LIN54 / DREAM (CHR)
LIN54 is the DNA-binding subunit of the MuvB core, the module shared by the repressive DREAM complex and the activating MMB (B-MYB-MuvB) and FOXM1-MuvB complexes. It reads a very short promoter element called the CHR, the cell cycle genes homology region, whose consensus is TTYGAA (most often TTTGAA or TTCGAA). Recognition is unusual: two tandem cysteine-rich CXC (tesmin/CRC) domains grip the duplex and two tyrosine side chains insert into the minor groove, with no zinc finger or helix-turn-helix involved. The CHR is the reason so many G2/M promoters - CCNB1, CCNB2, CDK1, CDC25C, PLK1, AURKA, UBE2C - share the same short TTYGAA, switching from repressed in G0/G1 to activated in G2/M.
The factors
LIN54 (also called MIP120, and CXCD1) is one of five subunits of the MuvB core, together with LIN9, LIN37, LIN52 and RBBP4 17531812,22391450. MuvB is the shared module of three complexes that act sequentially through the cell cycle. In quiescence and early G1 it assembles with E2F4, DP1 and the RB-family pocket protein p130 (RBL2) to form DREAM, which represses 17531812. On entry into S phase p130 and E2F4 leave and B-MYB (MYBL2) binds, giving MMB; later FOXM1 is recruited, giving FOXM1-MuvB, which activates the same promoters in G2 and M 22391450. LIN54 is the only subunit with sequence-specific DNA-binding activity, so it supplies the address for all three complexes 19725879,27465258. There is a single human LIN54 gene, so there is no paralogue ambiguity, and the protein is broadly expressed in proliferating and quiescent cells alike. Its DNA-binding module is not a zinc finger: it consists of two tandem cysteine-rich CXC domains, related to the tesmin/CRC domain family, and both are required for high-affinity binding 27465258. The Drosophila orthologue Mip120 is part of the dREAM/MMB complex with the same architecture 28522430.
The motif
The CHR was defined genetically in 1995 as a short element in the CCNA2, CDC25C and CDK1 promoters, sitting just downstream of a second element, the CDE, in a CDE-CHR tandem 7556094. The literature consensus is TTYGAA - in practice TTTGAA or TTCGAA - and the atlas data agree: the JASPAR LIN54 model is TTTGAAT and the CIS-BP model is ATTCAAA, which is the same element on the reverse strand 25215497. Family cohesion is 0.99, essentially one motif in two orientations.
One genuine disagreement is worth flagging. The genome-wide survey by Engeland's group defined the functional spectrum around TTYGAA 25106871, while the crystallographic study of LIN54 bound to DNA reported the biochemically selected consensus as TTYRAA, which admits TTTAAA and TTCAAA as well 27465258. Both statements are in the literature; the practical difference is whether a central G is required. The structure explains why the information content is so low: specificity comes from two tyrosine residues inserting into the minor groove rather than from major-groove base readout, a mode that reads a short AT-rich stretch with modest discrimination 27465258. That tyrosine-mediated contact is required for MuvB recruitment to target promoters in cells 27465258.
The element is 6 bp of low-complexity sequence. That is the single most important fact for reading a hit: TTTGAA occurs roughly every few kilobases in random sequence.
Where it acts
CHR elements are promoter elements, not enhancer elements, and they sit close to the transcription start site 19725879,27465258, typically within about 20-100 bp downstream of it. They occur in most late (G2/M) cell-cycle genes that bind DREAM, MMB or FOXM1-MuvB: CCNB1, CCNB2, CDK1, CDC25C, PLK1, AURKA, AURKB, BUB1, CENPF and UBE2C among many others 25106871. Inverse-orientation CHRs are functional 22064854. Some promoters use a CDE-CHR tandem in which an E2F4-contacted CDE enhances DREAM binding, and some use a CHR alone; the CHR, not the CDE, is the element that is strictly required 22064854. By contrast, canonical MYB-binding and forkhead-binding sites are under-represented in these promoters, even though B-MYB and FOXM1 act there - they arrive by protein interaction with MuvB rather than by binding their own sites 25106871,22391450. The structural work also suggests MuvB binding near the start site helps position downstream nucleosomes 27465258. The p53-p21-DREAM axis routes p53 signalling to these same CHR promoters, so CHR-containing G2/M genes are among the most reliably p53-repressed genes in the genome 20015071.
Biology and disease
The CHR is the mechanistic answer to a common observation: that G2/M genes behave as a tightly coordinated module with almost identical expression timing. They share one element and one binding protein. Loss of LIN54 or other MuvB subunits impairs mitotic gene expression and cell-cycle progression 19725879,22391450, and a LIN54 mutant in the CXC region mislocalizes to the cytoplasm and blocks the cycle 22895175. DREAM disruption de-represses G2/M genes in quiescence 17531812,28799433, which is one route by which RB-pathway and p53-pathway lesions in cancer produce the proliferation signature seen in tumour expression profiles. The CHR is therefore less a disease gene than the promoter grammar through which two of the most commonly disrupted tumour suppressor pathways act.
Reading a hit
A CHR match tells you a G2/M cell-cycle promoter is plausible; it does not tell you that LIN54 is bound. Six low-complexity bases match far too often for a single hit to be evidence. What raises confidence is context, not score: the match should be in a promoter, within roughly 100 bp of the transcription start site, in a gene whose expression peaks in G2/M, and ideally accompanied by a CDE a few bases away. Outside that context, treat TTTGAA as background. There is no paralogue problem, because LIN54 is the only protein known to read this element, but there is an interpretation problem in the other direction: because MuvB carries B-MYB, FOXM1, E2F4 and p130 to the DNA, ChIP-seq for any of those factors will return CHR elements without those factors binding DNA themselves, and a CHR hit under a FOXM1 or MYBL2 peak is usually indirect. The CIS-BP LIN54 model is inferred from chicken LIN54 at 99% DNA-binding-domain identity 25215497 rather than measured on the human protein, and note the TTYGAA-versus-TTYRAA disagreement when choosing how strict to be about the central base.
How this was worked out
The CHR is identified as an identical 5-bp region six nucleotides 3' of the CDE in the cyclin A, cdc25C and cdc2 promoters; mutating it deregulates all three in G0, and in vivo footprinting shows it occupied through the minor groove.
Still open then: The protein occupying the CHR was unknown.
The DREAM complex, p130/E2F4/DP plus the MuvB proteins LIN9, LIN37, LIN52, LIN54 and RBBP4, is identified as the repressor bound at more than 800 cell-cycle promoters in quiescence.
Still open then: Which subunit contacted DNA was not established.
The LIN54 CXC region is shown to be a new sequence-specific DNA-binding domain that binds the cdc2 promoter at the CHR overlapping the start site.
- 2012mediumPromoter mutagenesis; protein-DNA binding assays; ChIP; bioinformatic promoter screen22064854
DREAM is shown to bind the CHR of the cyclin B2 promoter in G0 without needing a CDE, MMB binds the same CHR in proliferating cells, and inverse CHRs are functional.
MuvB is shown to switch partners through the cycle, forming DREAM in quiescence, then recruiting B-MYB in S phase and FOXM1 in G2 to activate late cell-cycle genes.
- 2014mediumComputational meta-analysis of motif conservation, genome-wide binding and expression data25106871
A genome-wide definition of functional CHR variants (TTYGAA) places CHRs in most late cell-cycle genes bound by DREAM, MMB or FOXM1-MuvB, while MYB and forkhead sites are under-represented there.
A crystal structure of the LIN54 DNA-binding domain on a CHR shows two tyrosines reading the minor groove, explaining the 1995 minor-groove footprint, and binding studies define the consensus as TTYRAA rather than TTYGAA.
Still open then: The TTYRAA consensus conflicts with the TTYGAA spectrum derived from genomic promoters.
Still unresolved
- Whether the central G of the CHR is required is unsettled: the genome-wide promoter survey defines functional CHRs as TTYGAA, whereas binding studies with the LIN54 DNA-binding domain give TTYRAA, which also admits TTTAAA and TTCAAA.
- What confines MuvB to a few hundred promoters when TTYGAA occurs every few kilobases is not fully explained: proximity to the start site, an adjacent E2F4-bound CDE and NF-Y-bound CCAAT boxes are all implicated, but their separate contributions have not been resolved.
- Whether MuvB bound near the start site positions downstream nucleosomes is a model suggested by the structural study, not an established mechanism.
The CHR is 6 bp of low-complexity sequence (TTYGAA; TTTGAA and TTCGAA), so it matches frequently by chance and a single hit carries almost no information. Confidence comes from context: promoter location within roughly 100 bp of the transcription start site, a gene with G2/M-peaking expression, and often an adjacent CDE. Two consensus definitions coexist - TTYGAA from genome-wide promoter analysis and TTYRAA from in vitro selection with the LIN54 CXC domains - so whether a central G is required is unsettled. LIN54 is the only known reader, so there is no paralogue problem, but B-MYB, FOXM1, E2F4 and p130 all reach CHRs through MuvB, so their ChIP peaks contain CHRs indirectly. The CIS-BP model is inferred from chicken LIN54 (99% DBD identity).
References
- Zwicker J, Lucibello FC, Wolfraim LA, et al. Cell cycle regulation of the cyclin A, cdc25C and cdc2 genes is based on a common mechanism of transcriptional repression. EMBO J 1995;14:4514-22. PMID 7556094
- Litovchick L, Sadasivam S, Florens L, et al. Evolutionarily conserved multisubunit RBL2/p130 and E2F4 protein complex represses human cell cycle-dependent genes in quiescence. Mol Cell 2007;26:539-51. PMID 17531812
- Schmit F, Cremer S, Gaubatz S. LIN54 is an essential core subunit of the DREAM/LINC complex that binds to the cdc2 promoter in a sequence-specific manner. FEBS J 2009;276:5703-16. PMID 19725879
- Müller GA, Engeland K. The central role of CDE/CHR promoter elements in the regulation of cell cycle-dependent gene transcription. FEBS J 2010;277:877-93. PMID 20015071
- Müller GA, Quaas M, Schümann M, et al. The CHR promoter element controls cell cycle-dependent gene transcription and binds the DREAM and MMB complexes. Nucleic Acids Res 2012;40:1561-78. PMID 22064854
- Sadasivam S, Duan S, DeCaprio JA. The MuvB complex sequentially recruits B-Myb and FoxM1 to promote mitotic gene expression. Genes Dev 2012;26:474-89. PMID 22391450
- Matsuo T, Kuramoto H, Kumazaki T, et al. LIN54 harboring a mutation in CHC domain is localized to the cytoplasm and inhibits cell cycle progression. Cell Cycle 2012;11:3227-36. PMID 22895175
- Müller GA, Wintsche A, Stangner K, et al. The CHR site: definition and genome-wide identification of a cell cycle transcriptional element. Nucleic Acids Res 2014;42:10331-50. PMID 25106871
- Marceau AH, Felthousen JG, Goetsch PD, et al. Structural basis for LIN54 recognition of CHR elements in cell cycle-regulated promoters. Nat Commun 2016;7:12301. PMID 27465258
- Fischer M, Müller GA. Cell cycle transcription control: DREAM/MuvB and RB-E2F complexes. Crit Rev Biochem Mol Biol 2017;52:638-662. PMID 28799433
- Cheng MH, Andrejka L, Vorster PJ, et al. The Drosophila LIN54 homolog Mip120 controls two aspects of oogenesis. Biol Open 2017;6:967-978. PMID 28522430
- Weirauch MT, Yang A, Albu M, et al. Determination and inference of eukaryotic transcription factor sequence specificity. Cell 2014;158:1431-1443. PMID 25215497
2 motifs in this family — JASPAR 1 · CIS-BP 1
| motif | database | consensus | bits |
|---|---|---|---|
| M02527_2.00Gallus gallus 0.99 | CIS-BP | ATTcAAA | 11.3 |
| LIN54 (MA0619.2) | JASPAR | TTTgAAT | 11.1 |
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.