A chromatin landmark and transcription initiation at most promoters in human cells - PubMed (original) (raw)

Figure 4. Events Associated with Transcriptional Elongation Occur at a Minority of Genes

(A and B) Enrichment ratios are shown for H3K36me3, which is associated with elongation. The start site and direction of transcription are indicated by an arrow. (C) Composite enrichment profiles for H3K36me3 at genes called present or absent for mRNA transcripts using microarray data (as in Figure 2G). The start site and direction of transcription of the average gene are indicated by an arrow. (D) Single-probe enrichment ratios of H3K36me3 across the average 2.5 kb region downstream of the transcription start site (~10 probes per promoter). Enriched probes (blue) and unenriched probes (white) are shown for each gene. Individual genes are represented top to bottom and are ordered by average binding ratio across the entire region. (E) H3K36me3 maximum enrichment (blue horizontal line) between 1 kb and 3 kb of the transcription start site for each gene represented on the human promoter array. Genes are ordered as in (D). (F) Composite enrichment profiles for H3K79me2 at genes called present or absent for mRNA transcripts using microarray data (as in Figure 2G). (G) Composite enrichment profiles for Pol II (4H8) at genes called present or absent for mRNA transcripts using microarray data (as in Figure 2G). Both the initiating and elongating forms of Pol II are recognized by this antibody. The area from 1 kb to 3 kb downstream of the promoter (designated e) was used to determine genes enriched. The start site and direction of transcription of the average gene are indicated by an arrow. (H) Quantitative RT-PCR analysis of total RNA extracted from hES cells. Estimated transcripts per cell were obtained by dividing the number of molecules of cDNA, as determined by relative quantitation using the standard curve in Figure S5, by the number of cells used for the amplification. Positive control probes (active genes, blue bars) and test sample probes (Inactive genes, green bars) are as follows: (1) No probe, (2) RPLPO, (3) HMGB2, (4) CCNB1, (5) EIF2C3, (6) HOP, (7) GUCY1A3,(8) KITLG, (9) SOX9, (10) PLD1, (11) INCENP, (12) ERCC4, (13) CSF1, (14) HOXB1, (15) GPR143, (16) DSC3, (17) NFKBIL2, (18) ANG, (19) LEFTY1, (20) LNPEP, (21) TCF21, (22) RAP1GA1,(23) KLF2, (24) KCNJ3, (25) TNFSF7, (26) PRRG2, (27) FOXG1B, (28) DLX5, (29) KCNH1, (30) ACADL, (31) CXCL2, (32) HOXD12, (33) ONECUT1, (34) LYST, (35) PCSK2, (36) AVPR1B, (37) SMP3, (38) EPHX2, (39) UCP1, (40) AGC1, (41) ERAF, (42) HBA1, (43) MLNR. Measured values for the genes can be found in Table S6. Broken axis is indicated by white line. (I) H3K4me3 maximum enrichment (within 1 kb of the transcription start site) for each gene represented in (H).