HNF gene transcriptions

Editor-In-Chief: Henry A. Hoff

Hepatic nuclear factors (HNFs) bind through their DNA-binding domain (DBD) to consensus elements (A/G/T)(A/T)(A/G)T(C/T)(A/C/G)AT(A/C/G/T)(A/G/T), resulting in gene transcription.

HNF1s

Gene ID: 6927 is HNF1A HNF1 homeobox A aka TCF1 on 12q24.31: "The protein encoded by this gene is a transcription factor required for the expression of several liver-specific genes. The encoded protein functions as a homodimer and binds to the inverted palindrome 5'-GTTAATNATTAAC-3'. Defects in this gene are a cause of maturity onset diabetes of the young type 3 (MODY3) and also can result in the appearance of hepatic adenomas. Alternative splicing results in multiple transcript variants encoding different isoforms."

1. NP_000536.6 hepatocyte nuclear factor 1-alpha isoform 2 [variant 2].
2. NP_001293108.2 hepatocyte nuclear factor 1-alpha isoform 1: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1)."

Gene ID: 6928 is HNF1B HNF1 homeobox B aka HNF2, TCF2, on 17q12: "This gene encodes a member of the homeodomain-containing superfamily of transcription factors. The protein binds to DNA as either a homodimer, or a heterodimer with the related protein hepatocyte nuclear factor 1-alpha. The gene has been shown to function in nephron development, and regulates development of the embryonic pancreas. Mutations in this gene result in renal cysts and diabetes syndrome and noninsulin-dependent diabetes mellitus, and expression of this gene is altered in some types of cancer. Multiple transcript variants encoding different isoforms have been found for this gene."

1. NP_000449.1 hepatocyte nuclear factor 1-beta isoform 1: "Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1)."
2. NP_001159395.1 hepatocyte nuclear factor 1-beta isoform 2: "Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1."
3. NP_001291215.1 hepatocyte nuclear factor 1-beta isoform 3: "Transcript Variant: This variant (3) differs in the 3' UTR, uses an alternate in-frame splice site in the central coding region, and lacks two alternate exons in the 3' coding region, resulting in a frameshift compared to variant 1. The resulting isoform (3) is shorter, and contains a distinct C-terminus, compared to isoform 1."

Gene ID: 79618 is HMBOX1 homeobox containing 1 aka hepatocyte nuclear factor 1 (HNF-1), N terminus (HNF1LA) on 8p21.1-p12.

1. NP_001129198.1 homeobox-containing protein 1 isoform 1: "Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 all encode the same isoform (1)."
2. NP_001311311.1 homeobox-containing protein 1 isoform 1: "Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 all encode the same isoform (1)."
3. NP_001311312.1 homeobox-containing protein 1 isoform 2 [variant 4].
4. NP_001311313.1 homeobox-containing protein 1 isoform 2 [variant 5].
5. NP_001311314.1 homeobox-containing protein 1 isoform 3 [variant 6].
6. NP_001311315.1 homeobox-containing protein 1 isoform 4 [variant 7].
7. NP_001311316.1 homeobox-containing protein 1 isoform 5 [variant 8].
8. NP_001311317.1 homeobox-containing protein 1 isoform 5 [variant 9].
9. NP_001311318.1 homeobox-containing protein 1 isoform 6 [variant 10].
10. NP_001311319.1 homeobox-containing protein 1 isoform 6 [variant 11].
11. NP_001311320.1 homeobox-containing protein 1 isoform 7 [variant 12].
12. NP_001311321.1 homeobox-containing protein 1 isoform 7 [variant 13].
13. NP_001311322.1 homeobox-containing protein 1 isoform 8 [variant 14].
14. NP_001311323.1 homeobox-containing protein 1 isoform 8 [variant 15].
15. NP_001311324.1 homeobox-containing protein 1 isoform 9 [variant 16].
16. NP_001317427.1 homeobox-containing protein 1 isoform 10 [variant 19].
17. NP_078843.2 homeobox-containing protein 1 isoform 1: "Transcript Variant: This variant (1) encodes isoform 1. Variants 1, 2, and 3 all encode the same isoform (1)."

HNF3s

Gene ID: 2305 is FOXM1 forkhead box M1 aka HNF-3 on 12p13.33. "The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene."

1. NP_001230017.1 forkhead box protein M1 isoform 4: "Transcript Variant: This variant (4) lacks two alternate in-frame exons and uses two alternate in-frame splice junctions compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1."
2. NP_001230018.1 forkhead box protein M1 isoform 5: "Transcript Variant: This variant (5) lacks two alternate in-frame exons and uses an alternate in-frame splice site compared to variant 1. The resulting isoform (5) has the same N- and C-termini but is shorter compared to isoform 1."
3. NP_068772.2 forkhead box protein M1 isoform 2: "Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1."
4. NP_973731.1 forkhead box protein M1 isoform 1: "Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1)."
5. NP_973732.1 forkhead box protein M1 isoform 3: "Transcript Variant: This variant (3) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1."

Gene ID: 3169 is FOXA1 forkhead box A1 aka HNF3A on 14q21.1: "This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver."

Gene ID: 3170 is FOXA2 forkhead box A2 aka HNF3B on 20p11.21. "This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific genes such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. This gene has been linked to sporadic cases of maturity-onset diabetes of the young. Transcript variants encoding different isoforms have been identified for this gene."

1. NP_068556.2 hepatocyte nuclear factor 3-beta isoform 1: "Transcript Variant: This variant (1) encodes the longer isoform (1)."
2. NP_710141.1 hepatocyte nuclear factor 3-beta isoform 2: "Transcript Variant: This variant (2) has a different splice pattern at the 5' end compared to transcript variant 1, resulting in translation initiation from a downstream AUG, and a shorter isoform (2) missing 6 aa from the N-terminus compared to isoform 1."

Gene ID: 3171 is FOXA3 forkhead box A3 aka HNF3G on 19q13.32: "This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. The crystal structure of a similar protein in rat has been resolved."

Gene ID: 27022 is FOXD3 forkhead box D3 aka HNF3/FH transcription factor genesis on 1p31.3: "This gene belongs to the forkhead family of transcription factors which is characterized by a distinct forkhead domain. Mutations in this gene cause autoimmune susceptibility 1."

"Computer analysis of the 2.3 kb rat a1bg promoter fragment revealed [...] one HNF6/HNF3 binding site at [...] −137/−128 [...]."

The "GH-dependent sexually dimorphic expression conveyed by the 2.3 kb a1bg promoter is enhanced by the HNF6/HNF3 site [...]."

"By extending the electrophoresis run and including nuclear extract from hypophysectomized rats, devoid of GH and thereby lacking HNF6 (Lahuna et al. 1997), the two different complexes were clearly visualized. The complex with the lower mobility is most probably due to the binding of HNF3, in analogy with what was shown by Lahuna et al. for the CYP2C12 HNF6 binding site; HNF3 can bind to the site in the absence of HNF6 (Lahuna et al. 1997)."

HNF4s

Gene ID: 3172 is HNF4A hepatocyte nuclear factor 4 alpha on 20q13.12: "The protein encoded by this gene is a nuclear transcription factor which binds DNA as a homodimer. The encoded protein controls the expression of several genes, including hepatocyte nuclear factor 1 alpha, a transcription factor which regulates the expression of several hepatic genes. This gene may play a role in development of the liver, kidney, and intestines. Mutations in this gene have been associated with monogenic autosomal dominant non-insulin-dependent diabetes mellitus type I. Alternative splicing of this gene results in multiple transcript variants encoding several different isoforms."

1. NP_000448.3 hepatocyte nuclear factor 4-alpha isoform 2: "Transcript Variant: This variant (2) encodes the longest isoform (2, also known as HNF4alpha2)."
2. NP_001025174.1 hepatocyte nuclear factor 4-alpha isoform 4: "Transcript Variant: This variant (4) contains an alternate 5' terminal exon (resulting in translation initiation from an alternate upstream start codon) and uses an alternate in-frame donor splice site in the 3' coding region compared to variant 2. The resulting shorter isoform (4, also known as HNF4alpha7) has a distinct N-terminus and lacks a 10 aa protein segment in the C-terminal region compared to isoform 2."
3. NP_001025175.1 hepatocyte nuclear factor 4-alpha isoform 6: "Transcript Variant: This variant (6) contains an alternate 5' terminal exon (resulting in translation initiation from an alternate upstream start codon) and differs at the 3' end that causes a frame-shift compared to variant 2. The resulting shorter isoform (6, also known as HNF4alpha9) has distinct N- and C-termini compared to isoform 2."
4. NP_001245284.1 hepatocyte nuclear factor 4-alpha isoform 7: "Transcript Variant: This variant (7) contains an additional coding exon in the 5' region that results in translation initiation from an alternate downstream start codon compared to variant 2. The resulting shorter isoform (7) has a distinct N-terminus compared to isoform 2."
5. NP_001274111.1 hepatocyte nuclear factor 4-alpha isoform 8: "Transcript Variant: This variant (8) differs at the 5' end (resulting in translation initiation from an alternate upstream start codon) and uses an alternate in-frame donor splice site in the 3' coding region compared to variant 2. The resulting shorter isoform (8, also known as HNF4alpha10) has a distinct N-terminus and lacks a 10 aa protein segment in the C-terminal region compared to isoform 2."
6. NP_001274112.1 hepatocyte nuclear factor 4-alpha isoform 9: "Transcript Variant: This variant (9) differs at the 5' end, which results in translation initiation from an alternate upstream start codon compared to variant 2. The resulting shorter isoform (9, also known as HNF4alpha11) has a distinct N-terminus compared to isoform 2."
7. NP_001274113.1 hepatocyte nuclear factor 4-alpha isoform 10: "Transcript Variant: This variant (10) differs at the 5' end (resulting in translation initiation from an alternate upstream start codon) and at the 3' end (that causes a frame-shift) compared to variant 2. The resulting shorter isoform (10, also known as HNF4alpha12) has distinct N- and C-termini compared to isoform 2."
8. NP_787110.2 hepatocyte nuclear factor 4-alpha isoform 5: "Transcript Variant: This variant (5) contains an alternate 5' terminal exon, which results in translation initiation from an alternate upstream start codon compared to variant 2. The resulting shorter isoform (5, also known as HNF4alpha8) has a distinct N-terminus compared to isoform 2."
9. NP_849180.1 hepatocyte nuclear factor 4-alpha isoform 1: "Transcript Variant: This variant (1) uses an alternate in-frame donor splice site in the 3' coding region compared to variant 2. The resulting shorter isoform (1, also known as HNF4alpha1) lacks a 10 aa protein segment compared to isoform 2."
10. NP_849181.1 hepatocyte nuclear factor 4-alpha isoform 3: "Transcript Variant: This variant (3) has a different 3' end that causes a frame-shift compared to variant 2. The resulting shorter isoform (3, also known as HNF4alpha3) has a distinct C-terminus compared to isoform 2."

Gene ID: 3174 is HNF4G hepatocyte nuclear factor 4 gamma on 8q21.13.

1. NP_001317490.1 hepatocyte nuclear factor 4-gamma isoform 2 [variant 2].
2. NP_004124.5 hepatocyte nuclear factor 4-gamma isoform 1 [variant 1].

"NF1 factors have also been shown to interact directly with the basal transcription machinery as well as with other transcription factors, including Stat5 (Kim & Roeder 1994, Mukhopadhyay et al. 2001) and synergistic effects with HNF4 have been reported (Ulvila et al. 2004). In addition to the HNF6, Stat5 and NF1/Oct sites, the a1bg promoter harbours an imperfect HNF4 site at −51/−39 with two mismatches compared with the HNF4 consensus site. HNF4 is clearly important for the expression of CYP2C12 (Sasaki et al. 1999), however, the −51/−39 region in a1bg was not protected in the footprinting analysis and was therefore not analysed further."

HNF6s

File:Liver expression of a1bg-luciferase constructs.jpg

Liver expression of a1bg-luciferase constructs is diagrammed. Credit: Cissi Gardmo and Agneta Mode.{{fairuse}}

HNF6 is actually produced by GeneID: 3175 ONECUT1 one cut homeobox 1: "This gene encodes a member of the Cut homeobox family of transcription factors. Expression of the encoded protein is enriched in the liver, where it stimulates transcription of liver-expressed genes, and antagonizes glucocorticoid-stimulated gene transcription. This gene may influence a variety of cellular processes including glucose metabolism, cell cycle regulation, and it may also be associated with cancer. Alternative splicing results in multiple transcript variants."

Both "the 2.3 kb and the 160 bp proximal parts of the a1bg promoter direct sex-specific expression of the reporter gene, and that a negative regulatory element resides in the −1 kb to −160 bp region."

The "binding of [...] HNF6 to the respective site by electromobility shift analysis (EMSA) [was verified] using female-derived [rat] liver nuclear extracts. [...] HNF6 bound to the a1bg HNF6 oligonucleotide, but in this case, the mutated oligonucleotide was able to compete for binding when added in large excess [...]. However, [...] the HNF6 binding capacity of the mutated oligonucleotide was clearly reduced. A 20 molar excess of the mutated oligonucleotide had only a marginal effect on the binding of HNF6 [...], whereas a 20 molar excess of unlabelled probe [...] completely abolished binding. Supershift analysis with an HNF6 antibody revealed a complex with a slightly lower mobility than the HNF6 complex [...]. [...] HNF6 could bind to [its] respective site in the a1bg promoter in vitro, and the mutations introduced in respective site abolished binding of the corresponding factor."

The "expression of a −116/−89 deletion construct in which also the HNF6 site was mutated, (−116/−89) delmutHNF6-Luc, [...] the generated luciferase activities were reduced in both sexes [...]. This is in contrast to that mutation/deletion of the sites separately only affected the expression in female livers."

The "−116/−89 region contains a site(s) of importance for the GH-dependent and female-specific expression of the a1bg gene, and that the impact of this region together with the HNF6 site is more complex than mere enhancement of the expression in females."

HNF6 is expressed at higher levels in female than in male rat liver (Lahuna et al. 1997). Indeed, following mutation of the HNF6-binding element, mutHNF6-Luc, the sex-differentiated expression was attenuated due to reduced expression in females. Thus, for a1bg, the sex-related difference in amount of HNF6 is likely to contribute to the sex-differentiated and female characteristic expression."

Nuclear "proteins binding to the a1bg −116/−89 region [are] members of the [nuclear factor 1] NF1 and the [octamer transcription factor] Oct families of transcription factors. NF1 genes are expressed in most adult tissues (Osada et al. 1999). It is not known how NF1 modulates transcriptional activity, and both activation and repression of transcription have been reported (Gronostajski 2000). Cofactors such as [CREB binding protein] CBP/p300 [E1A binding protein p300] and [histone deacetylase] HDAC have been shown to interact with NF1 proteins suggesting modulation of chromatin structure (Chaudhry et al. 1999)."

"Like NF1, Oct proteins have been reported to be involved in activation as well as repression of gene expression (Phillips & Luisi 2000). [...] NF1 and Oct-1 have been shown to, reciprocally, facilitate each other’s binding (O’Connor & Bernard 1995, Belikov et al. 2004)."

In the diagram on the right is liver "expression of a1bg-luciferase constructs. (A) Stat5 and HNF6 consensus sequences and corresponding sites in the 2.3 kb a1bg promoter alongside with the used mutations. (B) Female (black bars) and male (open bars) rats [results]."

Samplings HNF6

For the Basic programs (starting with SuccessablesHNF6.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 in the negative direction (from ZSCAN22 to A1BG) is SuccessablesHNF6--.bas, looking for 3'-(A/G/T)(A/T)(A/G)T(C/T)(A/C/G)AT(A/C/G/T)(A/G/T)-5', 3, 3'-GTGTTAATAA-5', 1725, 3'-TAGTTGATAA-5', 3527, 3'-TTATTAATCG-5', 4229,
2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesHNF6-+.bas, looking for 3'-(A/G/T)(A/T)(A/G)T(C/T)(A/C/G)AT(A/C/G/T)(A/G/T)-5', 3, 3'-ATGTCCATGG-5', 3581, 3'-TTATTAATCA-5', 4147, 3'-TTATTGATTA-5', 4164,
3. positive strand in the negative direction is SuccessablesHNF6+-.bas, looking for 3'-(A/G/T)(A/T)(A/G)T(C/T)(A/C/G)AT(A/C/G/T)(A/G/T)-5', 1, 3'-AAATTGATAA-5', 3361,
4. positive strand in the positive direction is SuccessablesHNF6++.bas, looking for 3'-(A/G/T)(A/T)(A/G)T(C/T)(A/C/G)AT(A/C/G/T)(A/G/T)-5', 1, 3'-GAGTCCATTG-5', 3732,
5. complement, negative strand, negative direction is SuccessablesHNF6c--.bas, looking for 3'-(A/C/T)(A/T)(C/T)A(A/G)(C/G/T)TA(A/C/G/T)(A/C/T)-5', 1, 3'-TTTAACTATT-5', 3361,
6. complement, negative strand, positive direction is SuccessablesHNF6c-+.bas, looking for 3'-(A/C/T)(A/T)(C/T)A(A/G)(C/G/T)TA(A/C/G/T)(A/C/T)-5', 1, 3'-CTCAGGTAAC-5', 3732,
7. complement, positive strand, negative direction is SuccessablesHNF6c+-.bas, looking for 3'-(A/C/T)(A/T)(C/T)A(A/G)(C/G/T)TA(A/C/G/T)(A/C/T)-5', 3, 3'-CACAATTATT-5', 1725, 3'-ATCAACTATT-5', 3527, 3'-AATAATTAGC-5', 4229,
8. complement, positive strand, positive direction is SuccessablesHNF6c++.bas, looking for 3'-(A/C/T)(A/T)(C/T)A(A/G)(C/G/T)TA(A/C/G/T)(A/C/T)-5', 3, 3'-TACAGGTACC-5', 3581, 3'-AATAATTAGT-5', 4147, 3'-AATAACTAAT-5', 4164,
9. inverse complement, negative strand, negative direction is SuccessablesHNF6ci--.bas, looking for 3'-(A/C/T)(A/C/G/T)AT(C/G/T)(A/G)A(C/T)(A/T)(A/C/T)-5', 2, 3'-ACATGGACAT-5', 802, 3'-TAATGAACTT-5', 1301,
10. inverse complement, negative strand, positive direction is SuccessablesHNF6ci-+.bas, looking for 3'-(A/C/T)(A/C/G/T)AT(C/G/T)(A/G)A(C/T)(A/T)(A/C/T)-5', 1, 3'-TTATTGATTA-5', 4164,
11. inverse complement, positive strand, negative direction is SuccessablesHNF6ci+-.bas, looking for 3'-(A/C/T)(A/C/G/T)AT(C/G/T)(A/G)A(C/T)(A/T)(A/C/T)-5', 3, 3'-AAATTGATAA-5', 3361, 3'-TCATCAACTA-5', 3525, 3'-TTATTAATTC-5', 4542,
12. inverse complement, positive strand, positive direction is SuccessablesHNF6ci++.bas, looking for 3'-(A/C/T)(A/C/G/T)AT(C/G/T)(A/G)A(C/T)(A/T)(A/C/T)-5', 2, 3'-CCATTGACTC-5', 3736, 3'-ATATTAACAA-5', 4172,
13. inverse, negative strand, negative direction, is SuccessablesHNF6i--.bas, looking for 3'-(A/G/T)(A/C/G/T)TA(A/C/G)(C/T)T(A/G)(A/T)(A/G/T)-5', 3, 3'-TTTAACTATT-5', 3361, 3'-AGTAGTTGAT-5', 3525, 3'-AATAATTAAG-5', 4542,
14. inverse, negative strand, positive direction, is SuccessablesHNF6i-+.bas, looking for 3'-(A/G/T)(A/C/G/T)TA(A/C/G)(C/T)T(A/G)(A/T)(A/G/T)-5', 2, 3'-GGTAACTGAG-5', 3736, 3'-TATAATTGTT-5', 4172,
15. inverse, positive strand, negative direction, is SuccessablesHNF6i+-.bas, looking for 3'-(A/G/T)(A/C/G/T)TA(A/C/G)(C/T)T(A/G)(A/T)(A/G/T)-5', 2, 3'-TGTACCTGTA-5', 802, 3'-ATTACTTGAA-5', 1301,
16. inverse, positive strand, positive direction, is SuccessablesHNF6i++.bas, looking for 3'-(A/G/T)(A/C/G/T)TA(A/C/G)(C/T)T(A/G)(A/T)(A/G/T)-5', 1, 3'-AATAACTAAT-5', 4164.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

Initial content for this page in some instances came from Wikiversity.

See also

• HNF6 gene transcription laboratory