The 7SK snRNP - a stable RNA core with a reversibly docked kinase, which is why the reservoir is a switch and not a sink
also called 7SK snRNP · 7SK RNP · large P-TEFb complex · inactive P-TEFb
The 7SK snRNP is a small particle built around an RNA that holds the elongation enzyme P-TEFb switched off until the cell releases it. Its inner parts are permanently bolted together and the enzyme is the part that comes and goes, which is what makes it a usable switch rather than a dead end.
The same thing, for a scientist
The 7SK snRNP has two tiers. The **core** is 7SK RNA with MEPCE on its 5' methylphosphate cap and LARP7 on its 3' U-rich end: LARP7 remains bound to 7SK whether or not P-TEFb is present, immunodepleting LARP7 removes most cellular 7SK, and MEPCE and LARP7 act cooperatively to stabilise the RNA, with LARP7 occluding MEPCE's catalytic centre so that capping happens before assembly [E1][E2]. The **reversible tier** is a HEXIM1 or HEXIM2 dimer plus P-TEFb, which dock and undock according to CDK9 T-loop phosphorylation and cellular stress [E1][E3]. Only the assembled particle inhibits: 7SK alone binds P-TEFb without inhibiting it, and HEXIM supplies the inhibition [E3]. AFF1 is also present in the particle, bound through its N-terminal cyclin T1-binding sequence, which means the SEC scaffold and the reservoir share a subunit [E4] - and that the shared subunit is precisely the part of AFF1 that KMT2A::AFF1 lacks.
What is bolted on and what comes off
| component | tier | how it holds on |
|---|---|---|
| 7SK RNA (332 nt) | core scaffold | - |
| MEPCE | core | 5' gamma-monomethyl phosphate cap; its catalytic centre is occluded once LARP7 is present 2 |
| LARP7 | core | 3' U-rich stretch via the xRRM; stays bound after P-TEFb leaves 1 |
| HEXIM1 / HEXIM2 | reversible | homo- and heterodimers; supplies the actual kinase inhibition 35 |
| CDK9 / cyclin T | reversible | requires CDK9 T186 phosphorylation for capture 6 |
| AFF1 | reversible, travels with P-TEFb | via AFF1 N-terminal CBS on cyclin T1 4 |
| hnRNP A1/A2/Q/R | exchange partners | take over 7SK when P-TEFb and HEXIM1 leave 7 |
The consequence of the two tiers is that the reservoir cannot be emptied by destroying it. Knocking down LARP7 or 7SK raises free P-TEFb transiently and then lowers total P-TEFb protein, because the core also stabilises the kinase 1.
Stoichiometry, and what is honestly unknown
HEXIM1 and HEXIM2 form stable homo- and heterodimers that probably nucleate particle assembly, and HEXIM2 can quantitatively substitute for HEXIM1 to keep the amount of 7SK/HEXIM-bound P-TEFb constant when HEXIM1 is knocked down 5. That is a homeostatic, self-correcting system, and it is the single most important fact for anyone proposing to attack the reservoir pharmacologically.
What is not settled: the exact number of P-TEFb molecules per particle in a living cell, whether HEXIM1 and HEXIM2 occupy the same particle in vivo, and whether the composition differs between cell types. There is no structure of the intact snRNP. Treat any stated stoichiometry as model-dependent.
Nothing in this section was measured in leukaemia
Every experiment cited here is HeLa, HEK293 or an HIV model. There is no published composition, abundance or partition measurement of the 7SK snRNP in KMT2A-rearranged leukaemia, in infant B-ALL, or in any primary blast. A reader should carry that forward into every downstream entry in this beat.
| complex name | 7SK small nuclear ribonucleoprotein (7SK snRNP) |
|---|---|
| fraction of ptefb sequestered | more than half in HeLa (PMID 11713533); never measured in any leukaemia cell |
| structures | no structure of the assembled snRNP; apical stem-loop 1 with HEXIM or Tat arginine-rich motifs only (PMID 35970937) |
| measured in leukaemia | false |
core subunits
[
{
"component": "RN7SK",
"node": "noncoding-rn7sk",
"tier": "core scaffold"
},
{
"component": "MEPCE",
"uniprot": "Q7L2J0",
"node": "gene-mepce",
"tier": "core"
},
{
"component": "LARP7",
"uniprot": "Q4G0J3",
"node": "gene-larp7",
"tier": "core"
}
]reversible subunits
[
{
"component": "HEXIM1",
"uniprot": "O94992",
"node": "gene-hexim1"
},
{
"component": "HEXIM2",
"uniprot": "Q96MH2",
"node": "gene-hexim2"
},
{
"component": "CDK9",
"uniprot": "P50750",
"node": "gene-cdk9"
},
{
"component": "CCNT1",
"uniprot": "O60563",
"node": "gene-ccnt1"
},
{
"component": "CCNT2",
"uniprot": "O60583",
"node": "gene-ccnt2"
},
{
"component": "AFF1",
"uniprot": "P51825",
"node": "gene-aff1",
"note": "via AFF1 1-308 cyclin T1-binding sequence, which KMT2A::AFF1 lacks"
}
]exchange partners
[ "hnRNP A1", "hnRNP A2", "hnRNP Q", "hnRNP R" ]
related entries
[ "protein-ptefb-cdk9-ccnt1", "concept-transcription-elongation", "protein-nelf-complex" ]
- The core stabilises P-TEFb as well as inhibiting it: knocking down LARP7 or 7SK eventually lowers total P-TEFb protein, so 'release the brake' and 'destroy the brake' are different interventions with opposite long-run effects.
- HEXIM2 quantitatively compensates for HEXIM1 loss to hold bound P-TEFb constant, so a single-gene intervention on either HEXIM is buffered by design.
- What is the composition of the 7SK snRNP in a KMT2A-rearranged blast? No purification has ever been done in one.
- Does the particle differ between fetal-liver-derived and adult-derived haematopoietic cells, given that infant KMT2A::AFF1 arises in utero?
- Is there a structure of the intact snRNP that would show whether HEXIM1 and HEXIM2 can occupy the same particle?
- E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
LARP7 is a stable component of the 7SK snRNP while P-TEFb, HEXIM1 and hnRNP A1 are reversibly associated; immunodepleting LARP7 removes most cellular 7SK, and knocking down LARP7 or 7SK raises free P-TEFb initially and then decreases total P-TEFb protein.
LARP7 is a stable component of the 7SK snRNP while P-TEFb, HEXIM1 and hnRNP A1 are reversibly associated. · Krueger BJ, Jeronimo C, Roy BB, Bouchard A, Barrandon C, Byers SA, Searcey CE, Cooper JJ, Bensaude O, Cohen EA, Coulombe B, Price DH · Nucleic Acids Res 2008What this evidence cannot show
Glycerol gradient sedimentation and siRNA in human cell lines (HeLa-type), with P-TEFb inhibitors used to force reorganisation. Not a leukaemia experiment and not a quantitative stoichiometry.
Evidence that argues against this (1)
- An independent group reaching the same conclusion about LARP7's identity nonetheless frames LARP7 primarily as a negative transcriptional regulator whose knockdown increases Pol II output, which emphasises the opposite half of the same result - the system is not simply a store, it actively restrains transcription. Markert A et al. 2008
- E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
BCDIN3/MEPCE is the 7SK methylphosphate capping enzyme, and within the assembled snRNP it loses capping activity while retaining a capping-independent function that promotes the LARP7-7SK interaction and stabilises the RNA.
A capping-independent function of MePCE in stabilizing 7SK snRNA and facilitating the assembly of 7SK snRNP. · Xue Y, Yang Z, Chen R, Zhou Q · Nucleic Acids Res 2010What this evidence cannot show
Biochemistry and co-IP in human cell lines; the occlusion of MePCE's catalytic centre by LARP7 is inferred ('probably due to') rather than shown structurally in that paper.
Evidence that argues against this (1)
- The identification of BCDIN3 as the capping enzyme came from a proteomic survey of the transcription machinery rather than from a dedicated enzymology study, so the assignment rests on complex membership plus activity rather than on structure. Jeronimo C et al. 2007
- E3established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
7SK binding alone does not inhibit P-TEFb; HEXIM1 inhibits P-TEFb in a process that specifically requires 7SK to mediate the HEXIM1:P-TEFb interaction, and P-TEFb dissociates from HEXIM1 and 7SK in cells undergoing a stress response.
Inhibition of P-TEFb (CDK9/Cyclin T) kinase and RNA polymerase II transcription by the coordinated actions of HEXIM1 and 7SK snRNA. · Yik JH, Chen R, Nishimura R, Jennings JL, Link AJ, Zhou Q · Mol Cell 2003What this evidence cannot show
HeLa biochemistry and in vitro transcription. The stress stimuli used are chemical and physical rather than physiological signalling.
Evidence that argues against this (1)
- A reconstituted system shows the 7SK-P-TEFb interaction can form independently of HEXIM1 and is controlled by CDK9 T-loop phosphorylation, so HEXIM1 is the inhibitor but not necessarily the first thing to bind. Chen R et al. 2004
- E4established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
AFF1 co-immunoprecipitates with the 7SK snRNP components LARP7 and HEXIM1 as well as with the SEC subunits ELL2 and ENL, and the tripartite CDK9-cyclin T-AFF1 unit is transferred as a single unit between complexes of the P-TEFb network.
AFF1 is a ubiquitous P-TEFb partner to enable Tat extraction of P-TEFb from 7SK snRNP and formation of SECs for HIV transactivation. · Lu H, Li Z, Xue Y, Schulze-Gahmen U, Johnson JR, Krogan NJ, Alber T, Zhou Q · Proc Natl Acad Sci U S A 2014What this evidence cannot show
HeLa nuclear extracts, co-IP and deletion mapping; anti-LARP7 and anti-HEXIM1 immunoprecipitates did not contain ELL2 or ENL, so AFF1's presence in the snRNP is as a P-TEFb partner and not as a whole SEC.
Evidence that argues against this (1)
- An earlier purification of Tat-associated complexes describes a 7SK snRNP-containing complex that lacks HEXIM, which indicates the particle's composition is heterogeneous enough that a single co-IP series does not fix it. Sobhian B et al. 2010
- E5established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
HEXIM1 and HEXIM2 form stable homo- and hetero-oligomers, both inhibit P-TEFb through a 7SK-mediated interaction, and in HEXIM1-knockdown cells HEXIM2 compensates functionally and quantitatively to hold the amount of 7SK/HEXIM-bound P-TEFb constant.
Compensatory contributions of HEXIM1 and HEXIM2 in maintaining the balance of active and inactive positive transcription elongation factor b complexes for control of transcription. · Yik JH, Chen R, Pezda AC, Zhou Q · J Biol Chem 2005What this evidence cannot show
HeLa and transfected cells; the compensation is measured as the amount of P-TEFb in the bound fraction, not as a phenotype. HEXIM1 and HEXIM2 expression patterns differ across tissues and lines, so the compensation may not be universal.
Evidence that argues against this (1)
- An independent characterisation of HEXIM2 published simultaneously agrees on compensation but concludes that which HEXIM is used can be differentially regulated in vivo, so 'redundant' is not the right word for the pair. Byers SA et al. 2005
- E6established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
Capture of P-TEFb by 7SK requires phosphorylation of CDK9 at the conserved T-loop threonine, and dephosphorylation is what releases it under stress.
Phosphorylated positive transcription elongation factor b (P-TEFb) is tagged for inhibition through association with 7SK snRNA. · Chen R, Yang Z, Zhou Q · J Biol Chem 2004What this evidence cannot show
In vitro reconstitution plus in vivo binding, HeLa. The kinase responsible was unidentified at the time.
Evidence that argues against this (1)
- The released heterodimer is later shown to dissociate into CDK9 and cyclin T1 monomers, which are then reassembled on Brd4 or the SEC with T186 autophosphorylation, so the phosphorylation state is not a simple upstream switch. Zhou K et al. 2022
- E7strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
hnRNPs Q, R, A1 and A2 are major 7SK-associated proteins whose association increases when P-TEFb and HEXIM1 are released, and knocking down hnRNP A1 and A2 attenuates the transcription-dependent dissociation of the P-TEFb-HEXIM1-7SK complex.
The transcription-dependent dissociation of P-TEFb-HEXIM1-7SK RNA relies upon formation of hnRNP-7SK RNA complexes. · Barrandon C, Bonnet F, Nguyen VT, Labas V, Bensaude O · Mol Cell Biol 2007What this evidence cannot show
Proteomics plus siRNA in human cell lines; the model that hnRNPs 'trap' 7SK is inferred from association kinetics rather than shown directly.
Evidence that argues against this (1)
- A separate route to release requires no RNA-binding protein at all: SEC components can concentrate P-TEFb out of the soluble HEXIM1-containing pool by multivalent condensation, which predicts hnRNP loading is a consequence of release rather than its cause. Guo C et al. 2020
reversibly captured when CDK9 T186 is phosphorylated
the 332-nt scaffold the whole particle is built on
holds more than half of nuclear P-TEFb in an inactive state in HeLa
- regulates →Plain-English: what transcription elongation is, and why a traffic light explains this leukemia
the negative arm of the elongation switch
AFF1 is present in the particle through its N-terminal cyclin T1-binding sequence
supplies the kinase inhibition; reversibly associated
reversibly associated inhibitory subunit; buffers HEXIM1 loss
stable core component; clamps the 3' U-rich end of 7SK
stable core component; caps 7SK before assembly and stabilises the particle afterwards
the fusion cannot join the reservoir, so it cannot be switched off by it
the disassembly/reassembly cycle that sets the free P-TEFb pool
proposed route by which SEC multivalency draws P-TEFb out of the soluble HEXIM1-bound pool
Tat binds 7SK stem-loop 1 and displaces HEXIM to extract P-TEFb
the partition this hypothesis is about
reported to bind 7SK snRNA and release P-TEFb; single unreplicated paper
7SK snRNP associates with LEC at snRNA genes; depleting 7SK snRNA or LARP7 disrupts LEC integrity
three of the four 7SK snRNP subunits (HEXIM2, LARP7, MEPCE) are in the 8-member real-gap floor while HEXIM1 is covered
gives the particle a genome-wide enhancer address and a nucleosome-level mechanism