Affinage

NELFB

Negative elongation factor B · UniProt Q8WX92

Length
580 aa
Mass
65.7 kDa
Annotated
2026-04-29
16 papers in source corpus 10 papers cited in narrative 10 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

NELF-B (COBRA1) is a core subunit of the four-subunit NELF complex that enforces promoter-proximal RNA polymerase II pausing, thereby gating the expression of developmental and differentiation genes. Knockout studies demonstrate that NELF-B is essential for embryonic viability, mammary gland morphogenesis, and adipogenesis, where it stabilizes Pol II occupancy and maintains open chromatin at key regulatory promoters such as Pparg and Cebpa; BRCA1 genetically antagonizes this NELF-B–dependent transcriptional programme in a DNA-repair-independent, domain-specific manner (PMID:19340312, PMID:26941120, PMID:29426838, PMID:40960263). Beyond its nuclear Pol II-pausing function, NELF-B possesses a genetically separable cytoplasmic role in which it physically engages PI3K/AKT pro-survival kinases to promote cell proliferation, and it can shuttle the TrkC killer fragment to mitochondria to trigger Bax-dependent apoptosis (PMID:37717699, PMID:24034695). The high-resolution crystal structure of the NELF-B/C/E ternary complex reveals the inter-subunit contacts that organize the NELF core (PMID:37591184).

Mechanistic history

Synthesis pass · year-by-year structured walk · 7 steps
  1. 2004 Medium

    Establishing that NELF-B (COBRA1) functions as a nuclear transcriptional coregulator: prior to this, its molecular role was undefined; co-immunoprecipitation showed it interacts with BRCA1 in the nucleus and physically binds AP-1 components (c-Jun/c-Fos) to dose-dependently inhibit AP-1-driven transcription via a mappable c-Fos-binding domain.

    Evidence Co-IP of endogenous proteins, reporter assays, deletion mutagenesis in human breast cancer and other cell lines

    PMID:15185750 PMID:15530430

    Open questions at the time
    • BRCA1–COBRA1 interaction shown by single Co-IP without reciprocal validation or functional consequence defined
    • AP-1 inhibition demonstrated only by overexpression/reporter, lacking genome-wide or endogenous target validation
    • Relationship to Pol II pausing not yet established
  2. 2009 High

    Demonstrating that NELF-B is an essential NELF complex subunit required for Pol II pausing in vivo: knockout causes embryonic lethality due to inner cell mass failure, and ChIP showed direct promoter occupancy modulating Pol II abundance at developmental genes in embryonic stem cells.

    Evidence Nelfb knockout mouse, knockdown in mESCs, chromatin immunoprecipitation

    PMID:19340312

    Open questions at the time
    • Genome-wide target repertoire of NELF-B in ESCs not determined
    • Whether ICM deficiency reflects specific gene derepression or general transcription failure not resolved
  3. 2013 High

    Revealing two previously unknown functions — attenuation of glucocorticoid receptor signaling and cytoplasmic apoptotic signaling: NELF-B acts as a competitive decelerator of GR-driven gene induction via a conserved motif, and separately shuttles the TrkC killer fragment to mitochondria to initiate Bax/cytochrome c-dependent apoptosis in neural progenitors.

    Evidence Stable knockdown with ChIP and competition assay for GR; reciprocal Co-IP, mitochondrial fractionation, and in vivo silencing in chick neural tube for TrkC KF

    PMID:24034695 PMID:24097989

    Open questions at the time
    • Mechanism by which NELF-B recognizes and transports TrkC KF to mitochondria not structurally defined
    • Whether GR attenuation requires the intact NELF tetrameric complex or only NELF-B is unclear
    • Relationship between cytoplasmic apoptotic role and nuclear Pol II pausing function not addressed
  4. 2016 High

    Establishing a functional antagonism between BRCA1 and NELF-B in tissue development: conditional Cobra1 deletion blocked mammary gland morphogenesis and lactogenesis, and co-deletion of full-length Brca1 rescued these defects, demonstrating that BRCA1 counteracts NELF-B-dependent transcriptional control independently of DNA repair.

    Evidence Tissue-specific conditional knockout, double-KO genetic epistasis, transcriptional profiling in mouse mammary gland

    PMID:26941120

    Open questions at the time
    • Molecular mechanism by which BRCA1 antagonizes NELF-B-dependent pausing not identified
    • Whether this genetic interaction extends to non-mammary tissues not tested
  5. 2018 High

    Refining the BRCA1–NELF-B genetic interaction to require full-length BRCA1: separation-of-function mutations in BRCA1 RING or BRCT domains and Palb2 deletion all failed to rescue Cobra1 KO mammary defects, demonstrating specificity beyond BRCA1's known enzymatic activities.

    Evidence Conditional knockout with multiple separation-of-function alleles and Palb2 deletion in vivo

    PMID:29426838

    Open questions at the time
    • Which BRCA1 domain or activity mediates the antagonism remains unidentified
    • No biochemical reconstitution of BRCA1-mediated NELF eviction or pausing release
  6. 2023 High

    Solving the structural basis of the NELF core and uncoupling nuclear from cytoplasmic functions: the NELF-B/C/E crystal structure revealed inter-subunit interaction surfaces, while separation-of-function mutations demonstrated that cytoplasmic NELF-B promotes proliferation via PI3K/AKT independently of Pol II pausing.

    Evidence X-ray crystallography of NELF-B/C/E; separation-of-function mutants, Co-IP with PI3K/AKT, ectopic AKT rescue, Pol II ChIP

    PMID:37591184 PMID:37717699

    Open questions at the time
    • How cytoplasmic NELF-B activates PI3K/AKT at the molecular level is unknown
    • Whether NELF-B's cytoplasmic pool is regulated by signaling-dependent nuclear-cytoplasmic shuttling not addressed
    • Full tetrameric NELF complex structure (with NELF-A and RNA Pol II) not yet available
  7. 2025 High

    Extending NELF-B's developmental role to adipogenesis: conditional Nelfb deletion from preadipocytes abolished fat depot formation, and ChIP showed NELF-B maintains open chromatin and Pol II binding at Pparg, Cebpa, Krox20, and Stat3 promoters; Pparg re-expression or pharmacological activation rescued differentiation, placing NELF-B upstream of the master adipogenic regulator.

    Evidence Conditional knockout in preadipocyte lineage, ChIP for Pol II and chromatin accessibility, retroviral Pparg rescue, rosiglitazone treatment in vivo and in vitro

    PMID:40960263

    Open questions at the time
    • Whether NELF-B's role in adipogenesis is separable from the cytoplasmic PI3K/AKT function not tested
    • Genome-wide pausing landscape in preadipocytes not characterized

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key open questions include: the molecular mechanism by which BRCA1 antagonizes NELF-B–dependent pausing, how cytoplasmic NELF-B engages and activates PI3K/AKT, and whether the nuclear pausing and cytoplasmic signaling functions are coordinately regulated during development and disease.
  • No reconstituted biochemical system for BRCA1-mediated pausing release at NELF-B targets
  • Structural basis of cytoplasmic NELF-B–PI3K/AKT interaction unknown
  • Regulation of nuclear-cytoplasmic partitioning of NELF-B not characterized

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0098772 molecular function regulator activity 4 GO:0003677 DNA binding 2
Localization
GO:0005634 nucleus 4 GO:0005829 cytosol 2 GO:0005739 mitochondrion 1
Pathway
R-HSA-74160 Gene expression (Transcription) 4 R-HSA-1266738 Developmental Biology 3 R-HSA-162582 Signal Transduction 1 R-HSA-5357801 Programmed Cell Death 1
Partners
AKT1BRCA1FOSJUNNELF-ANELF-CNELF-ENTRK3
Complex memberships
NELF complex (NELF-A/B/C/E)

Evidence

Reading pass · 10 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2009 NELF-B (COBRA1) is a subunit of the four-subunit NELF complex that controls RNA polymerase II pausing in transcription; knockout of mouse NELF-B causes inner cell mass deficiency and embryonic lethality, and ChIP shows COBRA1 binds to the Lef1 promoter to modulate promoter-bound RNA polymerase abundance, preventing unscheduled expression of developmental genes in embryonic stem cells. Knockout mouse model, knockdown in mESCs, chromatin immunoprecipitation (ChIP) PloS one High 19340312
2004 COBRA1 physically interacts with BRCA1 in the nucleus of human breast cancer cells, as shown by co-immunoprecipitation of endogenous proteins, and localizes to the nucleus. Co-immunoprecipitation of endogenous proteins, immunofluorescence IUBMB life Medium 15185750
2004 COBRA1 inhibits AP-1 transcriptional activity in a dose-dependent manner by physically interacting with c-Jun and c-Fos; the middle region of COBRA1 binds c-Fos, and deletion of the c-Fos binding site abolishes COBRA1-mediated AP-1 inhibition. Transfection/overexpression, siRNA knockdown, reporter assay, co-immunoprecipitation, deletion mutagenesis Biochemical and biophysical research communications Medium 15530430
2013 NELF-B attenuates glucocorticoid receptor (GR)-mediated gene induction, reduces partial agonist activity, and increases agonist EC50; ChIP shows NELF-B diminishes GR recruitment to promoter regions; NELF-A and NELF-B each act independently as competitive decelerators after the site of GR action; a conserved motif in each subunit is required for full modulatory activity. Stable knockdown, ChIP, competition assay, mutagenesis of conserved motif The Journal of biological chemistry High 24097989
2013 The neurotrophin receptor TrkC killer fragment (TrkC KF) interacts with COBRA1 (NELF-B); COBRA1 shuttles TrkC KF to the mitochondria where it promotes Bax activation, cytochrome c release, and apoptosome-dependent apoptosis. Cobra1 silencing rescues neuroepithelial cell death caused by NT-3 silencing in chick neural tube. Co-immunoprecipitation, subcellular fractionation, in vivo silencing in chick neural tube, Bax/cytochrome c release assay Molecular cell High 24034695
2016 Tissue-specific deletion of Cobra1 in mouse mammary gland blocks ductal morphogenesis, alveologenesis, and lactogenesis; additional loss of full-length Brca1 largely rescues these defects and restores developmental transcription, demonstrating that BRCA1 antagonizes COBRA1-dependent transcription programme in a DNA repair-independent manner. Conditional (tissue-specific) knockout, genetic epistasis (double KO), transcriptional profiling Nature communications High 26941120
2018 The genetic interaction between Brca1 and Cobra1 in mammary gland development is domain-specific: separation-of-function mutations abrogating either BRCA1 RING E3 ligase activity or BRCT phospho-recognition fail to rescue Cobra1 KO mammary defects, and deletion of Palb2 does not rescue Cobra1 KO, placing the interaction specifically with full-length BRCA1. Conditional knockout, separation-of-function mutations, genetic epistasis Scientific reports High 29426838
2023 Crystal structure of the human NELF-B/C/E ternary complex was solved at high resolution, revealing detailed inter-subunit interaction surfaces and residues important for the association between NELF-B and NELF-E. X-ray crystallography Biochemical and biophysical research communications High 37591184
2023 Cytoplasmic NELFB supports cell proliferation independently of Pol II pausing: separation-of-function mutations that sequester NELFB in the cytoplasm decouple its role in cell proliferation from Pol II pausing. Cytoplasmic NELFB physically and functionally interacts with PI3K/AKT prosurvival kinases, and ectopic membrane-tethered PI3K/AKT partially bypasses the proliferative role of NELFB but not its effect on Pol II occupancy. Separation-of-function mutations, subcellular localization experiments, co-immunoprecipitation, AKT ectopic expression rescue, Pol II ChIP The Journal of biological chemistry High 37717699
2025 Nelfb deletion from preadipocyte lineages in mice causes failure of dermal white adipose tissue and other fat depot formation; Nelfb promotes open chromatin and stabilizes RNA Polymerase II binding at Pparg, Cebpa, Krox20, and Stat3 promoters; retroviral Pparg expression or rosiglitazone (Pparg agonist) treatment rescues adipocyte differentiation in Nelfb-depleted cells or mice, placing Nelfb upstream of Pparg in the adipogenic gene regulatory hierarchy. Conditional knockout, ChIP (Pol II, chromatin accessibility), retroviral rescue, pharmacological rescue (rosiglitazone) Development (Cambridge, England) High 40960263

Source papers

Stage 0 corpus · 16 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2009 Mouse cofactor of BRCA1 (Cobra1) is required for early embryogenesis. PloS one 52 19340312
2021 NSUN6, an RNA methyltransferase of 5-mC controls glioblastoma response to temozolomide (TMZ) via NELFB and RPS6KB2 interaction. Cancer biology & therapy 32 34705606
2016 Genetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development. Nature communications 22 26941120
2013 The dependence receptor TrkC triggers mitochondria-dependent apoptosis upon Cobra-1 recruitment. Molecular cell 20 24034695
2007 Concerted transcriptional regulation by BRCA1 and COBRA1 in breast cancer cells. International journal of biological sciences 16 18071589
2004 COBRA1 inhibits AP-1 transcriptional activity in transfected cells. Biochemical and biophysical research communications 12 15530430
2013 A conserved protein motif is required for full modulatory activity of negative elongation factor subunits NELF-A and NELF-B in modifying glucocorticoid receptor-regulated gene induction properties. The Journal of biological chemistry 11 24097989
2017 Knockdown of COBRA1 decreases the proliferation and migration of hepatocellular carcinoma cells. Oncology reports 9 28112367
2018 BRCA1 Interacting Protein COBRA1 Facilitates Adaptation to Castrate-Resistant Growth Conditions. International journal of molecular sciences 5 30036938
2004 Characterization of COBRA1 in human breast cancer cell lines using a new polyclonal antibody against COBRA1. IUBMB life 5 15185750
2025 Nelfb promotes dermal white adipose tissue formation through RNA polymerase II-mediated adipogenic gene regulation. Development (Cambridge, England) 4 40960263
2023 Structural basis of the human negative elongation factor NELF-B/C/E ternary complex. Biochemical and biophysical research communications 4 37591184
2018 Gene-Specific Genetic Complementation between Brca1 and Cobra1 During Mouse Mammary Gland Development. Scientific reports 4 29426838
2000 COBRA-1, a rationally-designed epoxy-THF containing compound with potent tubulin depolymerizing activity as a novel anticancer agent. Bioorganic & medicinal chemistry letters 4 10866379
2021 Role of NELF-B in supporting epithelial-mesenchymal transition and cell proliferation during hepatocellular carcinoma progression. Oncology letters 2 34539865
2023 An essential signaling function of cytoplasmic NELFB is independent of RNA polymerase II pausing. The Journal of biological chemistry 0 37717699