2. Hashimshony T
    3. Wagner F
    4. Yanai I

    (2012) Developmental milestones punctuate gene expression in the Caenorhabditis embryo

    Developmental Cell 22:1101–1108.

    https://doi.org/10.1016/j.devcel.2012.04.004

    • PubMed
    • Google Scholar
16. 1. Levin M
    2. Anavy L
    3. Cole AG
    4. Winter E
    5. Mostov N
    6. Khair S
    7. Senderovich N
    8. Kovalev E
    9. Silver DH
    10. Feder M
    11. Fernandez-Valverde SL
    12. Nakanishi N
    13. Simmons D
    14. Simakov O
    15. Larsson T
    16. Liu SY
    17. Jerafi-Vider A
    18. Yaniv K
    19. Ryan JF
    20. Martindale MQ
    21. Rink JC
    22. Arendt D
    23. Degnan SM
    24. Degnan BM
    25. Hashimshony T
    26. Yanai I

    (2016) The mid-developmental transition and the evolution of animal body plans

    Nature 531:637–641.

    https://doi.org/10.1038/nature16994

    • PubMed
    • Google Scholar
17. 1. MacAlpine DM
    2. Almouzni G

    (2013) Chromatin and DNA replication

    Cold Spring Harbor Perspectives in Biology 5:a010207.

    https://doi.org/10.1101/cshperspect.a010207

    • PubMed
    • Google Scholar
18. 1. McGuffee SR
    2. Smith DJ
    3. Whitehouse I

    (2013) Quantitative, genome-wide analysis of eukaryotic replication initiation and termination

    Molecular Cell 50:123–135.

    https://doi.org/10.1016/j.molcel.2013.03.004

    • PubMed
    • Google Scholar
19. 1. Ooi SL
    2. Henikoff JG
    3. Henikoff S

    (2010) A native chromatin purification system for epigenomic profiling in Caenorhabditis elegans

    Nucleic Acids Research 38:e26.

    https://doi.org/10.1093/nar/gkp1090

    • PubMed
    • Google Scholar
20. 1. Petryk N
    2. Kahli M
    3. d'Aubenton-Carafa Y
    4. Jaszczyszyn Y
    5. Shen Y
    6. Silvain M
    7. Thermes C
    8. Chen CL
    9. Hyrien O

    (2016) Replication landscape of the human genome

    Nature Communications 7:10208.

    https://doi.org/10.1038/ncomms10208

    • PubMed
    • Google Scholar
21. 1. Robertson S
    2. Lin R

    (2015) The Maternal-to-Zygotic Transition in C. elegans

    Current Topics in Developmental Biology 113:1–42.

    https://doi.org/10.1016/bs.ctdb.2015.06.001

    • PubMed
    • Google Scholar
22. 1. Royce TE
    2. Carriero NJ
    3. Gerstein MB

    (2007) An efficient pseudomedian filter for tiling microrrays

    BMC Bioinformatics 8:186.

    https://doi.org/10.1186/1471-2105-8-186

    • PubMed
    • Google Scholar
23. 1. Samson M
    2. Jow MM
    3. Wong CC
    4. Fitzpatrick C
    5. Aslanian A
    6. Saucedo I
    7. Estrada R
    8. Ito T
    9. Park SK
    10. Yates JR
    11. Chu DS

    (2014) The specification and global reprogramming of histone epigenetic marks during gamete formation and early embryo development in C. elegans

    PLoS Genetics 10:e1004588.

    https://doi.org/10.1371/journal.pgen.1004588

    • PubMed
    • Google Scholar
24. 1. Smith DJ
    2. Whitehouse I

    (2012) Intrinsic coupling of lagging-strand synthesis to chromatin assembly

    Nature 483:434–438.

    https://doi.org/10.1038/nature10895

    • PubMed
    • Google Scholar
25. 1. Sulston JE
    2. Schierenberg E
    3. White JG
    4. Thomson JN

    (1983) The embryonic cell lineage of the nematode Caenorhabditis elegans

    Developmental Biology 100:64–119.

    https://doi.org/10.1016/0012-1606(83)90201-4

    • PubMed
    • Google Scholar
26. 1. Urban JM
    2. Foulk MS
    3. Casella C
    4. Gerbi SA

    (2015) The hunt for origins of DNA replication in multicellular eukaryotes

    F1000Prime Reports 7:30.

    https://doi.org/10.12703/P7-30

    • PubMed
    • Google Scholar
27. 1. Yadav T
    2. Whitehouse I

    (2016) Replication-coupled nucleosome assembly and positioning by ATP-dependent chromatin-remodeling enzymes

    Cell Reports 15:715–723.

    https://doi.org/10.1016/j.celrep.2016.03.059

    • Google Scholar
28. 1. Zhang Y
    2. Liu T
    3. Meyer CA
    4. Eeckhoute J
    5. Johnson DS
    6. Bernstein BE
    7. Nusbaum C
    8. Myers RM
    9. Brown M
    10. Li W
    11. Liu XS

    (2008) Model-based analysis of ChIP-Seq (MACS)

    Genome Biology 9:R137.

    https://doi.org/10.1186/gb-2008-9-9-r137

    • PubMed
    • Google Scholar

Author details

1. Ehsan Pourkarimi

   Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States

   Contribution

   EP, Conceptualization, Resources, Data curation, Software, Formal analysis, Supervision, Funding acquisition, Validation, Investigation, Visualization, Methodology, Writing—original draft, Project administration, Writing—review and editing

   Competing interests

   The authors declare that no competing interests exist.

   "This ORCID iD identifies the author of this article:" 0000-0001-9598-3465

2. James M Bellush

   1. Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
   2. BCMB Graduate Program, Weill Cornell Medical College, New York, United States

   Contribution

   JMB, Conceptualization, Data curation, Formal analysis, Validation, Methodology, Writing—review and editing

   Competing interests

   The authors declare that no competing interests exist.

3. Iestyn Whitehouse

   Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States

   Contribution

   IW, Conceptualization, Resources, Data curation, Software, Formal analysis, Supervision, Funding acquisition, Validation, Investigation, Visualization, Methodology, Writing—original draft, Project administration, Writing—review and editing

   For correspondence

   whitehoi@mskcc.org

   Competing interests

   The authors declare that no competing interests exist.

   "This ORCID iD identifies the author of this article:" 0000-0003-0385-3116

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