Table 1 Genomic and functional annotation of D4Z4-like loci.

From: Rethinking genomics of facioscapulohumeral muscular dystrophy in the telomere-to-telomere era: pitfalls in the hidden landscape of D4Z4 repeats

Chrom. location

N. of D4Z4-like Units

Flanking seq.

Completeness KpnI/KpnI with promoter

DBE >20 bp

Exon1 (DUX4 ORF) >1200 bp

pLAM

Number

Identity %

Exon2

Exon3

PolyA

Chr4 q35

DUX4L9-201

(DUXc)

FRG2_201

1 Partial

0/1

1/1

95.2

1/1

0/1

0/1

Chr4 q35

34

D4Z4 subtel

33 Complete*

1 Partial 1st rep

33/33

0/1

33/33

0/1

99.7-100

n.d.

33/33

1/1

1/33 last rep

0/1

1/33

0/1

Chr10 q26

34

D4Z4-subtel

33 Complete*

1 Partial 1st rep

33/33

0/1

33/33

0/1

98.6-99.2

n.d.

33/33

1/1

1/33 last rep

0/1

0/34

0/1

Chr10 q11

3 including

DUXL16 & 18

bsat_10_1

3 Partial

2/3

3/3

88.4-90.5

0/3

0/3

0/3

Chr1 q12

57

bsat_1_1

1 Complete*

56 Partial

1/1

34/56

1/1

31/56

89.9

85.9-90.4

1/1

21 /56

1/1

2/56

0/1

0/56

Chr13 p11

26

bsat_13_4

1 Complete*

25 Partial

1/1

20/25

1/1

15/25

89.6

87.8–90.7

1/1

13/25

0/1

0/25

0/1

0/25

Chr13 p13

2

bsat_13_4

2 Partial

1/2

1/2

90.4

1/2

0/2

0/2

Chr14 p13

17

bsat_14_1

17 Partial

16/17

14/17

87.9–90.5

8/17

2/17

0/17

Chr14 p13

2

bsat_14_2

2 Partial

1/2

1/2

90.6

1/2

0/2

0/2

Chr14 p11

26

bsat_14_5

1 Complete*

25 Partial

1/1

19/25

1/1

14/25

89.7

85.9–90.4

1/1

12/25

0/1

0/25

0/1

0/25

Chr14 p11

36

bsat_14_8

2 Complete*

34 Partial

2/2

26/34

2/2

21/34

93.5–96.7

87.4–90.5

2/2

11/34

0/2

0/36

0/2

3/34**

Chr14 p11

56

bsat_14_9

56 Partial

46/56

42/56

86.2–90.1

28/56

3/56

1/56**

Chr15 p13

19

bsat_15_1

19 Partial

16/19

12/19

86.1–90.2

13/19

2/19

0/19

Chr15 p13

1

bsat_15_2

1 Partial

1/1

1/1

90.7

0/1

0/1

0/1

Chr15 p11

25

bsat_15_5

1 Complete*

24 Partial

1/1

19/24

1/1

14/24

89.5

86–90.9

1/1

12/24

0/1

0/24

0/1

0/24

Chr18 p11

1

Intron-subtel

1 Partial

0/1

0/1

n.d.

1/1

1/1

0/1

Chr21 p13

26

bsat_21_1

26 Partial

23/26

19/26

86.6–90.7

15/26

2/26

0/26

Chr21 p13

2

bsat_21_2

2 Partial

1/2

1/2

90.4

1/2

0/2

0/2

Chr21 p11

38

bsat_21_7

38 Partial

29/38

28/38

86.4–89.8

15/38

3/38

0/38

Chr22 p13

23

bsat_22_1

23 Partial

22/23

19/23

86.4–90.6

14/23

3/23

1/23**

Chr22 p13

2

bsat_22_2

2 Partial

1/1

1/1

90.7

1/2

0/2

0/2

Chr22 p11

28

bsat_22_6

28 Partial

25/28

20/28

87.3–91.3

14/28

2/28

2/28**

Chr22 p11

11

bsat_22_8

11 Partial

11/11

10/11

87.4–90.8

4/11

0/11

0/11

Chr22 p11

43

bsat_22_12

2 Complete*

41 Partial

2/2

30/41

2/2

26/41

89.5–90.4

88–90.7

2/2

12/41

0/2

5/41

0/2

1/41**

Chr3 q11

2

bsat_3_1

2 Partial

1/2

1/2

88.3–90.6

0/2

0/2

0/2

Chr3 p12

DUX4L26-201

(DUXo)

FRG2C_201

1 Partial

0/1

1/1

88.8

0/1

0/1

0/1

Chr9 q12

1

bsat_9_5

1 Partial

1/1

1/1

87.9

0/1

0/1

0/1

ChrY q11

4

DUXL16,17,18 &19

bsat_Y_11

4 Partial

3/4

4/4

89.1–92

4/4

0/4

0/4

  1. (i) Chromosomal location and cytoband;(ii) Copy number and organization (tandem arrays vs isolated monomers);(iii) Flanking sequence context relevant to transcriptional activity and chromatin organization;(iv) Completeness of the repeat unit, defined as the canonical 3.3 kb KpnI–KpnI D4Z4 monomer containing the putative DUX4 promoter (truncated/degenerate elements classified as incomplete);(v) Presence of the D4Z4 Binding Element (DBE; as defined in Methods); (vi) Presence of an Exon 1–containing DUX4 ORF and its sequence identity to the 4q35 last-repeat sequence;(vii) Presence of a pLAM-like downstream cassette (DUX4 exon 2, exon 3, and canonical polyadenylation signal), which together determine the potential to generate full-length DUX4 transcripts.
  2. *Complete but lacking the PolyA signal.
  3. **Carrying a putative PolyA signal but lacking Exon 3 or Exon 2 and 3.
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