HMG box gene transcriptions

File:Large lymphocytes-9.JPG

This is a large lymphocyte. Credit: Guy Waterval.{{free media}}

"Upstream Binding Factor (UBF) is important for activation of ribosomal RNA transcription and belongs to a family of proteins containing nucleic acid binding domains, termed HMG-boxes, with similarity to High Mobility Group (HMG) chromosomal proteins."

Chromosomal proteins

"Most HMG box proteins contain two or more HMG boxes and appear to bind DNA in a relatively sequence-aspecific manner (5, 13, 15, 16 and references therein). [...] they all appear to bind to the minor groove of the A/T A/T C A A A G-motif (10, 14, 18-20)."

"Previous studies in lymphocytes have described two DNA-binding HMG box proteins, TCF-1 and LEF-1, with affinity for the A/TA/TCAAAG motif found in several T cell-specific enhancers."

"The high mobility group-1 (HMG) box was originaly identified by Tjian and co-workers in the transcription factor UBF as a region of homology to HMG-1 proteins (Jantzen et al., 1990). UBF reportedly contained four such regions of -80 amino acids; one of these boxes was shown to mediate DNA binding."

"Interestingly, the sequence-specific HMG boxes characterized to date display high afinity to the A/TA/TCAAAG motif despite a low level of amino acid homology (typically <25% identity)."

"Human LEF-1 was originally identified as a T cell-specific protein binding to the TTCAAAG motif in the TCR-α enhancer (Waterman et al., 1991)."

"As analysed by gel retardation, the Sox-4 HMG box indeed bound to the AACAAAG motif (probe MWε-1; Figure 2B, lane 1). As described for other HMG boxes, Sox-4 interacted with DNA bases within the minor groove: substitution of A/T pairs for I/C pairs, which leaves the surface of the minor groove intact (Star and Hawley, 1991), had no apparent effect on binding affinity (lanes 2 and 4)."

Consensus sequences

"In mammals, the Tcf/Lef family consists of four genes: Tcf‐1, Lef‐1, Tcf‐3 and Tcf‐4. All TCF/LEF proteins display several common structural features (48,49). They contain a nearly identical DNA‐binding domain, the HMG box, recognizing the consensus sequence A/T A/T CAAA."

"Both directed and random screen studies have identified a consensus recognition sequence for the HMG DBD; 5′-SCTTTGATS-3′ [...] (van de Wetering et al. 1997; van Beest et al. 2000; Hallikas and Taipale 2006; Atcha et al. 2007)."

"The domain is called the “C clamp” to highlight the absolute requirement for four cysteine residues in DNA binding (Atcha et al. 2007) [...]."

"The C clamp carries specificity for a secondary, GC-rich sequence called a “Helper site” [(C/G)C(C/G)G(C/G)] that can occur with variable spacing and orientation relative to the Wnt response element (Atcha et al. 2007; Chang et al. 2008)."

High mobility group proteins

Gene ID: 6932 is TCF7 transcription factor 7 on 5q31.1: "This gene encodes a member of the T-cell factor/lymphoid enhancer-binding factor family of high mobility group (HMG) box transcriptional activators. This gene is expressed predominantly in T-cells and plays a critical role in natural killer cell and innate lymphoid cell development. The encoded protein forms a complex with beta-catenin and activates transcription through a Wnt/beta-catenin signaling pathway. Mice with a knockout of this gene are viable and fertile, but display a block in T-lymphocyte differentiation. Alternative splicing results in multiple transcript variants. Naturally-occurring isoforms lacking the N-terminal beta-catenin interaction domain may act as dominant negative regulators of Wnt signaling."

1. NP_001128323.2 transcription factor 7 isoform 3: "Transcript Variant: This variant (3, also known as A), differs in the 5' UTR, has multiple coding region differences, uses a downstream start codon, and differs in the 3' UTR, compared to variant 1. The resulting isoform (3) is shorter at the N-terminus and has a distinct C-terminus, compared to isoform 1."
2. NP_001333354.1 transcription factor 7 isoform 5: "Transcript Variant: This variant (8) contains an alternate exon in the coding region, compared to variant 1. The resulting isoform (5) is longer, compared to isoform 1."
3. NP_001333379.1 transcription factor 7 isoform 7: "Transcript Variant: This variant (9) differs in the 5' UTR, has multiple coding region differences, and uses a downstream start codon, compared to variant 1. The resulting isoform (7) is shorter at the N-terminus and has a distinct C-terminus, compared to isoform 1."
4. NP_001353431.1 transcription factor 7 isoform 8 [variant 10].
5. NP_003193.2 transcription factor 7 isoform 1: "Transcript Variant: This variant (1) encodes isoform (1)."
6. NP_963963.1 transcription factor 7 isoform 2: "Transcript Variant: This variant (2, also known as B), differs in the 5' UTR, has multiple coding region differences, and uses a downstream start codon, compared to variant 1. The resulting isoform (2) is shorter at the N-terminus, compared to isoform 1. Both variants 2 and 5 encode the same isoform."
7. NP_963965.1 transcription factor 7 isoform 4: "Transcript Variant: This variant (4, also known as C), differs in the 5' UTR, has multiple coding region differences, uses a downstream start codon, and differs in the 3' UTR, compared to variant 1. The resulting isoform (4) is shorter at the N-terminus and has a distinct C-terminus, compared to isoform 1."
8. NP_998813.1 transcription factor 7 isoform 2: "Transcript Variant: This variant (5) differs in the 5' UTR, has multiple coding region differences, and uses a downstream start codon, compared to variant 1. The resulting isoform (2) is shorter at the N-terminus, compared to isoform 1. Both variants 2 and 5 encode the same isoform."

Gene ID: 6934 is TCF7L2 transcription factor 7 like 2 on 10q25.2-q25.3: "This gene encodes a high mobility group (HMG) box-containing transcription factor that plays a key role in the Wnt signaling pathway. The protein has been implicated in blood glucose homeostasis. Genetic variants of this gene are associated with increased risk of type 2 diabetes. Several transcript variants encoding multiple different isoforms have been found for this gene."

1. NP_001139746.1 transcription factor 7-like 2 isoform 1: "Transcript Variant: This variant (1) encodes the longest isoform."
2. NP_001139755.1 transcription factor 7-like 2 isoform 3: "Transcript Variant: This variant (3) has multiple differences in the coding region, compared to variant 1, one of which results in a translational frameshift. The resulting protein (isoform 3) has a distinct C-terminus and is shorter than isoform 1."
3. NP_001139756.1 transcription factor 7-like 2 isoform 4: "Transcript Variant: This variant (4) has multiple differences in the coding region, compared to variant 1, one of which results in a translational frameshift. The resulting protein (isoform 4) has a distinct C-terminus and is shorter than isoform 1."
4. NP_001139757.1 transcription factor 7-like 2 isoform 5: "Transcript Variant: This variant (5) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform 5, which is shorter than isoform 1."
5. NP_001139758.1 transcription factor 7-like 2 isoform 6: "Transcript Variant: This variant (6) has multiple differences in the coding region, compared to variant 1, one of which results in a translational frameshift. The resulting protein (isoform 6) has a distinct C-terminus and is shorter than isoform 1."
6. NP_001185454.1 transcription factor 7-like 2 isoform 7: "Transcript Variant: This variant (7) has multiple differences in the coding region, compared to variant 1, one of which results in a translational frameshift. The resulting protein (isoform 7) has a distinct C-terminus and is shorter than isoform 1."
7. NP_001185455.1 transcription factor 7-like 2 isoform 8: "Transcript Variant: This variant (8) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform 8, which is shorter than isoform 1."
8. NP_001185456.1 transcription factor 7-like 2 isoform 9: "Transcript Variant: This variant (9) has multiple differences in the coding region, compared to variant 1, one of which results in a translational frameshift. The resulting protein (isoform 9) has a distinct C-terminus and is shorter than isoform 1."
9. NP_001185457.1 transcription factor 7-like 2 isoform 10: "Transcript Variant: This variant (10) has multiple differences in the coding region, compared to variant 1, one of which results in a translational frameshift. The resulting protein (isoform 10) has a distinct C-terminus and is shorter than isoform 1."
10. NP_001185458.1 transcription factor 7-like 2 isoform 11: "Transcript Variant: This variant (11) has multiple differences in the coding region, compared to variant 1, one of which results in a translational frameshift. The resulting protein (isoform 11) has a distinct C-terminus and is shorter than isoform 1."
11. NP_001185459.1 transcription factor 7-like 2 isoform 12: "Transcript Variant: This variant (12) has multiple differences in the coding region, compared to variant 1, one of which results in a translational frameshift. The resulting protein (isoform 12) has a distinct C-terminus and is shorter than isoform 1."
12. NP_001185460.1 transcription factor 7-like 2 isoform 13: "Transcript Variant: This variant (13) has multiple differences in the coding region, compared to variant 1, one of which results in a translational frameshift. The resulting protein (isoform 13) has a distinct C-terminus and is shorter than isoform 1."
13. NP_001336799.1 transcription factor 7-like 2 isoform 14: "Transcript Variant: This variant (14) lacks alternate exons in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (14) has a distinct N-terminus and is shorter than isoform 1."
14. NP_001336800.1 transcription factor 7-like 2 isoform 15: "Transcript Variant: This variant (15) lacks alternate exons in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (15) has a distinct N-terminus and is shorter than isoform 1."
15. NP_001350430.1 transcription factor 7-like 2 isoform 16 [variant 16].
16. NP_001354872.1 transcription factor 7-like 2 isoform 17 [variant 17].
17. NP_110383.2 transcription factor 7-like 2 isoform 2: "Transcript Variant: This variant (2) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform 2, which is shorter than isoform 1."

Gene ID: 51176 is LEF1 lymphoid enhancer binding factor 1: "This gene encodes a transcription factor belonging to a family of proteins that share homology with the high mobility group protein-1. The protein encoded by this gene can bind to a functionally important site in the T-cell receptor-alpha enhancer, thereby conferring maximal enhancer activity. This transcription factor is involved in the Wnt signaling pathway, and it may function in hair cell differentiation and follicle morphogenesis. Mutations in this gene have been found in somatic sebaceous tumors. This gene has also been linked to other cancers, including androgen-independent prostate cancer. Alternative splicing results in multiple transcript variants."

1. NP_001124185.1 lymphoid enhancer-binding factor 1 isoform 2: "Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1. [...] SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif."
2. NP_001124186.1 lymphoid enhancer-binding factor 1 isoform 3: "Transcript Variant: This variant (3) lacks both an in-frame exon in the central coding region and an exon in the 3' coding region that causes a frameshift, compared to variant 1. The encoded isoform (3) has a distinct C-terminus and is shorter than isoform 1."
3. NP_001159591.1 lymphoid enhancer-binding factor 1 isoform 4: "Transcript Variant: This variant (4) differs in the 5' UTR and 5' coding region, and lacks an alternate in-frame exon in the central coding region, compared to variant 1. The encoded isoform (4) has a distinct N-terminus and is shorter than isoform 1."
4. NP_057353.1 lymphoid enhancer-binding factor 1 isoform 1: "Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1)."

HMG box samplings

Main article: Model samplings

Copying a responsive elements consensus sequence (A/T)(A/T)CAAAG and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (A/T)(A/T)CAAAG (starting with SuccessablesHMG.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

1. negative strand, negative direction, looking for (A/T)(A/T)CAAAG, 0.
2. negative strand, positive direction, looking for (A/T)(A/T)CAAAG, 0.
3. positive strand, negative direction, looking for (A/T)(A/T)CAAAG, 1, ATCAAAG at 2891.
4. positive strand, positive direction, looking for (A/T)(A/T)CAAAG, 0.
5. complement, negative strand, negative direction, looking for (A/T)(A/T)GTTTC, 1, TAGTTTC at 2891.
6. complement, negative strand, positive direction, looking for (A/T)(A/T)GTTTC, 0.
7. complement, positive strand, negative direction, looking for (A/T)(A/T)GTTTC, 0.
8. complement, positive strand, positive direction, looking for (A/T)(A/T)GTTTC, 0.
9. inverse complement, negative strand, negative direction, looking for CTTTG(A/T)(A/T), 2, CTTTGTT at 1585, CTTTGTT at 229.
10. inverse complement, negative strand, positive direction, looking for CTTTG(A/T)(A/T), 0.
11. inverse complement, positive strand, negative direction, looking for CTTTG(A/T)(A/T), 0.
12. inverse complement, positive strand, positive direction, looking for CTTTG(A/T)(A/T), 0.
13. inverse negative strand, negative direction, looking for GAAAC(A/T)(A/T), 0.
14. inverse negative strand, positive direction, looking for GAAAC(A/T)(A/T), 0.
15. inverse positive strand, negative direction, looking for GAAAC(A/T)(A/T), 2, GAAACAA at 1585, GAAACAA at 229.
16. inverse positive strand, positive direction, looking for GAAAC(A/T)(A/T), 0.

HMG UTRs

1. Positive strand, negative direction: ATCAAAG at 2891.

HMG distal promoters

1. Negative strand, negative direction: CTTTGTT at 1585, CTTTGTT at 229.

HMG random dataset samplings

1. HMGr0: 3, TTCAAAG at 4166, AACAAAG at 3503, TTCAAAG at 3338.
2. HMGr1: 2, TACAAAG at 3722, TACAAAG at 2071.
3. HMGr2: 0.
4. HMGr3: 1, AACAAAG at 278.
5. HMGr4: 3, TACAAAG at 3777, AACAAAG at 3593, ATCAAAG at 672.
6. HMGr5: 1, TACAAAG at 3734.
7. HMGr6: 1, TACAAAG at 1499.
8. HMGr7: 2, ATCAAAG at 2949, TTCAAAG at 252.
9. HMGr8: 4, AACAAAG at 2658, ATCAAAG at 1142, TTCAAAG at 935, AACAAAG at 620.
10. HMGr9: 0.
11. HMGr0ci: 5, CTTTGTT at 4178, CTTTGAT at 3842, CTTTGAA at 3415, CTTTGTA at 986, CTTTGTT at 617.
12. HMGr1ci: 1, CTTTGTT at 1640.
13. HMGr2ci: 0.
14. HMGr3ci: 0.
15. HMGr4ci: 0.
16. HMGr5ci: 1, CTTTGTT at 1983.
17. HMGr6ci: 2, CTTTGAA at 1712, CTTTGAT at 257.
18. HMGr7ci: 0.
19. HMGr8ci: 3, CTTTGTA at 2944, CTTTGTT at 1167, CTTTGAT at 1149.
20. HMGr9ci: 0.

HMGr arbitrary UTRs

1. HMGr0: TTCAAAG at 4166, AACAAAG at 3503, TTCAAAG at 3338.
2. HMGr4: TACAAAG at 3777, AACAAAG at 3593.
3. HMGr0ci: CTTTGTT at 4178, CTTTGAT at 3842, CTTTGAA at 3415.
4. HMGr8ci: CTTTGTA at 2944.

HMGr alternate UTRs

1. HMGr1: TACAAAG at 3722.
2. HMGr5: TACAAAG at 3734.
3. HMGr7: ATCAAAG at 2949.

HMGr arbitrary negative direction proximal promoters

1. HMGr8: AACAAAG at 2658.

HMGr alternate positive direction proximal promoters

1. HMGr0: TTCAAAG at 4166.
2. HMGr0ci: CTTTGTT at 4178.

HMGr arbitrary negative direction distal promoters

1. HMGr4: ATCAAAG at 672.
2. HMGr6: TACAAAG at 1499.
3. HMGr8: ATCAAAG at 1142, TTCAAAG at 935, AACAAAG at 620.
4. HMGr0ci: CTTTGTA at 986, CTTTGTT at 617.
5. HMGr6ci: CTTTGAA at 1712, CTTTGAT at 257.
6. HMGr8ci: CTTTGTT at 1167, CTTTGAT at 1149.

HMGr alternate negative direction distal promoters

1. HMGr1: TACAAAG at 2071.
2. HMGr3: AACAAAG at 278.
3. HMGr7: TTCAAAG at 252.
4. HMGr1ci: CTTTGTT at 1640.
5. HMGr5ci: CTTTGTT at 1983.

HMGr arbitrary positive direction distal promoters

1. HMGr1: TACAAAG at 3722, TACAAAG at 2071.
2. HMGr3: AACAAAG at 278.
3. HMGr5: TACAAAG at 3734.
4. HMGr7: ATCAAAG at 2949, TTCAAAG at 252.
5. HMGr1ci: CTTTGTT at 1640.
6. HMGr5ci: CTTTGTT at 1983.

HMGr alternate positive direction distal promoters

1. HMGr0: AACAAAG at 3503, TTCAAAG at 3338.
2. HMGr4: TACAAAG at 3777, AACAAAG at 3593, ATCAAAG at 672.
3. HMGr6: TACAAAG at 1499.
4. HMGr8: AACAAAG at 2658, ATCAAAG at 1142, TTCAAAG at 935, AACAAAG at 620.
5. HMGr0ci: CTTTGAT at 3842, CTTTGAA at 3415, CTTTGTA at 986, CTTTGTT at 617.
6. HMGr6ci: CTTTGAA at 1712, CTTTGAT at 257.
7. HMGr8ci: CTTTGTA at 2944, CTTTGTT at 1167, CTTTGAT at 1149.

HMG box analysis and results

Main article: Complex locus A1BG and ZNF497 § HMG boxes

"Most HMG box proteins contain two or more HMG boxes and appear to bind DNA in a relatively sequence-aspecific manner (5, 13, 15, 16 and references therein). [...] they all appear to bind to the minor groove of the A/T A/T C A A A G-motif (10, 14, 18-20)."

Reals or randoms	Promoters	direction	Numbers	Strands	Occurrences	Averages (± 0.1)
Reals	UTR	negative	1	2	0.5	0.5 ± 0.5 (--0,+-1)
Randoms	UTR	arbitrary negative	9	10	0.9	0.6
Randoms	UTR	alternate negative	3	10	0.3	0.6
Reals	Core	negative	0	2	0	0
Randoms	Core	arbitrary negative	0	10	0	0
Randoms	Core	alternate negative	0	10	0	0
Reals	Core	positive	0	2	0	0
Randoms	Core	arbitrary positive	0	10	0	0
Randoms	Core	alternate positive	0	10	0	0
Reals	Proximal	negative	0	2	0	0
Randoms	Proximal	arbitrary negative	1	10	0.1	0.05
Randoms	Proximal	alternate negative	0	10	0	0.05
Reals	Proximal	positive	0	2	0	0
Randoms	Proximal	arbitrary positive	0	10	0	0.1
Randoms	Proximal	alternate positive	2	10	0.2	0.1
Reals	Distal	negative	2	2	1	1 ± 1 (--2,+-0)
Randoms	Distal	arbitrary negative	11	10	1.1	0.8
Randoms	Distal	alternate negative	5	10	0.5	0.8
Reals	Distal	positive	0	2	0	0
Randoms	Distal	arbitrary positive	8	10	0.8	1.35
Randoms	Distal	alternate positive	19	10	1.9	1.35

Comparison:

The occurrences of real HMG boxes are greater than the randoms. This suggests that the real HMG boxes are likely active or activable.

Helper site samplings

Copying a responsive elements consensus sequence AAAAAAAA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (C/G)C(C/G)G(C/G) (starting with SuccessablesHelp.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

1. negative strand, negative direction, looking for AAAAAAAA, 0.
2. positive strand, negative direction, looking for AAAAAAAA, 0.
3. negative strand, positive direction, looking for AAAAAAAA, 0.
4. positive strand, positive direction, looking for AAAAAAAA, 0.
5. inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
6. inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
7. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
8. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.

See also

• GA responsive complex gene transcription laboratory