SREBP
SREBP-1 and SREBP-2 are bHLH-LZ factors made as ER membrane precursors and activated by sterol-regulated proteolysis, so only the cleaved nuclear fragment binds DNA. They are unusual in having dual specificity: a tyrosine replaces the arginine that is otherwise invariant in bHLH basic regions, letting them bind both the palindromic E-box CACGTG and the non-palindromic sterol regulatory element SRE-1, TCACNCCAC. Sites sit in promoters of cholesterol and fatty acid synthesis genes and work with a neighbouring NF-Y CCAAT box or SP1 GC box, which an isolated SRE needs for activity. The pathway controls the LDL receptor, hepatic lipogenesis and the response to statins, and is central to fatty liver disease and insulin resistance.
The factors
SREBF1 and SREBF2 encode SREBP-1 and SREBP-2, basic helix-loop-helix leucine zipper (bHLH-LZ) factors that are unusual in being synthesized as membrane-anchored precursors in the endoplasmic reticulum. SREBF1 produces two isoforms from alternative first exons, SREBP-1a and SREBP-1c (also called ADD1), which differ in the length of their activation domain 11994399. Each precursor has two transmembrane segments and is held in the ER by SCAP; when sterols are low, SCAP escorts it to the Golgi, where sequential cleavage by Site-1 and Site-2 proteases releases the N-terminal bHLH-LZ fragment, which enters the nucleus and dimerizes 9150132. Regulation is therefore proteolytic rather than transcriptional at the level of DNA binding, and only the cleaved nuclear form is a transcription factor. SREBP-2 is the principal driver of cholesterol synthesis genes, SREBP-1c of fatty acid synthesis genes, and SREBP-1a is a stronger general activator expressed mainly in proliferating cells and cell lines 11994399. Both genes are broadly expressed, with SREBF1 highest in liver and adipose tissue. The atlas assigns 12 motifs to this family (4 JASPAR, 5 HOCOMOCO, 2 CIS-BP, 1 Vierstra archetype) over SREBF1 and SREBF2, with cohesion 0.89 - the lowest in the E-box group - and SREBF1 (MA0595.1) as the representative.
The motif
SREBP has dual DNA-binding specificity, and this is the single most important fact about the family. It binds the canonical palindromic E-box CACGTG, usually with T/A flanks (ATCACGTGAT), and it also binds a non-palindromic, non-E-box element, the sterol regulatory element SRE-1, written TCACNCCAC 8402897,7739539. Mutagenesis of the LDL receptor promoter identified the nucleotides that make SRE-1 an active element 2298751, and biochemistry then showed the structural cause: in SREBP the arginine that is otherwise invariant in the basic region of every bHLH protein is replaced by a tyrosine, and that single substitution is sufficient to add SRE recognition to E-box recognition 7739539. The co-crystal of the SREBP-1a bHLH-LZ bound to an SRE showed a quasi-symmetric dimer with an asymmetric DNA interface: one monomer reads the E-box-like ATCAC half-site with typical bHLH contacts, and the other reads the non-E-box half through entirely different contacts 9634703. This is why the atlas cannot give the family one consensus. Roughly half of the assigned models are SRE-type (aTCACCCCAc, or its reverse complement aTGGgGTGAt), including the Vierstra archetype AC0486:SREBF:bHLH; the rest are E-box-type (ATCACGTGAT, ATCACcTGAT, gTCAgGTGAt). The published SRE consensus TCACNCCAC and the data consensus aTCACCCCAc agree, with the databases simply filling the degenerate position with the commonest base, C 8402897. The two motif classes are not variants of each other in any alignment sense, and a scan using one will miss the other.
Where it acts
SREBP sites are promoter-proximal, typically within a few hundred base pairs of the transcription start site of lipid-metabolism genes, and they rarely work alone. An isolated SRE is a weak element; efficient activation requires a co-regulatory factor bound nearby, most often NF-Y at a CCAAT box or SP1 at a GC box 9271397,9430668. At the LDLR promoter, synergy with SP1 (or SP3, which can substitute) requires a region of SP1 that includes the buttonhead (Btd) box, whereas the FAS and ACC promoters, which carry two SREBP sites, do not need it 9271397; at HMGCS1, SREBP interacts directly with the assembled NF-Y trimer through its bHLH-zipper 9430668. Genome-wide mapping of SREBP1 together with NFY and SP1 confirmed that the three co-occupy a large fraction of SREBP-bound promoters 18654640. The canonical composite arrangements are the LDLR promoter (SRE-1 plus SP1 sites) and the HMGCS1 promoter (SRE plus NF-Y) 8314806,9430668. Because the nuclear form is generated by proteolysis, occupancy is switched by sterol depletion, statin treatment, insulin (for SREBP-1c) or feeding rather than by changes in site availability 9150132.
Biology and disease
SREBP-2 activates essentially the whole cholesterol biosynthetic pathway plus the LDL receptor, which is why statin treatment, by lowering hepatic sterols, raises LDLR expression through this pathway 11994399. SREBP-1c activates fatty acid and triglyceride synthesis and is induced by insulin and by LXR agonists 11994399,28849786. Targeted disruption of Srebf1 in mice causes partial embryonic lethality, and surviving animals show elevated SREBP-2 and increased cholesterol synthesis, an example of cross-compensation within the family 9329978. In humans the pathway sits at the centre of non-alcoholic fatty liver disease, hypertriglyceridemia and insulin resistance, and SREBP-driven lipogenesis is also co-opted by tumours; reviews describe the physiology as convergent but the pathophysiology as divergent between the two genes 28849786.
Reading a hit
Decide first which motif you matched. An ATCACGTGAT hit is a T/A-flanked canonical E-box and is indistinguishable from USF, MITF/TFE, BHLHE41 or CLOCK-BMAL1 sites; it is weak evidence for SREBP on its own. A TCACNCCAC hit is much more specific, because few other human factors read that asymmetric sequence, and it becomes considerably stronger if an NF-Y CCAAT box or an SP1 GC box lies within about 50 bp in a lipid-gene promoter. SREBF1 and SREBF2 cannot be distinguished from each other by sequence, and the SREBP-1a/1c isoforms share one DNA-binding domain entirely. Several HOCOMOCO models here are ChIP-only, and one grade-C model (tCgCGTGA) is a degenerate half-site that should not be used for scanning.
How this was worked out
Single-base substitutions across the LDL receptor promoter map sterol regulation to the central 10 bp of Repeat 2, the SRE-1, a conditional positive element that works with neighbouring elements.
Still open then: The protein that binds SRE-1 was unknown.
- 1993highDNA-affinity purification, cross-linking, DNase I footprinting, cDNA cloning, reporter assays8314806 8402897
SREBP is purified by SRE-1 affinity and cloned as SREBP-1, a bHLH-ZIP protein whose target is a direct repeat of CAC rather than the inverted CANNTG repeat read by all other known bHLH-ZIP proteins.
Still open then: How a bHLH-ZIP dimer could read a non-palindromic site.
ADD1/SREBP1 binds both the E-box ATCACGTGA and SRE-1; a single basic-region tyrosine controls the dual specificity, since Tyr-to-Arg restricts SREBP to E-boxes and Arg-to-Tyr gives USF SRE binding.
The pathway is consolidated: SREBPs are ER-membrane precursors released by sterol-regulated, two-step proteolysis, so nuclear SREBP levels, not site availability, set target-gene activity.
Srebf1-null mice show partial embryonic lethality, and survivors raise nuclear SREBP-2 and hepatic cholesterol synthesis, showing cross-compensation within the family.
SREBP activation requires a co-regulator bound nearby: SP1 or SP3 through the Btd region at the LDLR promoter, and the trimeric NF-Y, which interacts directly with the SREBP bHLH-ZIP, at HMGCS1.
The SREBP-1a co-crystal on an SRE reveals a quasi-symmetric dimer with an asymmetric interface: one monomer reads the E-box-like ATCAC half and the other the GTGGG half through different contacts.
Genome-wide mapping in hepatocyte-derived cells finds SREBP1 at 1,141 promoters, extensively co-occupied with NF-Y and SP1 in combinations that mark distinct pathways.
Still unresolved
- How many SREBP target promoters act through the SRE rather than through an E-box is not settled: the classic sterol-regulated promoters (LDLR, HMGCS1) use SRE-type sites, the protein binds E-boxes as well in vitro, and the atlas splits its models roughly evenly between the two classes.
- Why SREBP-2 favours cholesterol genes and SREBP-1c lipogenic genes is not explained by DNA sequence: their models are indistinguishable, and proposed explanations rest on activation-domain strength and promoter architecture, such as the number of SREs and the type of co-regulator site.
This family has two unrelated motif classes and the databases hold both, so check which one you matched. An ATCACGTGAT E-box hit is shared with USF, MITF/TFE, BHLHE41 and CLOCK-BMAL1 and is weak evidence for SREBP. A TCACNCCAC SRE hit is far more specific, but SREBPs bind it weakly on their own and real elements are usually accompanied by NF-Y or SP1 within about 50 bp. SREBF1 and SREBF2 are indistinguishable by sequence, as are the SREBP-1a and -1c isoforms. Cohesion here is only 0.89 because of the two motif classes, several models are ChIP-only, and one grade-C model is a degenerate half-site not suitable for scanning.
References
- Smith JR, Osborne TF, Goldstein JL, et al. Identification of nucleotides responsible for enhancer activity of sterol regulatory element in low density lipoprotein receptor gene. J Biol Chem 1990;265:2306-10. PMID 2298751
- Wang X, Briggs MR, Hua X, et al. Nuclear protein that binds sterol regulatory element of low density lipoprotein receptor promoter. II. Purification and characterization. J Biol Chem 1993;268:14497-504. PMID 8314806
- Yokoyama C, Wang X, Briggs MR, et al. SREBP-1, a basic-helix-loop-helix-leucine zipper protein that controls transcription of the low density lipoprotein receptor gene. Cell 1993;75:187-97. PMID 8402897
- Kim JB, Spotts GD, Halvorsen YD, et al. Dual DNA binding specificity of ADD1/SREBP1 controlled by a single amino acid in the basic helix-loop-helix domain. Mol Cell Biol 1995;15:2582-8. PMID 7739539
- Párraga A, Bellsolell L, Ferré-D'Amaré AR, et al. Co-crystal structure of sterol regulatory element binding protein 1a at 2.3 A resolution. Structure 1998;6:661-72. PMID 9634703
- Brown MS, Goldstein JL. The SREBP pathway: regulation of cholesterol metabolism by proteolysis of a membrane-bound transcription factor. Cell 1997;89:331-40. PMID 9150132
- Athanikar JN, Sanchez HB, Osborne TF. Promoter selective transcriptional synergy mediated by sterol regulatory element binding protein and Sp1: a critical role for the Btd domain of Sp1. Mol Cell Biol 1997;17:5193-200. PMID 9271397
- Dooley KA, Millinder S, Osborne TF. Sterol regulation of 3-hydroxy-3-methylglutaryl-coenzyme A synthase gene through a direct interaction between sterol regulatory element binding protein and the trimeric CCAAT-binding factor/nuclear factor Y. J Biol Chem 1998;273:1349-56. PMID 9430668
- Shimano H, Shimomura I, Hammer RE, et al. Elevated levels of SREBP-2 and cholesterol synthesis in livers of mice homozygous for a targeted disruption of the SREBP-1 gene. J Clin Invest 1997;100:2115-24. PMID 9329978
- Horton JD, Goldstein JL, Brown MS. SREBPs: activators of the complete program of cholesterol and fatty acid synthesis in the liver. J Clin Invest 2002;109:1125-31. PMID 11994399
- Reed BD, Charos AE, Szekely AM, et al. Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes. PLoS Genet 2008;4:e1000133. PMID 18654640
- Shimano H, Sato R. SREBP-regulated lipid metabolism: convergent physiology - divergent pathophysiology. Nat Rev Endocrinol 2017;13:710-730. PMID 28849786
12 motifs in this family — JASPAR 4 · HOCOMOCO 5 · CIS-BP 2 · Vierstra 1
| motif | database | consensus | bits |
|---|---|---|---|
| SREBF2 (MA0828.3) | JASPAR | ATCACGTGAT | 17.1 |
| SREBF2 (MA0596.1) | JASPAR | aTGGgGTGAt | 13.6 |
| M08059_2.00 | CIS-BP | aTCACcCCAt | 13.6 |
| SREBF1 (MA0595.1) | JASPAR | aTCACCCCAc | 13.5 |
| M08048_2.00 | CIS-BP | aTCACCCCAc | 13.5 |
| SREBF1 (MA0829.3) | JASPAR | ATCACcTGAT | 13.3 |
| SRBP2.H14CORE.0.S.BSB | HOCOMOCO | gTgGCGTGAT | 12.5 |
| SRBP1.H14CORE.0.P.BPB | HOCOMOCO | gTCAgGTGAt | 12.2 |
| SRBP2.H14CORE.2.M.CMC | HOCOMOCO | aTcagGTGAT | 11.5 |
| SRBP1.H14CORE.1.S.CSC | HOCOMOCO | tCgCGTGA | 11.2 |
| AC0486:SREBF:bHLH | Vierstra | TCACcCCAc | 10.4 |
| SRBP2.H14CORE.1.P.BPB | HOCOMOCO | gTGGgGtGA | 8.2 |
HOCOMOCO tags read as assay + quality grade: P ChIP-seq, S HT-SELEX, M methyl-HT-SELEX, G GHT-SELEX, I SMiLE-seq, B PBM; grade A means two or more assay types agreed. A P-only matrix is a record of where the protein was crosslinked, which need not be a sequence it binds itself.
The factors, elsewhere
These entries are written from the primary literature and every citation is checked against PubMed, but this one can still be out of date, too confident, or simply wrong — especially where a motif’s published site and its database matrices disagree. Corrections and additions are welcome, and they are the fastest way to make this page better for everyone.