CoChat
Sign Up
Cited by 65Genomics and Chromatin DynamicsDevelopmental Biology and Gene RegulationEpigenetics and DNA Methylation

Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis

Open access
Koenecke, Nina, Johnston, Jeff, Gaertner, Bjoern, Natarajan, Malini, Zeitlinger, Julia·2016·Genome Biology
DOI 10.1186/s13059-016-1057-2PMC PMC5037609
Open this paper in CoChat — free accountOpen PDF

Abstract

BACKGROUND: Drosophila dorso-ventral (DV) patterning is one of the best-understood regulatory networks to date, and illustrates the fundamental role of enhancers in controlling patterning, cell fate specification, and morphogenesis during development. Histone acetylation such as H3K27ac is an excellent marker for active enhancers, but it is challenging to obtain precise locations for enhancers as the highest levels of this modification flank the enhancer regions. How to best identify tissue-specific enhancers in a developmental system de novo with a minimal set of data is still unclear. RESULTS: Using DV patterning as a test system, we develop a simple and effective method to identify tissue-specific enhancers de novo. We sample a broad set of candidate enhancer regions using data on CREB-binding protein co-factor binding or ATAC-seq chromatin accessibility, and then identify those regions with significant differences in histone acetylation between tissues. This method identifies hundreds of novel DV enhancers and outperforms ChIP-seq data of relevant transcription factors when benchmarked with mRNA expression data and transgenic reporter assays. These DV enhancers allow the de novo discovery of the relevant transcription factor motifs involved in DV patterning and contain additional motifs that are evolutionarily conserved and for which the corresponding transcription factors are expressed in a DV-biased fashion. Finally, we identify novel target genes of the regulatory network, implicating morphogenesis genes as early targets of DV patterning. CONCLUSIONS: Taken together, our approach has expanded our knowledge of the DV patterning network even further and is a general method to identify enhancers in any developmental system, including mammalian development.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1186/s13059-016-1057-2

Cites

9 of 9 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Enhancers can reside in a poised state exhibiting both H3K4me1 and H3K27me3 that is associated with Polycomb repressive complexes.

    “In addition to the ‘primed’ and active states, enhancers can also reside in a ‘poised’ state exhibiting both H3K4me1 and H3 lysine 27 trimethylation (H3K27me3) that is associated with Polycomb repressive complexes [131, 135, 136, 138].”

    From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [138]

    The Background discusses H3K27ac as a marker of active enhancers, not the claimed combination of H3K4me1 and H3K27me3 at poised enhancers. Searches for those marks, poised enhancers, and Polycomb found only related reference titles, not a passage in this paper stating the claim. The indexed passages have no page numbers. (LLM, conf=0.73)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 69

  1. [1]Bier E De Robertis EM EMBRYO DEVELOPMENT. BMP gradients: a paradigm for morphogen-mediated developmental patterning Science 2015 348 aaa5838 10.1126/science.aaa5838 26113727 · DOI
  2. [2]Roth S Stein D Nusslein-Volhard C A gradient of nuclear localization of the dorsal protein determines dorsoventral pattern in the Drosophila embryo Cell 1989 59 1189 202 10.1016/0092-8674(89)90774-5 2688897 · DOI
  3. [3]Jiang J Kosman D Ip YT Levine M The dorsal morphogen gradient regulates the mesoderm determinant twist in early Drosophila embryos Genes Dev 1991 5 1881 91 10.1101/gad.5.10.1881 1655572 · DOI · Paper page
  4. [4]Ip YT Park RE Kosman D Yazdanbakhsh K Levine M Dorsal-twist interactions establish snail expression in the presumptive mesoderm of the Drosophila embryo Genes Dev 1992 6 1518 30 10.1101/gad.6.8.1518 1644293 · DOI
  5. [5]Kosman D Ip YT Levine M Arora K Establishment of the mesoderm-neuroectoderm boundary in the Drosophila embryo Science 1991 254 118 22 10.1126/science.1925551 1925551 · DOI · Paper page
  6. [6]Huang JD Schwyter DH Shirokawa JM Courey AJ The interplay between multiple enhancer and silencer elements defines the pattern of decapentaplegic expression Genes Dev 1993 7 694 704 10.1101/gad.7.4.694 8458580 · DOI · Paper page
  7. [7]Jiang J Rushlow CA Zhou Q Small S Levine M Individual dorsal morphogen binding sites mediate activation and repression in the Drosophila embryo EMBO J 1992 11 3147 54 1322296 PMC556799
  8. [8]Doyle HJ Kraut R Levine M Spatial regulation of zerknullt: a dorsal-ventral patterning gene in Drosophila Genes Dev 1989 3 1518 33 10.1101/gad.3.10.1518 2612903 · DOI
  9. [9]Ferguson EL Anderson KV Decapentaplegic acts as a morphogen to organize dorsal-ventral pattern in the Drosophila embryo Cell 1992 71 451 61 10.1016/0092-8674(92)90514-D 1423606 · DOI
  10. [10]Ray RP Arora K Nusslein-Volhard C Gelbart WM The control of cell fate along the dorsal-ventral axis of the Drosophila embryo Development 1991 113 35 54 1765005
  11. [11]Lin MC Park J Kirov N Rushlow C Threshold response of C15 to the Dpp gradient in Drosophila is established by the cumulative effect of Smad and Zen activators and negative cues Development 2006 133 4805 13 10.1242/dev.02689 17092951 · DOI
  12. [12]Raftery LA Twombly V Wharton K Gelbart WM Genetic screens to identify elements of the decapentaplegic signaling pathway in Drosophila Genetics 1995 139 241 54 7705627 PMC1206322
  13. [13]Bier E Jan LY Jan YN rhomboid, a gene required for dorsoventral axis establishment and peripheral nervous system development in Drosophila melanogaster Genes Dev 1990 4 190 203 10.1101/gad.4.2.190 2110920 · DOI · Paper page
  14. [14]Markstein M Markstein P Markstein V Levine MS Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo Proc Natl Acad Sci U S A 2002 99 763 8 10.1073/pnas.012591199 11752406 PMC117379 · DOI · Paper page
  15. [16]Stathopoulos A Van Drenth M Erives A Markstein M Levine M Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo Cell 2002 111 687 701 10.1016/S0092-8674(02)01087-5 12464180 · DOI
  16. [19]Zeitlinger J Zinzen RP Stark A Kellis M Zhang H Young RA Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo Genes Dev 2007 21 385 90 10.1101/gad.1509607 17322397 PMC1804326 · DOI · Paper page
  17. [20]Ozdemir A Fisher-Aylor KI Pepke S Samanta M Dunipace L McCue K High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation Genome Res 2011 21 566 77 10.1101/gr.104018.109 21383317 PMC3065704 · DOI
  18. [21]He Q Bardet AF Patton B Purvis J Johnston J Paulson A High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species Nat Genet 2011 43 414 20 10.1038/ng.808 21478888 · DOI
  19. [22]MacArthur S Li XY Li J Brown JB Chu HC Zeng L Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions Genome Biol 2009 10 R80 10.1186/gb-2009-10-7-r80 19627575 PMC2728534 · DOI
  20. [23]He Q Johnston J Zeitlinger J ChIP-nexus enables improved detection of in vivo transcription factor binding footprints Nat Biotechnol 2015 33 4 395 401 10.1038/nbt.3121 25751057 PMC4390430 · DOI
  21. [24]Moorman C Sun LV Wang J de Wit E Talhout W Ward LD Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster Proc Natl Acad Sci U S A 2006 103 12027 32 10.1073/pnas.0605003103 16880385 PMC1567692 · DOI
  22. [26]Hager GL McNally JG Misteli T Transcription dynamics Mol Cell 2009 35 741 53 10.1016/j.molcel.2009.09.005 19782025 PMC6326382 · DOI
  23. [29]Creyghton MP Cheng AW Welstead GG Kooistra T Carey BW Steine EJ Histone H3K27ac separates active from poised enhancers and predicts developmental state Proc Natl Acad Sci U S A 2010 107 21931 6 10.1073/pnas.1016071107 21106759 PMC3003124 · DOI · Paper page
  24. [30]Zentner GE Tesar PJ Scacheri PC Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions Genome Res 2011 21 1273 83 10.1101/gr.122382.111 21632746 PMC3149494 · DOI · Paper page
  25. [31]Bonn S Zinzen RP Girardot C Gustafson EH Perez-Gonzalez A Delhomme N Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development Nat Genet 2012 44 148 56 10.1038/ng.1064 22231485 · DOI · Paper page
  26. [32]Buenrostro JD Giresi PG Zaba LC Chang HY Greenleaf WJ Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position Nat Methods 2013 10 1213 8 10.1038/nmeth.2688 24097267 PMC3959825 · DOI · Paper page
  27. [33]Schneider DS Hudson KL Lin TY Anderson KV Dominant and recessive mutations define functional domains of Toll, a transmembrane protein required for dorsal-ventral polarity in the Drosophila embryo Genes Dev 1991 5 797 807 10.1101/gad.5.5.797 1827421 · DOI · Paper page
  28. [34]Konrad KD Goralski TJ Mahowald AP Developmental genetics of the gastrulation defective locus in Drosophila melanogaster Dev Biol 1988 127 133 42 10.1016/0012-1606(88)90195-9 3129326 · DOI
  29. [35]Visel A Blow MJ Li Z Zhang T Akiyama JA Holt A ChIP-seq accurately predicts tissue-specific activity of enhancers Nature 2009 457 854 8 10.1038/nature07730 19212405 PMC2745234 · DOI · Paper page
  30. [36]Negre N Brown CD Ma L Bristow CA Miller SW Wagner U A cis-regulatory map of the Drosophila genome Nature 2011 471 527 31 10.1038/nature09990 21430782 PMC3179250 · DOI
  31. [37]Philip P Boija A Vaid R Churcher AM Meyers DJ Cole PA CBP binding outside of promoters and enhancers in Drosophila melanogaster Epigen Chromatin 2015 8 48 10.1186/s13072-015-0042-4 PMC4657240 26604986 · DOI
  32. [38]Tie F Banerjee R Stratton CA Prasad-Sinha J Stepanik V Zlobin A CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing Development 2009 136 3131 41 10.1242/dev.037127 19700617 PMC2730368 · DOI
  33. [39]Kvon EZ Kazmar T Stampfel G Yanez-Cuna JO Pagani M Schernhuber K Genome-scale functional characterization of Drosophila developmental enhancers in vivo Nature 2014 512 7512 91 5 24896182
  34. [41]Akimaru H Chen Y Dai P Hou DX Nonaka M Smolik SM Drosophila CBP is a co-activator of cubitus interruptus in hedgehog signalling Nature 1997 386 735 8 10.1038/386735a0 9109493 · DOI
  35. [42]Holmqvist PH Boija A Philip P Crona F Stenberg P Mannervik M Preferential genome targeting of the CBP co-activator by Rel and Smad proteins in early Drosophila melanogaster embryos PLoS Genet 2012 8 e1002769 10.1371/journal.pgen.1002769 22737084 PMC3380834 · DOI
  36. [43]Love MI Huber W Anders S Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2 Genome Biol 2014 15 550 10.1186/s13059-014-0550-8 25516281 PMC4302049 · DOI · Paper page
  37. [45]Zhu LJ Christensen RG Kazemian M Hull CJ Enuameh MS Basciotta MD FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system Nucleic Acids Res 2011 39 D111 7 10.1093/nar/gkq858 21097781 PMC3013762 · DOI
  38. [46]Mathelier A Fornes O Arenillas DJ Chen CY Denay G Lee J JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles Nucleic Acids Res 2016 44 D110 5 10.1093/nar/gkv1176 26531826 PMC4702842 · DOI · Paper page
  39. [47]Grant CE Bailey TL Noble WS FIMO: scanning for occurrences of a given motif Bioinformatics 2011 27 1017 8 10.1093/bioinformatics/btr064 21330290 PMC3065696 · DOI · Paper page
  40. [48]Bodmer R The gene tinman is required for specification of the heart and visceral muscles in Drosophila Development 1993 118 719 29 7915669
  41. [49]Azpiazu N Frasch M tinman and bagpipe: two homeo box genes that determine cell fates in the dorsal mesoderm of Drosophila Genes Dev 1993 7 1325 40 10.1101/gad.7.7b.1325 8101173 · DOI
  42. [50]Sivasankaran R Vigano MA Muller B Affolter M Basler K Direct transcriptional control of the Dpp target omb by the DNA binding protein Brinker EMBO J 2000 19 6162 72 10.1093/emboj/19.22.6162 11080162 PMC305821 · DOI
  43. [51]Kirkpatrick H Johnson K Laughon A Repression of Dpp targets by binding of brinker to Mad sites J Biol Chem 2001 276 18216 22 10.1074/jbc.M101365200 11262410 · DOI
  44. [52]Rushlow C Colosimo PF Lin MC Xu M Kirov N Transcriptional regulation of the Drosophila gene zen by competing Smad and Brinker inputs Genes Dev 2001 15 340 51 10.1101/gad.861401 11159914 PMC312624 · DOI
  45. [53]Zhang H Levine M Ashe HL Brinker is a sequence-specific transcriptional repressor in the Drosophila embryo Genes Dev 2001 15 261 6 10.1101/gad.861201 11159907 PMC312626 · DOI
  46. [54]Liang HL Xu M Chuang YC Rushlow C Response to the BMP gradient requires highly combinatorial inputs from multiple patterning systems in the Drosophila embryo Development 2012 139 1956 64 10.1242/dev.079772 22513375 PMC3347688 · DOI
  47. [55]Jack J Myette G The genes raw and ribbon are required for proper shape of tubular epithelial tissues in Drosophila Genetics 1997 147 243 53 9286684 PMC1208108
  48. [56]Gonzalez-Gaitan M Rothe M Wimmer EA Taubert H Jackle H Redundant functions of the genes knirps and knirps-related for the establishment of anterior Drosophila head structures Proc Natl Acad Sci U S A 1994 91 8567 71 10.1073/pnas.91.18.8567 8078924 PMC44647 · DOI
  49. [57]Schroeder MD Pearce M Fak J Fan H Unnerstall U Emberly E Transcriptional control in the segmentation gene network of Drosophila PLoS Biol 2004 2 E271 10.1371/journal.pbio.0020271 15340490 PMC514885 · DOI
  50. [58]Ashe HL Mannervik M Levine M Dpp signaling thresholds in the dorsal ectoderm of the Drosophila embryo Development 2000 127 3305 12 10887086
  51. [59]Frank LH Rushlow C A group of genes required for maintenance of the amnioserosa tissue in Drosophila Development 1996 122 1343 52 8625823
  52. [60]Bjorum SM Simonette RA Alanis R Jr Wang JE Lewis BM Trejo MH The Drosophila BTB domain protein Jim Lovell has roles in multiple larval and adult behaviors PLoS One 2013 8 e61270 10.1371/journal.pone.0061270 23620738 PMC3631165 · DOI
  53. [61]Duret L Bucher P Searching for regulatory elements in human noncoding sequences Curr Opin Struct Biol 1997 7 399 406 10.1016/S0959-440X(97)80058-9 9204283 · DOI
  54. [62]Margulies EH Birney E Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes Nat Rev Genet 2008 9 303 13 10.1038/nrg2185 18347593 · DOI
  55. [63]Martin-Bermudo MD Dunin-Borkowski OM Brown NH Specificity of PS integrin function during embryogenesis resides in the alpha subunit extracellular domain EMBO J 1997 16 4184 93 10.1093/emboj/16.14.4184 9250662 PMC1170044 · DOI
  56. [64]Lawrence M Daujat S Schneider R Lateral thinking: how histone modifications regulate gene expression Trends Genet 2016 32 42 56 10.1016/j.tig.2015.10.007 26704082 · DOI
  57. [65]Langmead B Trapnell C Pop M Salzberg SL Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol 2009 10 R25 10.1186/gb-2009-10-3-r25 19261174 PMC2690996 · DOI · Paper page
  58. [66]Bardet AF Steinmann J Bafna S Knoblich JA Zeitlinger J Stark A Identification of transcription factor binding sites from ChIP-seq data at high resolution Bioinformatics 2013 29 2705 13 10.1093/bioinformatics/btt470 23980024 PMC3799470 · DOI
  59. [67]Kim D Pertea G Trapnell C Pimentel H Kelley R Salzberg SL TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Genome Biol 2013 14 R36 10.1186/gb-2013-14-4-r36 23618408 PMC4053844 · DOI · Paper page
  60. [68]Trapnell C Williams BA Pertea G Mortazavi A Kwan G van Baren MJ Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nat Biotechnol 2010 28 511 5 10.1038/nbt.1621 20436464 PMC3146043 · DOI · Paper page
  61. [69]Zhang Y Liu T Meyer CA Eeckhoute J Johnson DS Bernstein BE Model-based analysis of ChIP-Seq (MACS) Genome Biol 2008 9 R137 10.1186/gb-2008-9-9-r137 18798982 PMC2592715 · DOI · Paper page
  62. [71]Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010;330:doi:10.1126/science.1198374. PMC3192495 21177974 · DOI
  63. [73]Hammonds AS Bristow CA Fisher WW Weiszmann R Wu S Hartenstein V Spatial expression of transcription factors in Drosophila embryonic organ development Genome Biol 2013 14 R140 10.1186/gb-2013-14-12-r140 24359758 PMC4053779 · DOI
  64. [74]Tomancak P Berman BP Beaton A Weiszmann R Kwan E Hartenstein V Global analysis of patterns of gene expression during Drosophila embryogenesis Genome Biol 2007 8 R145 10.1186/gb-2007-8-7-r145 17645804 PMC2323238 · DOI
  65. [75]Tomancak P, Beaton A, Weiszmann R, Kwan E, Shu S, Lewis SE, et al. Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 2002;3:RESEARCH0088. PMC151190 12537577
  66. [76]Lecuyer E Yoshida H Parthasarathy N Alm C Babak T Cerovina T Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function Cell 2007 131 174 87 10.1016/j.cell.2007.08.003 17923096 · DOI · Paper page
  67. [77]Wilk R Hu J Blotsky D Krause HM Diverse and pervasive subcellular distributions for both coding and long noncoding RNAs Genes Dev 2016 30 594 609 10.1101/gad.276931.115 26944682 PMC4782052 · DOI
  68. [78]Russell J Gennissen A Nusse R Isolation and expression of two novel Wnt/wingless gene homologues in Drosophila Development 1992 115 475 85 1425336
  69. [79]Yan R Small S Desplan C Dearolf CR Darnell JE Jr Identification of a Stat gene that functions in Drosophila development Cell 1996 84 421 30 10.1016/S0092-8674(00)81287-8 8608596 · DOI

Cited by

Sorted by citations

Authors
Koenecke, N., Johnston, J., Gaertner, B., Natarajan, M., & Zeitlinger, J.
Affiliations
Stowers Institute for Medical Research (US)
Corresponding author
Zeitlinger, Julia
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2016-09-27
Volume
17
Issue
1
Pages
196-196
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/s13059-016-1057-2
PMC
PMC5037609
OpenAlex
W2526877120
Cited by
65
References
9
Citations by year
2026: 2 · 2025: 8 · 2024: 6 · 2023: 12 · 2022: 8 · 2021: 9 · 2020: 1 · 2019: 6 · 2018: 9 · 2017: 4
FWCI
3.29
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Genome biology (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
Stowers Institute for Medical Research
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
enhancer identification, dorsoventral patterning, Drosophila, histone acetylation, H3K27ac, tissue-specific enhancers, transcription factor binding motifs, CREB-binding protein, chromatin accessibility, developmental regulatory networks, enhancer target genes

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review