Affinage

LEO1

RNA polymerase-associated protein LEO1 · UniProt Q8WVC0

Round 2 corrected
Length
666 aa
Mass
75.4 kDa
Annotated
2026-04-28
42 papers in source corpus 15 papers cited in narrative 15 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

LEO1 is a core subunit of the evolutionarily conserved PAF1 complex (PAF1C) that associates with elongating RNA polymerase II and functions in transcription elongation through chromatin, co-transcriptional histone modification, and chromatin state maintenance. LEO1 directly binds nascent RNA to stabilize PAF1C at actively transcribed loci, promoting histone H2B monoubiquitination and downstream H3K4/H3K79 methylation, while also maintaining nucleosome turnover to prevent heterochromatin spreading into euchromatin (PMID:20732871, PMID:16307923, PMID:26518661). CDK12-mediated phosphorylation of LEO1 promotes PAF1C–Pol II association and processive elongation, whereas Integrator-PP2A (INTAC)-mediated dephosphorylation attenuates it, constituting a kinase–phosphatase switch that tunes transcription elongation (PMID:37205756). LEO1 also directly interacts with Cockayne syndrome protein B (CSB) and is required for CSB chromatin recruitment and efficient transcription-coupled nucleotide excision repair following UV or cisplatin damage (PMID:34096589).

Mechanistic history

Synthesis pass · year-by-year structured walk · 7 steps
  1. 1994 Medium

    Initial cloning of LEO1 in S. cerevisiae established it as a non-essential, constitutively expressed gene encoding a highly hydrophilic protein, but its molecular function remained unknown.

    Evidence Gene disruption, sequencing, and expression analysis in yeast

    PMID:8018723

    Open questions at the time
    • No function assigned — deletion had no obvious phenotype under standard conditions
    • No physical interactors or complex membership identified
  2. 2002 High

    Identification of Leo1 as a bona fide subunit of the yeast Paf1/RNA Pol II complex resolved its molecular context, showing it functions within a transcription-associated complex distinct from the Srb-Mediator.

    Evidence Tandem affinity purification, mass spectrometry, and genetic epistasis in yeast

    PMID:11884586

    Open questions at the time
    • Leo1-specific molecular activity within PAF1C undefined
    • Whether a human PAF1C containing LEO1 exists was not yet shown
  3. 2005 High

    Purification of a human PAF1 complex containing LEO1 that associates with multiple phosphorylated forms of RNA Pol II, together with demonstration that PAF1C is required for H2B monoubiquitination and subsequent H3K4/H3K79 methylation, established the co-transcriptional histone modification axis of the complex.

    Evidence Affinity purification with mass spectrometry, co-IP, in vitro ubiquitination assays, RNAi, and ChIP in human cells

    PMID:15632063 PMID:16307923

    Open questions at the time
    • LEO1's individual contribution to histone modification versus other PAF1C subunits not dissected
    • Mechanism by which PAF1C stimulates RNF20/40 activity not resolved
  4. 2010 High

    Three concurrent advances resolved distinct LEO1 functions: Leo1 directly binds nascent RNA to stabilize PAF1C at transcribed chromatin; reconstituted PAF1C facilitates Pol II elongation through chromatin cooperatively with TFIIS; and zebrafish Leo1 is essential for cardiac and neural crest development, requiring nuclear localization.

    Evidence In vitro RNA binding and RNA-IP in yeast; reconstituted chromatin transcription system with human PAF1C; forward genetic screen with phenotypic and localization analysis in zebrafish

    PMID:20178742 PMID:20178782 PMID:20732871

    Open questions at the time
    • RNA-binding domain of Leo1 not mapped to specific residues
    • Whether RNA binding is separable from chromatin elongation function not tested
    • Zebrafish cardiac phenotype not linked to a specific PAF1C biochemical activity
  5. 2015 High

    Demonstration that the Leo1–Paf1 subcomplex promotes nucleosome turnover to prevent heterochromatin spreading resolved how PAF1C maintains euchromatin–heterochromatin boundaries, independently of RNAi.

    Evidence ChIP-exo, random mutant library screen, and reporter silencing assay in fission yeast

    PMID:26518661

    Open questions at the time
    • Mechanism by which Leo1–Paf1 promotes histone turnover not biochemically defined
    • Whether this boundary-maintenance function is conserved in mammals not tested
  6. 2021 High

    Discovery that LEO1 directly binds CSB and is required for CSB chromatin recruitment and transcription-coupled DNA repair extended LEO1's role beyond transcription elongation into the DNA damage response.

    Evidence Yeast two-hybrid, recombinant protein binding, co-IP, fractionation, knockout/knockdown survival and repair assays in human cells

    PMID:34096589

    Open questions at the time
    • Whether LEO1–CSB interaction is regulated by LEO1 phosphorylation unknown
    • Structural basis of the LEO1(381–568)–CSB interface not resolved
  7. 2023 High

    Identification of LEO1 as a direct CDK12 substrate whose phosphorylation state is toggled by Integrator-PP2A revealed a kinase–phosphatase switch controlling PAF1C–Pol II association and processive transcription elongation.

    Evidence Chemical genetic CDK12 substrate screen, phosphoproteomics, alanine substitution mutagenesis, acute depletion, and elongation assays in human cells

    PMID:37205756

    Open questions at the time
    • Specific LEO1 phosphoresidues critical for Pol II binding not individually assigned
    • How INTAC is itself recruited to dephosphorylate LEO1 is unknown
    • Whether the CDK12–INTAC switch also modulates LEO1's RNA-binding or CSB-interaction functions not addressed

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key open questions include the structural basis for LEO1's RNA-binding and CSB-interaction surfaces, whether the CDK12/INTAC phosphorylation switch coordinately regulates LEO1's non-elongation functions (e.g., TC-NER, chromatin boundary maintenance), and the mechanism by which the Leo1–Paf1 subcomplex drives nucleosome turnover to prevent heterochromatin spreading.
  • No high-resolution structure of LEO1 in complex with RNA, CSB, or PAF1C available
  • Functional separation of LEO1's RNA-binding, CSB-binding, and phosphoregulatory activities not achieved
  • Conservation of the heterochromatin boundary function in mammals not tested

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140110 transcription regulator activity 3 GO:0003723 RNA binding 1
Localization
GO:0005694 chromosome 3 GO:0005634 nucleus 1
Pathway
R-HSA-4839726 Chromatin organization 3 R-HSA-74160 Gene expression (Transcription) 3 R-HSA-73894 DNA Repair 1
Partners
CDC73CDK12CSBCTR9INTS11PAF1
Complex memberships
PAF1 complex (PAF1C)

Evidence

Reading pass · 15 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1994 LEO1 encodes a non-essential, extremely hydrophilic protein of 53.9 kDa on S. cerevisiae chromosome XV; the gene is constitutively expressed at a low level and deletion mutants show no obvious phenotype. Gene disruption, nucleotide sequencing, expression analysis Biochimica et biophysica acta Medium 8018723
2002 Leo1 (along with Ctr9 and Rtf1) is a bona fide component of the yeast Paf1/RNA polymerase II complex, biochemically distinct from the Srb-mediator; deletion of LEO1 suppresses many paf1Δ phenotypes, suggesting Leo1 contributes to a functional Paf1 complex required for transcription. Tandem affinity purification, mass spectrometry, genetic epistasis (double mutant analysis) Molecular and cellular biology High 11884586
2005 A human counterpart of the yeast Paf1 complex was identified that includes a human Leo1 homolog along with hPaf1 and hCtr9; this complex associates with the nonphosphorylated, Ser2-phosphorylated, and Ser5-phosphorylated forms of RNA polymerase II, and parafibromin (hCdc73) can interact with a histone H3K4 methyltransferase complex. Affinity purification of cellular parafibromin, mass spectrometry, co-immunoprecipitation, immunofluorescence Molecular and cellular biology High 15632063
2005 The human PAF complex (containing Leo1 homolog) is required for H2B monoubiquitination at Lys120 in vivo; UbcH6 physically interacts with RNF20/40 and hPAF, and formation of a trimeric complex with hPAF stimulates H2B monoubiquitination activity in vitro, which subsequently promotes H3K4 and H3K79 methylation. In vitro ubiquitination assay, co-immunoprecipitation, RNAi knockdown, chromatin immunoprecipitation Molecular cell High 16307923
2006 Drosophila Hyrax and its human ortholog Parafibromin (components of the PAF1 complex together with Leo1) are required for Wnt/Wg target gene transcription and bind directly to the C-terminal region of beta-catenin/Armadillo, linking PAF1C (including Leo1) to Wnt signaling output. Genetic screen, co-immunoprecipitation, direct binding assay, epistasis analysis in Drosophila Cell High 16630820
2009 hPAF complex (containing human LEO1) is recruited to transcribed genes and is required for efficient H2B ubiquitylation; hPAF-mediated transcription is required for hBRE1-hRAD6 recruitment and subsequent H2B-K120 ubiquitylation, which directly stimulates hSET1-dependent H3K4 di- and trimethylation. Chromatin immunoprecipitation, co-immunoprecipitation, reconstituted in vitro transcription system, RNAi Cell High 19410543
2010 Leo1 in yeast binds RNA in vitro and is necessary for PAF1C association with RNA in vivo (RNA-IP); loss of Leo1 reduces PAF1C recruitment to transcribed genes and decreases histone H3 and H3K4me3 levels within transcribed chromatin, demonstrating that RNA binding by Leo1 stabilizes PAF1C at actively transcribed regions. RNA immunoprecipitation (RNA-IP), in vitro RNA binding assay, chromatin immunoprecipitation, gene deletion The Journal of biological chemistry High 20732871
2010 Human PAF1C (containing LEO1) has an intrinsic ability to facilitate chromatin transcription elongation in a biochemically defined reconstituted system; hPAF1C directly interacts with elongation factor SII/TFIIS and cooperatively binds RNA polymerase II to promote elongation through chromatin. Reconstituted in vitro chromatin transcription assay, co-immunoprecipitation, direct binding assay Cell High 20178742
2010 Zebrafish leo1 encodes a nuclear protein; a truncated Leo1(LA1186) mutant lacking a nuclear localization signal is mislocalized to the cytoplasm and causes defects in cardiomyocyte differentiation at the atrioventricular boundary and loss of neural crest cell populations (melanocytes, xanthophores, craniofacial cartilage, glial cells), establishing Leo1's nuclear function as essential for cardiac and neural crest development. Forward genetic screen, phenotypic analysis, localization studies (nuclear vs. cytoplasmic distribution of truncated protein), marker expression analysis Developmental biology Medium 20178782
2011 During human embryonic stem cell differentiation, the PAF1 transcriptional elongation complex (containing LEO1) is recruited to promoters of pluripotency genes OCT4 and NANOG; a specific interaction of DNA methyltransferases with PAF1C was detected during early differentiation, suggesting a mechanism for silencing of pluripotency genes. Quantitative proteomics, phosphoproteomics, co-immunoprecipitation, chromatin immunoprecipitation Science signaling Medium 21406692
2014 In acute myelogenous leukemia, LEO1 is transcriptionally upregulated by PRL-3 phosphatase through increased JMJD2C histone demethylase occupancy at the LEO1 promoter, reducing H3K9me3 repressive marks; elevated LEO1 in turn stabilizes the PAF complex and upregulates SOX2 and SOX4 oncogenes, mediating PRL-3's oncogenic phenotype. SILAC-based quantitative proteomics, ChIP, RNAi knockdown, stable overexpression, co-immunoprecipitation Cancer research Medium 24686170
2015 In fission yeast, the Leo1-Paf1 subcomplex of PAF1C is required to prevent heterochromatin spreading into euchromatin; deletion of Leo1 decreases nucleosome turnover at euchromatic regions, leading to stabilization of H3K9me2 heterochromatin marks at facultative heterochromatin loci in an RNAi-independent manner. ChIP-exo (high-resolution genome-wide), random mutant library screen, reporter gene silencing assay, gene deletion EMBO reports High 26518661
2017 Drosophila Leo1 (PAF1C component) physically interacts with Myc and helps recruit Myc to target gene promoters; since PAF1C associates with active genes, Leo1 contributes to Myc targeting to open chromatin promoters. Co-immunoprecipitation, chromatin immunoprecipitation, genetic interaction analysis Proceedings of the National Academy of Sciences of the United States of America Medium 29078288
2021 Human LEO1 directly interacts with Cockayne syndrome protein B (CSB) via the Phe381-Ser568 region of LEO1 and the C-terminal domain of CSB; both proteins are co-recruited to chromatin in a transcription-dependent manner following UV or cisplatin treatment; LEO1 knockdown/knockout reduces CSB chromatin recruitment, increases UV/cisplatin sensitivity, impairs RNA synthesis recovery, and slows repair of cyclobutane pyrimidine dimers, establishing LEO1 as a partner of CSB in transcription-coupled DNA repair. Yeast two-hybrid, in vitro direct binding with recombinant proteins, co-immunoprecipitation, cell fractionation, fluorescence imaging of DNA damage recruitment, knockdown/knockout phenotypic analysis (survival, RNA synthesis recovery, CPD repair assay) Nucleic acids research High 34096589
2023 Human LEO1 is a direct cellular substrate of CDK12 kinase; CDK12 phosphorylates LEO1, and acute depletion of LEO1 or substitution of its phosphorylation sites with alanine attenuates PAF1C association with elongating RNA polymerase II and impairs processive transcription elongation. Additionally, LEO1 interacts with and is dephosphorylated by the Integrator-PP2A complex (INTAC), and INTAC depletion promotes PAF1C-Pol II association, revealing a kinase/phosphatase switch regulating LEO1 phosphorylation status and PAF1C function. Chemical genetic CDK12 substrate screening, phosphoproteomics, alanine substitution mutagenesis, acute protein depletion, co-immunoprecipitation, ChIP/elongation assays Science advances High 37205756

Source papers

Stage 0 corpus · 42 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2006 Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2861 17081983
2014 Synaptic, transcriptional and chromatin genes disrupted in autism. Nature 2092 25363760
2002 Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America 1479 12477932
2006 A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nature biotechnology 1336 16964243
2004 Large-scale characterization of HeLa cell nuclear phosphoproteins. Proceedings of the National Academy of Sciences of the United States of America 1159 15302935
2017 Prevalence and architecture of de novo mutations in developmental disorders. Nature 1121 28135719
2015 The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 1118 26186194
2017 Architecture of the human interactome defines protein communities and disease networks. Nature 1085 28514442
2015 A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 1015 26496610
2014 A proteome-scale map of the human interactome network. Cell 977 25416956
2020 A reference map of the human binary protein interactome. Nature 849 32296183
2003 Complete sequencing and characterization of 21,243 full-length human cDNAs. Nature genetics 754 14702039
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2012 A census of human soluble protein complexes. Cell 689 22939629
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2018 High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies. Molecular cell 580 29395067
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2022 OpenCell: Endogenous tagging for the cartography of human cellular organization. Science (New York, N.Y.) 432 35271311
2009 RAD6-Mediated transcription-coupled H2B ubiquitylation directly stimulates H3K4 methylation in human cells. Cell 426 19410543
2015 Panorama of ancient metazoan macromolecular complexes. Nature 407 26344197
2005 Monoubiquitination of human histone H2B: the factors involved and their roles in HOX gene regulation. Molecular cell 400 16307923
2011 System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. Science signaling 382 21406692
2007 Functional specialization of beta-arrestin interactions revealed by proteomic analysis. Proceedings of the National Academy of Sciences of the United States of America 360 17620599
2021 A proximity-dependent biotinylation map of a human cell. Nature 339 34079125
2012 A high-throughput approach for measuring temporal changes in the interactome. Nature methods 273 22863883
2006 Parafibromin/Hyrax activates Wnt/Wg target gene transcription by direct association with beta-catenin/Armadillo. Cell 258 16630820
2005 The parafibromin tumor suppressor protein is part of a human Paf1 complex. Molecular and cellular biology 228 15632063
2018 Mapping the Genetic Landscape of Human Cells. Cell 225 30033366
2010 The human PAF1 complex acts in chromatin transcription elongation both independently and cooperatively with SII/TFIIS. Cell 222 20178742
2017 Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification. Nature communications 221 28524877
2002 Ctr9, Rtf1, and Leo1 are components of the Paf1/RNA polymerase II complex. Molecular and cellular biology 204 11884586
2015 The Paf1 complex factors Leo1 and Paf1 promote local histone turnover to modulate chromatin states in fission yeast. EMBO reports 68 26518661
2010 The PAF1 complex component Leo1 is essential for cardiac and neural crest development in zebrafish. Developmental biology 49 20178782
2010 Leo1 subunit of the yeast paf1 complex binds RNA and contributes to complex recruitment. The Journal of biological chemistry 39 20732871
2017 PAF1 complex component Leo1 helps recruit Drosophila Myc to promoters. Proceedings of the National Academy of Sciences of the United States of America 28 29078288
2014 LEO1 is regulated by PRL-3 and mediates its oncogenic properties in acute myelogenous leukemia. Cancer research 28 24686170
2023 CDK12 and Integrator-PP2A complex modulates LEO1 phosphorylation for processive transcription elongation. Science advances 23 37205756
2010 Integrated genomic profiling identifies candidate genes implicated in glioma-genesis and a novel LEO1-SLC12A1 fusion gene. Genes, chromosomes & cancer 22 20196086
2005 Expression of the Leo1-like domain of replicative senescence down-regulated Leo1-like (RDL) protein promotes senescence of 2BS fibroblasts. FASEB journal : official publication of the Federation of American Societies for Experimental Biology 17 15791002
2021 LEO1 is a partner for Cockayne syndrome protein B (CSB) in response to transcription-blocking DNA damage. Nucleic acids research 16 34096589
1994 The gene LEO1 on yeast chromosome XV encodes a non-essential, extremely hydrophilic protein. Biochimica et biophysica acta 14 8018723
2025 LEO1 haploinsufficiency is associated with developmental delays and autism spectrum disorder. Journal of human genetics 0 40993282