Skip to main content

Table 1 Characteristics of landing sites1

From: Quantitative analysis of polycomb response elements (PREs) at identical genomic locations distinguishes contributions of PRE sequence and genomic environment

Site

Cytological location2

Genomic location2

Gene density3

Adjacent genes4

Next PC binding sites5

Chromatin type6

GTGTG8

GAGAG8

GCCAT8

1

chr. 2L, 38E3

20,716,266

2

+8 kb: CG9316

+42 kb: dia

Red

59

36

51

    

-1.7 kb: Hr38

-947 kb: bsh

    

2

chr. 2R, 46E1

5,965,083

4

+0.8 kb: egr

+1396 kb: inv

Red

47

25

53

    

-1.9 kb: CG1371

-97 kb: eve

    

3

chr. 2R, 58F4

18,549,410

12

+29 bp: CG42566

+205 kb: fd59A

Blue

43

26

36

    

-0.5 kb: CG42565

-375 kb: dve

    

4

chr. 3R, 100E3

27,899,491

1

Telomeric region

-

Yellow

41

38

17

    

-5.3 kb: Map205

-5.3 kb: Map205

    
  1. 1All four landing sites are located in intergenic regions with no PcG binding within a window or ±5 kb [9, 11].
  2. 2Cytological and genomic locations are shown according to FlyBase version FB2010_05.
  3. 3Gene density: number of genes whose gene span overlaps a ±10 kb window from the landing site.
  4. 4Adjacent genes: distance between genomic coordinate of the landing site and that of the closest edge of the next adjacent gene span in both directions (- = upstream, + = downstream according to genomic coordinates). Note that site 3 is located in the telomeric region of chromosome 3R, thus there is no downstream gene.
  5. 5Next PC binding sites: the closest Polycomb binding site up and downstream of the landing site was identified according to [9, 11].
  6. 6Chromatin type: Drosophila chromatin type according to [66] in which each landing site is located. 'Red' and 'yellow' chromatin types share features of transcriptionally active euchromatin but differ in the presence of specific factors (see Discussion for details). Note that the border of 'yellow' chromatin extends to 1.7kb upstream of site 4. This site is not assigned to a chromatin type in [66]. 'Blue' chromatin is enriched for PcG proteins and H3K27me3.
  7. 8GTGTG, GAGAG, GCCAT: the number of occurrences of each of these motifs within 10kb up and downstream of each landing site is shown.