The application of deep sequencing to map 5′ capped transcripts has confirmed the existence of at least two distinct promoter classes in metazoans: “focused” promoters with transcription start sites (TSSs) that occur in a narrowly defined genomic span and “dispersed” promoters with TSSs that are spread over a larger window. Previous studies have explored the presence of genomic features, such as CpG islands and sequence motifs, in these promoter classes, but virtually no studies have directly investigated the relationship with chromatin features. Here, we show that promoter classes are significantly differentiated by nucleosome organization and chromatin structure. Dispersed promoters display higher associations with well-positioned nucleosomes downstream of the TSS and a more clearly defined nucleosome free region upstream, while focused promoters have a less organized nucleosome structure, yet higher presence of RNA polymerase II. These differences extend to histone variants (H2A.Z) and marks (H3K4 methylation), as well as insulator binding (such as CTCF), independent of the expression levels of affected genes. Notably, differences are conserved across mammals and flies, and they provide for a clearer separation of promoter architectures than the presence and absence of CpG islands or the occurrence of stalled RNA polymerase. Computational models support the stronger contribution of chromatin features to the definition of dispersed promoters compared to focused start sites. Our results show that promoter classes defined from 5′ capped transcripts not only reflect differences in the initiation process at the core promoter but also are indicative of divergent transcriptional programs established within gene-proximal nucleosome organization.
Ni T, Corcoran DL, Rach EA, Song S, Spana EP, et al. (2010) A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nat Methods 7: 521–527.
Juven-Gershon T, Kadonaga JT (2010) Regulation of gene expression via the core promoter and the basal transcriptional machinery. Dev Biol 339: 225–229.
Nechaev S, Fargo DC, Dos Santos G, Liu L, Gao Y, et al. (2009) Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila. Science 327: 335–338.
Jin C, Zang C, Wei G, Cui K, Peng W, et al. (2009) H3.3/H2A.Z double variant-containing nucleosomes mark ‘nucleosome-free regions’ of active promoters and other regulatory regions. Nat Genet 41: 941–945.
Raisner RM, Hartley PD, Meneghini MD, Bao MZ, Liu CL, et al. (2005) Histone variant H2A.Z marks the 5′ ends of both active and inactive genes in euchromatin. Cell 123: 233–248.
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, et al. (2007) High-resolution profiling of histone methylations in the human genome. Cell 129: 823–837.
Tsukiyama T, Becker PB, Wu C (1994) ATP-dependent nucleosome disruption at a heat-shock promoter mediated by binding of GAGA transcription factor. Nature 367: 525–532.
Fu Y, Sinha M, Peterson CL, Weng Z (2008) The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet 4: e1000138. doi:10.1371/journal.pgen.1000138.
Engstrom PG, Ho Sui SJ, Drivenes O, Becker TS, Lenhard B (2007) Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome Res 17: 1898–1908.
Ganapathi M, Srivastava P, Das Sutar SK, Kumar K, Dasgupta D, et al. (2005) Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes. BMC Bioinformatics 6: 126.
Ohler U (2006) Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction. Nucleic Acids Res 34: 5943–5950.
Saxonov S, Berg P, Brutlag DL (2006) A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A 103: 1412–1417.
Tillo D, Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, et al. (2010) High nucleosome occupancy is encoded at human regulatory sequences. PLoS ONE 5: e9129. doi:10.1371/journal.pone.0009129.
Ramirez-Carrozzi VR, Braas D, Bhatt DM, Cheng CS, Hong C, et al. (2009) A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell 138: 114–128.
Negre N, Brown CD, Shah PK, Kheradpour P, Morrison CA, et al. (2010) A comprehensive map of insulator elements for the Drosophila genome. PLoS Genet 6: e1000814. doi:10.1371/journal.pgen.1000814.
Rach EA, Yuan HY, Majoros WH, Tomancak P, Ohler U (2009) Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome. Genome Biol 10: R73.
Davey CS, Pennings S, Reilly C, Meehan RR, Allan J (2004) A determining influence for CpG dinucleotides on nucleosome positioning in vitro. Nucleic Acids Res 32: 4322–4331.
Kawaji H, Severin J, Lizio M, Waterhouse A, Katayama S, et al. (2009) The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Genome Biol 10: R40.
Tolstorukov MY, Kharchenko PV, Goldman JA, Kingston RE, Park PJ (2009) Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes. Genome Res 19: 967–977.
Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, et al. (2008) High-resolution mapping and characterization of open chromatin across the genome. Cell 132: 311–322.
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, et al. (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40: 897–903.
Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG (2009) A transcription factor affinity-based code for mammalian transcription initiation. Genome Res 19: 644–656.
Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, et al. (2009) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458: 362–366.
Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, et al. (2007) Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446: 572–576.
Parry TJ, Theisen JW, Hsu JY, Wang YL, Corcoran DL, et al. (2010) The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery. Genes Dev 24: 2013–2018.
Zeitlinger J, Stark A, Kellis M, Hong JW, Nechaev S, et al. (2007) RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet 39: 1512–1516.
Smith ST, Wickramasinghe P, Olson A, Loukinov D, Lin L, et al. (2009) Genome wide ChIP-chip analyses reveal important roles for CTCF in Drosophila genome organization. Dev Biol 328: 518–528.
Chernukhin I, Shamsuddin S, Kang SY, Bergstrom R, Kwon YW, et al. (2007) CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites genome-wide. Mol Cell Biol 27: 1631–1648.
Hendrix DA, Hong JW, Zeitlinger J, Rokhsar DS, Levine MS (2008) Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Proc Natl Acad Sci U S A 105: 7762–7767.
Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, et al. (2009) Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol 16: 847–852.
Manak JR, Dike S, Sementchenko V, Kapranov P, Biemar F, et al. (2006) Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nat Genet 38: 1151–1158.
Hochheimer A, Zhou S, Zheng S, Holmes MC, Tjian R (2002) TRF2 associates with DREF and directs promoter-selective gene expression in Drosophila. Nature 420: 439–445.
