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Cited by 126Kruppel-like factors researchDevelopmental Biology and Gene RegulationGenomics and Phylogenetic Studies

KLF/SP Transcription Factor Family Evolution: Expansion, Diversification, and Innovation in Eukaryotes

Open access
Presnell, Jason S., Schnitzler, Christine E., Browne, William E·2015·Genome Biology and Evolution
DOI 10.1093/gbe/evv141PMC PMC4558859
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Abstract

The Krüppel-like factor and specificity protein (KLF/SP) genes play key roles in critical biological processes including stem cell maintenance, cell proliferation, embryonic development, tissue differentiation, and metabolism and their dysregulation has been implicated in a number of human diseases and cancers. Although many KLF/SP genes have been characterized in a handful of bilaterian lineages, little is known about the KLF/SP gene family in nonbilaterians and virtually nothing is known outside the metazoans. Here, we analyze and discuss the origins and evolutionary history of the KLF/SP transcription factor family and associated transactivation/repression domains. We have identified and characterized the complete KLF/SP gene complement from the genomes of 48 species spanning the Eukarya. We have also examined the phylogenetic distribution of transactivation/repression domains associated with this gene family. We report that the origin of the KLF/SP gene family predates the divergence of the Metazoa. Furthermore, the expansion of the KLF/SP gene family is paralleled by diversification of transactivation domains via both acquisitions of pre-existing ancient domains as well as by the appearance of novel domains exclusive to this gene family and is strongly associated with the expansion of cell type complexity.

AI snapshot

Written from the paper’s full text.

TL;DR

The KLF/SP transcription factor family originated before the divergence of Metazoa, with bona fide KLF genes first appearing in the filasterean *Capsaspora* and the SP subfamily arising later in the metazoan stem lineage. Its expansion across eukaryotes involved gene duplication, domain shuffling, and rare de novo domain innovation, paralleling increased metazoan cell-type complexity.

Key findings

  • The KLF-DBD appears in the opisthokont stem lineage prior to the divergence of Holomycota, but bona fide KLF/SP orthologs were defined as containing only three zinc fingers and a canonical aspartic acid at position 44 (D44); 397 putative filozoan KLF/SP sequences had D44, while 13 nonfilozoan KLF-DBD sequences lacked it and had additional zinc fingers.
  • KLF genes first appear in the filasterean *Capsaspora*, whereas the SP subfamily is restricted to metazoans and is absent from ctenophores; the SP box motif appears coincident with the SP subfamily in poriferans.
  • Nonbilaterian metazoans, protostomes, and invertebrate deuterostomes have 6–12 KLF/SP genes; vertebrates average 24, teleosts average 33, cartilaginous fishes 22, and tetrapods 25.
  • Ancient domains (Btd box, PVDLS, R3, SID) are present in other eukaryotic genes and were shuffled into KLF/SPs, while the R2 domain is a de novo innovation restricted to vertebrate KLF10/11 genes and the SP box is a metazoan-specific de novo domain.

Methods

  • Searched 48 eukaryotic genomes—26 metazoans, 4 unicellular holozoans, 7 holomycotans, 1 apusozoan, 4 amoebozoans, and 6 bikonts—using HMMER 3.0 with the Pfam PF00096 C2H2 zinc finger HMM, followed by custom Perl scripts for the 81-amino-acid KLF-DBD and manual extension of partial gene models.
  • Identified transactivation/repression domains (Btd box, SP box, SID, PVDLS, R2, R3, 9aaTAD) and low-complexity regions (LCRs) using custom Perl models, a 9aaTAD prediction tool, and four LCR methods (CAST, ScanProsite, SEG, manual curation), then searched whole genomes and built domain co-occurrence networks.
  • Performed phylogenetic analysis on concatenated KLF-DBD plus transactivation/repression domains (excluding 9aaTAD and LCRs; aligned sequences 81–112 amino acids) using MUSCLE, ProtTest-selected LG+I+G, RAxML with 300 ML searches and 100 bootstrap replicates, and MrBayes with two 5-million-generation runs and 25% burn-in.

Limitations

  • The paper states that composite co-occurrence networks are additive and do not compensate for missing data due to poor genome annotations; it also notes that the lamprey genome was derived from somatic tissue and may underrepresent the true *Petromyzon marinus* KLF/SP complement.
  • The paper reports only moderate support for deeper nodes (e.g., BPP = 0.84) and an average standard deviation of split frequencies of 0.048635 in Bayesian runs, which is acceptable but above the strong-convergence threshold of 0.01.
  • Evident from the text: taxon sampling used one or few representatives per lineage, domain and LCR predictions rely on motif models without experimental validation, and the inference that SP genes arose after ctenophore divergence depends on an early-diverging ctenophore phylogeny; an alternate metazoan topology would imply SP origin before poriferans followed by ctenophore loss.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1093/gbe/evv141

Cites

139 of 139 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 62 cited sources checked · 0 supported · 0 flagged

  • Findingnone given

    A number of transactivation/repression domains found in KLF/SPs are also present in the genomes of ancient unicellular lineages that lack KLF/SPs.

    “A number of transactivation/repression domains found in KLF/SPs are also present in the genomes of ancient unicellular lineages that lack KLF/SPs”
    Quote in the paperSubstantial claim
  • Findingown data

    Phylogenetic analyses recover a moderately supported clade that represents the 397 filozoan genes possessing the canonical D44 aspartic acid residue in the second zinc finger of the KLF-DBD, to the exclusion of the remaining 13 nonfilozoan sequences, along with MleKLFX.

    “Our phylogenetic analyses consistently recover a moderately supported clade that represents the 397 filozoan genes possessing the canonical D44 aspartic acid residue in the second zinc finger of the KLF-DBD to the exclusion of the remaining 13 nonfilozoan sequences, along with MleKLFX (fig. 2).”
    Quote in the paperSubstantial claim
  • Findingown data

    The KLF-DBD was not present in any of the bikont genomes searched.

    “However, the KLF-DBD was not present in any of the bikont genomes searched (fig. 1).”
    Quote in the paperSubstantial claim
  • Findingown data

    The Btd box model identified all 9 human SP sequences.

    “For example, the search with the Btd box model identified all 9 human SP sequences.”
    Quote in the paperSubstantial claim
  • Findingown data

    The SP box domain motif first appears coincident with the SP subfamily in poriferans.

    “This domain motif first appears coincident with the SP subfamily in poriferans.”
    Quote in the paperNot a substantial claim
  • May combine two claims. 44
  • Classified as probably not a substantial claim. 35
  • The quote only partly states this claim. 1

  • May combine two claims.

    Findingown data

    In our analyses, KLF genes first appear in the filasterean Capsaspora while the SP subfamily first appears near the base of the metazoan lineage in sponges and is absent from ctenophores.

    “Thus in our analyses KLF genes first appear in the filasterean Capsaspora while the SP subfamily first appears near the base of the metazoan lineage in sponges and is absent from ctenophores (fig. 1).”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: The amorphean bikont split occurred at or near the origin of the Eukarya.

  • May combine two claims.

    Findingown data

    The D44 residue is absent from all nonfilozoan KLF-DBD motifs and the ctenophore sequence MleKLFX.

    “and is notably absent from all nonfilozoan KLF-DBD motifs and the ctenophore sequence MleKLFX”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Neither representative ctenophore, Mnemiopsis or Pleurobrachia, show evidence for SP genes and both have fewer KLF genes as compared with other nonbilaterian metazoans.

    “However, neither representative ctenophore, Mnemiopsis or Pleurobrachia, show evidence for SP genes and both have fewer KLF genes as compared with other nonbilaterian metazoans.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The SP box is present in one out of two SP genes in Oscarella but is not detected in the two SP genes identified in the Amphimedon genome.

    “The SP box is present in one out of two SP genes in Oscarella but is not detected in the two SP genes identified in the Amphimedon genome.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Both Btd and SP box motifs are absent in unicellular KLFs, absent in both ctenophore KLFs, but present in all other metazoan phyla.

    “Both Btd and SP box motifs are absent in unicellular KLFs, absent in both ctenophore KLFs, but present in all other metazoan phyla (fig. 3).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Uniquely within the poriferans, the SP box was not found in any Amphimedon KLF/SP, but was identified in Oscarella KLF/SPs.

    “Uniquely within the poriferans, the SP box was not found in any Amphimedon KLF/SP, but was identified in Oscarella KLF/SPs.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The total complement of KLF/SP genes substantially increases within the jawed vertebrates, and teleosts have an average of 33 KLF/SPs, which is slightly higher than cartilaginous fishes (22) and tetrapods (25).

    “The total complement of KLF/SP genes substantially increases within the jawed vertebrates (fig. 1) and teleosts have an average of 33 KLF/SPs, which is slightly higher than cartilaginous fishes (22) and tetrapods (25).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    S/T-rich LCR regions occur most frequently and are found in at least one KLF/SP family member in all filozoan taxa except the poriferan Oscarella.

    “S/T-rich LCR regions occur most frequently and are found in at least one KLF/SP family member in all filozoan taxa except the poriferan Oscarella (fig. 3).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    P-rich LCR regions have lower representation among KLF/SPs, and are found in all filozoans except for Ciona, Daphnia, Tribolium, Lottia, Trichoplax, Oscarella, and Monosiga.

    “P-rich LCR regions have lower representation among KLF/SPs, and are found in all filozoans except for Ciona, Daphnia, Tribolium, Lottia, Trichoplax, Oscarella, and Monosiga (fig. 3).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingcitation

    Several nonrandom LCRs implicated in transactivation/repression that are highly biased for a particular amino acid residue were identified.

    “We also identified several nonrandom LCRs implicated in transactivation/repression that are highly biased for a particular amino acid residue (Wootton and Federhen 1993).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Wootton and Federhen 1993

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    Our phylogenetic analyses recovered a KLF 1/2/4 clade including invertebrate bilaterians (BPP = 0.96), a teleost-specific KLF1 clade (BPP = 1), and a mammalian KLF1 clade (BPP = 1).

    “Our phylogenetic analyses recovered a KLF 1/2/4 clade including invertebrate bilaterians (BPP = 0.96), a teleost-specific KLF1 clade (BPP = 1), and a mammalian KLF1 clade (BPP = 1; fig. 2).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Although the S/T- and Q-rich LCR organization superficially resembles the architecture found among SP1-4 genes, these unicellular KLFs lack the characteristic Btd box and SP box motifs that define the SPs.

    “Although the S/T- and Q-rich LCR organization superficially resembles the architecture found among SP1–4 genes, these unicellular KLFs lack the characteristic Btd box and SP box motifs that define the SPs.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The overall topologies of the ML and Bayesian trees share significant overlap, albeit with only moderate support for deeper nodes, for example, BPP = 0.84.

    “The overall topologies of the ML and Bayesian trees share significant overlap, albeit with only moderate support for deeper nodes, for example, BPP = 0.84 (fig. 2).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The single Monosiga KLF gene superficially consists of a KLF6/7 domain architecture; however, phylogenetically this sequence groups with other unicellular KLFs.

    “The single Monosiga KLF gene superficially consists of a KLF6/7 domain architecture; however, phylogenetically this sequence groups with other unicellular KLFs.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Although a single unicellular KLF clade composed of CowKLFa, SroKLFa, and MbrKLFa branch sister to a highly supported cnidarian + bilaterian KLF15 clade (BPP = 0.99), the remaining unicellular KLF sequences are divergent and characterized by long branches.

    “Although a single unicellular KLF clade composed of CowKLFa, SroKLFa, and MbrKLFa branch sister to a highly supported cnidarian + bilaterian KLF15 clade (BPP = 0.99), the remaining unicellular KLF sequences are divergent and characterized by long branches (fig. 2; supplementary figs. S2 and S3, Supplementary Material online).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Our search revealed the presence of an R3 domain in all representative eukaryotic genomes, while the R2 domain was restricted to vertebrate KLF10/11 genes.

    “Our search revealed the presence of an R3 domain in all representative eukaryotic genomes, while the R2 domain was restricted to vertebrate KLF10/11 genes (Supplementary Material online).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    None of the transactivation/repression domains considered in this study were found in the nonfilozoan KLF-DBD containing sequences, despite several relevant domains being well represented in all eukaryotic genomes examined.

    “Furthermore, none of the transactivation/repression domains considered in this study were found in the nonfilozoan KLF-DBD containing sequences, despite several relevant domains being well represented in all eukaryotic genomes examined (fig. 6, Supplementary Material online).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    According to domain architecture, this class is found in all the jawed vertebrates and in the Endopterygota as represented in this study by Drosophila.

    “According to domain architecture, this class is found in all the jawed vertebrates and in the Endopterygota as represented in this study by Drosophila (fig. 5).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Within metazoans, there appears to be a gradient of network complexity; the nonbilaterian network is less complex than the invertebrate bilaterian network, and both of these are less complex than the vertebrate network.

    “Within metazoans, there appears to be a gradient of network complexity; the nonbilaterian network (fig. 4D) is less complex than the invertebrate bilaterian network (fig. 4E), and both of these are less complex than the vertebrate network (fig. 4F).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    All nonfilozoan KLF-DBD containing genes lacked this diagnostic residue and possess additional zinc fingers.

    “All nonfilozoan KLF-DBD containing genes lacked this diagnostic residue and possess additional zinc fingers.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The association of the PVDLS motif with KLF genes was not detected in other Drosophilid species, but was identified in two hymenopterans Apis millifera and Nasonia vitripennis.

    “Curiously, the association of this motif with KLF genes was not detected in other Drosophilid species, but was identified in two hymenopterans Apis millifera and Nasonia vitripennis (data not shown).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The Ctenophoran network is composed of only S/T-rich and P-rich LCRs, with the P-rich LCRs + KLF-DBD domain pair occurring at greater frequency.

    “For example, the Ctenophoran network (fig. 4G), in contrast to both the Poriferan network (fig. 4H) and larger nonbilaterian composite network (fig. 4D), is composed of only S/T-rich and P-rich LCRs, with the P-rich LCRs + KLF-DBD domain pair occurring at greater frequency.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Our exhaustive search uncovered no R2 domains in any invertebrate genome or outside of the KLF10/11 genes within the vertebrate genomes in this study.

    “Our exhaustive search uncovered no R2 domains in any invertebrate genome or outside of the KLF10/11 genes within the vertebrate genomes in this study.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The R3 domain is present in all eukaryote genomes but there is no evidence for it being shuffled into KLFs until much later than the SID motif.

    “Interestingly, the R3 domain is present in all eukaryote genomes but there is no evidence for it being shuffled into KLFs until much later than the SID motif (fig. 6).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The SP subfamily appears early in metazoan evolution in the Poriferan lineage, coincident with the appearance of the SP box motif.

    “The SP subfamily appears early in metazoan evolution in the Poriferan lineage (fig. 1) coincident with the appearance of the SP box motif (fig. 3).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingnone given

    The Btd box is found in SPs and together with the KLF-DBD represents the defining characteristic of the SP subfamily.

    “The Btd box is found in SPs and along with the KLF-DBD represents the defining characteristic of the SP subfamily.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    These four ancient domains first appear in differential combinations with the KLF-DBD in KLF/SP genes after the divergence of the metazoans and correlate strongly with the observed expansion of domain architecture repertoires.

    “These four ancient domains first appear in differential combinations with the KLF-DBD in KLF/SP genes after the divergence of the metazoans and correlate strongly with the observed expansion of domain architecture repertoires (fig. 5).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In our study, we recovered two SPs in sponges, two SP genes in Trichoplax, and four SP genes in Nematostella.

    “In our study, we recovered two SPs in sponges, two SP genes in Trichoplax, and four SP genes in Nematostella.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In our study, KLF genes first appear in the filasterian Capsaspora, while the SP subfamily is restricted to metazoans, notably excluding the ctenophores.

    “In our study, KLF genes first appear in the filasterian Capsaspora, while the SP subfamily is restricted to metazoans, notably excluding the ctenophores.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingnone given

    The second zinc finger of the btd gene is only 21 amino acids long, lacking 2 residues between the 2 C residues, and differs slightly from the corresponding zinc finger in the KLF-DBD.

    “However, the second zinc finger of the btd gene is slightly different than the corresponding zinc finger in the KLF-DBD. The second zinc finger of btd is only 21 amino acids long, lacking 2 residues between the 2 C residues.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In our analyses, the PVDLS domain appears in vertebrate KLFs defining the 3/8/12 architecture group and in a lone Drosophila KLF (CG42741).

    “In our analyses, the PVDLS domain appears in vertebrate KLFs defining the 3/8/12 architecture group and in a lone Drosophila KLF (CG42741).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    A more recent study focused on the phylogenetic distribution of C2H2 zinc finger families in eukaryotes showed that KLFs were present in Monosiga but absent in the fungal taxa surveyed.

    “A more recent study, focused on the phylogenetic distribution of C2H2 zinc finger families in eukaryotes, also showed that KLFs were present in Monosiga but absent in the fungal taxa surveyed (Seetharam and Stuart 2013).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Seetharam and Stuart 2013

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    A KLF gene was recently identified in the choanoflagellate Monosiga brevicollis genome, but that study's conclusions were restricted to examining porcine KLF paralogy.

    “A KLF gene was recently identified in the choanoflagellate Monosiga brevicollis genome; however, that study’s conclusions were restricted to examining porcine KLF paralogy (Chen et al. 2009).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Chen et al. 2009 source

      Not checked in the free run.

  • The quote only partly states this claim.

    Interpretationown data

    The expansion of the KLF/SP gene family is paralleled by diversification of transactivation domains via acquisitions of pre-existing ancient domains.

    “the expansion of the KLF/SP gene family is paralleled by diversification of transactivation domains via both acquisitions of pre-existing ancient domains as well as by the appearance of novel domains exclusive to this gene family”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The more N-terminal regions of KLF/SP transcription factors are typically highly variable and consist of different combinations of transactivation/repression domains.

  • May combine two claims.

    Premisecitation

    The KLF/SP transcription factor gene family is characterized by a highly conserved triple-C2H2 DNA-binding domain located toward the C-terminus, composed of three tandem zinc fingers evenly spaced by conserved linker regions, and shares similarity with the Drosophila Krüppel gene.

    “The Krüppel-like factor and specificity protein (KLF/SP) transcription factor gene family is characterized by a highly conserved triple-C2H2 DBD located toward the C-terminus composed of three tandem zinc fingers that are evenly spaced by conserved linker regions (Iuchi 2001) and share similarity with the Drosophila Krüppel gene (Rosenberg et al. 1986).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Iuchi 2001

      Not checked in the free run.

    • cites Rosenberg et al. 1986

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Historically, mammalian KLFs have been divided into 3 groups based on shared domain architecture: the KLF1, 2, 4, 5, 6, and 7 groups; the KLF3, 8, and 12 groups; and the KLF9, 10, 11, 13, 14, 16 groups.

    “Historically, mammalian KLFs have been divided into 3 groups based on shared domain architecture: The KLF1, 2, 4, 5, 6, and 7 groups; the KLF3, 8, and 12 groups; and the KLF9, 10, 11, 13, 14, 16 groups (McConnell and Yang 2010)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites McConnell and Yang 2010

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    SPs differ from KLFs by the presence of the Buttonhead (Btd) box domain just 5′ of the KLF-DBD and are typically divided into 2 groups: SP1-4 and SP5-9.

    “whereas SPs, which differ from KLFs by the presence of the Buttonhead (Btd) box domain just 5′ of the KLF-DBD, are typically divided into 2 groups: SP1–4 and SP5–9 (Suske et al. 2005).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Suske et al. 2005

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    The high stringency D44 KLF-DBD model is specific and sensitive.

    “Therefore the high stringency D44 KLF-DBD model is specific and sensitive.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The Btd box was first identified in the Drosophila gene buttonhead.

    “The Btd box was first identified in the Drosophila gene buttonhead (Wimmer et al. 1993)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Wimmer et al. 1993

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    The average standard deviation of split frequencies between the two Bayesian runs was 0.048635.

    “The “average standard deviation of split frequencies” between the two runs was 0.048635.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    We required a putative LCR to be detected by a minimum of two methods for annotation as an LCR.

    “We further required a putative LCR to be detected by a minimum of two methods for annotation as an LCR.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    LCRs are typically c-LCRs located centrally within the protein.

    “and are typically c-LCRs located centrally within the protein (Coletta et al. 2010)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Coletta et al. 2010

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Q-rich regions are known to interact with TAFII110 to activate transcription.

    “Q-rich regions, which are more frequently found among members of the SP subgroup, are known to interact with TAFII110 to activate transcription (Hoey et al. 1993; Gill et al. 1994).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Hoey et al. 1993

      Not checked in the free run.

    • cites Gill et al. 1994

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    The Sin3a protein acts as a transcriptional repressor, and is able to recruit and bind histone deacetylases.

    “The Sin3a protein acts as a transcriptional repressor, and is able to recruit and bind histone deacetylases (Laherty et al. 1997; Silverstein and Ekwall 2005).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Laherty et al. 1997

      Not checked in the free run.

    • cites Silverstein and Ekwall 2005

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    P-rich regions have been associated with transcriptional repression.

    “whereas P-rich regions have been associated with transcriptional repression (Hanna-Rose and Hansen 1996)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Hanna-Rose and Hansen 1996

      Not checked in the free run.

  • May combine two claims.

    Study design and conductown data

    The transactivation/repression domain models are both specific and sensitive enough to capture the intended domains.

    “Thus, our models are both specific and sensitive enough to capture the intended domains.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    The WT1 gene contains an extra zinc finger and is phylogenetically distinct.

    “The WT1 gene contains an extra zinc finger and is phylogenetically distinct (Shimeld 2008).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Shimeld 2008

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    LCRs are nonrandom regions of protein sequences that are highly biased for a particular amino acid residue.

    “LCRs are nonrandom regions of protein sequences that are highly biased for a particular amino acid residue (Wootton and Federhen 1993).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Wootton and Federhen 1993

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The SP box was subsequently discovered in SP5.

    “and the associated SP box was subsequently discovered in SP5 (Harrison et al. 2000)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Harrison et al. 2000

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The 9aaTAD has been shown to interact with TAF9 of the RNA polymerase II holoenzyme.

    “The 9aaTAD has been shown to interact with TAF9 of the RNA polymerase II holoenzyme and this domain motif has been identified in many transcription factors (Piskacek 2009).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Piskacek 2009

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    There is evidence suggesting that the Btd box is involved in transactivation.

    “Although not definitive, there is evidence suggesting that the Btd box is involved in transactivation (Athanikar et al. 1997).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Athanikar et al. 1997 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The 9aaTAD is a short motif highly conserved throughout eukaryotes.

    “The 9aaTAD, first identified in yeast transcription factors (Piskacek et al. 2007), is a short motif highly conserved throughout eukaryotes.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Piskacek et al. 2007

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductcitation

    A 25% burn-in was confirmed as adequate with Tracer v1.6.

    “25% burn-in was confirmed as adequate with Tracer v1.6; Rambaut and Drummond 2007”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Rambaut and Drummond 2007

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    S/T-rich regions are generally associated with enhanced transcriptional activation.

    “S/T-rich regions are generally associated with enhanced transcriptional activation, whereas P-rich regions have been associated with transcriptional repression (Hanna-Rose and Hansen 1996).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Hanna-Rose and Hansen 1996

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    LCRs are commonly found in transcription factors.

    “LCRs are commonly found in transcription factors (Faux et al. 2005)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Faux et al. 2005

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The 9aaTAD motif has been identified in many transcription factors.

    “and this domain motif has been identified in many transcription factors (Piskacek 2009)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Piskacek 2009

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    A putative low-complexity region (LCR) was assigned if it was identified in at least two of the four methods (CAST, ScanProsite, SEG, and manual curation).

    “A putative LCR was assigned if it was identified in at least two of the four methods (supplementary table S2, Supplementary Material online).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    LCRs have been shown to influence transcriptional regulation.

    “have been shown to influence transcriptional regulation (Gerber et al. 1994)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Gerber et al. 1994

      Not checked in the free run.

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductown data

    The Bayesian runs reached stationarity, and adjusting the burn-in did not affect the topology of the tree.

    “The runs reached stationarity, and adjusting the burn-in did not affect the topology of the tree.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductcitation

    ProtTest v2.4 determined the LG+I+G model as the best-fit model for protein evolution.

    “ProtTest v2.4 was used to determine the LG+I+G model as the best-fit model for protein evolution (Abascal et al. 2005).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Abascal et al. 2005

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Interpretationreasoning

    Therefore, we created a unicellular specific KLF architecture class.

    “Therefore, we created a unicellular specific KLF architecture class (fig. 5).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    C2H2 zinc finger domains are ubiquitous across a wide range of eukaryotes.

    “Although C2H2 zinc finger domains are ubiquitous across a wide range of eukaryotes (de Mendoza et al. 2013), the KLF-DBD first appears in the Holomycota (figs. 1 and 6).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites de Mendoza et al. 2013

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Premisecitation

    Historically, the single criteria for defining the KLF/SP gene family has been the presence of a highly conserved KLF-DBD composed of three C2H2 zinc fingers each separated by a seven amino acid linker region.

    “Historically, the single criteria for defining the KLF/SP gene family has been the presence of a highly conserved KLF-DBD composed of three C2H2 zinc fingers each separated by a seven amino acid linker region (McConnell and Yang 2010).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites McConnell and Yang 2010

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductreasoning

    The 9aaTAD was not used in determining domain architecture as it does not contribute to any unique domain combination.

    “The 9aaTAD was not used in determining domain architecture as it does not contribute to any unique domain combination.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The relationship of Ctenophora and Porifera to other metazoans shown in figure 4J and K are based on recent hypotheses of metazoan phylogeny.

    “The relationship of Ctenophora and Porifera to other metazoans shown in figure 4J and K are based on recent hypotheses of metazoan phylogeny (Dunn et al. 2008; Ryan et al. 2013).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Dunn et al. 2008

      Not checked in the free run.

    • cites Ryan et al. 2013

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductreasoning

    The composite networks are additive and thus do not compensate for missing data due to poor genome annotations.

    “The composite networks are additive and thus do not compensate for missing data due to poor genome annotations.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Domain architectures have been described for mammalian KLF/SP genes.

    “Domain architectures have been described for mammalian KLF/SP genes (Kaczynski et al. 2003; Suske et al. 2005; McConnell and Yang 2010; Archer 2011).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Kaczynski et al. 2003

      Not checked in the free run.

    • cites Suske et al. 2005

      Not checked in the free run.

    • cites McConnell and Yang 2010

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    We primarily focused on overlapping nodes with BPP ≥ 0.90.

    “We primarily focused on overlapping nodes with BPP ≥ 0.90.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    We infer that KLF16 arose by a tandem duplication of one of the two ancestral KLF9/13 genes in the mammalian stem lineage, followed by KLF14 evolution by RTE of KLF16.

    “Thus, we infer that KLF16 arose by a tandem duplication of one of the two ancestral KLF9/13 genes in the mammalian stem lineage followed by KLF14 evolution by RTE of KLF16 (supplementary fig. S5, Supplementary Material online).”
    Quote in the paperSubstantial claim
    • Rests on an assumption: In mammals, KLF14 and KLF16 are present.

  • May combine two claims.

    Interpretationown data

    A putative ancestral KLF3/8/12 gene most likely evolved early in the vertebrate stem lineage, whereas the PVDLS motif was likely also convergently acquired in the hexapod lineage leading to the Endopterygota.

    “Based on these additional results, we infer that a putative ancestral KLF3/8/12 gene most likely evolved early in the vertebrate stem lineage, whereas the PVDLS motif was likely also convergently acquired in the hexapod lineage leading to the Endopterygota.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    Variability, expansion, and extinction of LCRs have been associated with gene conversion due to mismatch repair of DNA heteroduplexes and higher rates of recombination relative to flanking sequences due to unequal crossing over and replication slippage.

    “Variability, expansion, and extinction of LCRs have been associated with gene conversion due to mismatch repair of DNA heteroduplexes (Radding 1982) and higher rates of recombination relative to flanking sequences due to unequal crossing over and replication slippage (DePristo et al. 2006).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Radding 1982

      Not checked in the free run.

    • cites DePristo et al. 2006

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    Thus we infer the origin of KLF genes in the filozoan stem lineage and a later origin of the SP genes after the divergence of the metazoan lineage.

    “Thus we infer the origin of KLF genes in the filozoan stem lineage and a later origin of the SP genes after the divergence of the metazoan lineage (figs. 1 and 6).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Our analyses suggest an ancestral complement of a single SP1-4 ortholog and a single SP5-9 ortholog in the early metazoan stem lineage, followed by an expansion after the divergence of the Placozoa.

    “Therefore, our analyses suggest an ancestral complement of a single SP1–4 ortholog and a single SP5–9 ortholog in the early metazoan stem lineage followed by an expansion after the divergence of the Placozoa (fig. 1).”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    Three SPs in the cnidarian Nematostella and the placozoan Trichoplax were identified and grouped into three separate clades: SP1-4, SP5/btd, and SP6-9.

    “Recently, three SPs in the cnidarian Nematostella and the placozoan Trichoplax were identified and grouped into three separate clades: SP1–4, SP5/btd, and SP6-9 (Schaeper et al. 2010)”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Schaeper et al. 2010

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Premisecitation

    Schaeper et al. (2010) proposed an ancestral complement of three SPs in the Metazoa.

    “leading to a proposed ancestral complement of three SPs in the Metazoa.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Schaeper et al. 2010

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationcitation

    According to the structural difference in the second zinc finger, btd would be classified in the Zif268/EGR-1 family of zinc finger transcription factors.

    “According to this structural difference, btd would be classified in the Zif268/EGR-1 family of zinc finger transcription factors (Iuchi 2001).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Iuchi 2001

      Not checked in the free run.

76 of 76

  • The paper relies on this without support.

    The more N-terminal regions of KLF/SP transcription factors are typically highly variable and consist of different combinations of transactivation/repression domains.

    “The more N-terminal regions of KLF/SP transcription factors are typically highly variable and consist of different combinations of transactivation/repression domains.”

  • The paper relies on this without support.

    No study to date has examined the phylogenetic context of the different transactivation/repression domains associated with the KLF/SP gene family.

    “No study to date has examined the phylogenetic context of the different transactivation/repression domains associated with the KLF/SP gene family.”

  • The paper relies on this without support.

    Hypotheses of metazoan gene evolution are greatly aided by sampling a wide range of taxa that include nonmetazoan representatives.

    “Hypotheses of metazoan gene evolution are greatly aided by sampling a wide range of taxa that include nonmetazoan representatives.”

  • The paper relies on this without support.

    The KLF/SP family shares a conserved 81-amino-acid triple-C2H2 zinc finger DNA-binding domain (KLF-DBD) with the given amino acid sequence.

    “We then used a perl script modified from Zeng et al. (2011) to search the protein sequences of the HMMER output for the 81 amino acid triple-C2H2 zinc finger DBD conserved in KLF/SPs (KLF-DBD). The amino acid sequence is as follows: C-X4-C-X12-H-X3-H-X7-C-X4-C-X12-H-X3-H-X7-C-X2-C-X12-H-X3-H, where X can be any amino acid.”

  • The authors state this as an assumption.

    The amorphean bikont split occurred at or near the origin of the Eukarya.

    “with the assumption that the amorphean bikont split occurred at or near the origin of the Eukarya (Derelle and Lang 2012).”

  • The paper relies on this without support.

    In mammals, KLF14 and KLF16 are present.

    “In mammals, two additional genes with similar domain architecture, KLF14 and KLF16, are present”
6 of 6

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • The study examined expression patterns of several transcription factor families (Fox, Klf, Lhx, Nkx, Nr, Pax, Pou, Prdm, Sox, Tbx), all of which have been shown to have important roles in spatial patterning, cell-type specification and differentiation during development.

    “We examined the expression patterns of several transcription factor families (Extended Data Fig. 13), including forkhead box (Fox), Krüppel-like factor (Klf), LIM homeobox (Lhx), NKX-homeodomain (Nkx), nuclear receptor (Nr), Paired box (Pax), POU domain (Pou), positive regulatory domain (Prdm), SRY-related HMG-box (Sox), and T-box (Tbx), all of which have been shown to have important roles in”

    From A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain (2023) · cites this paper as [103]

    Split into 2 atoms — 0 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 1 unverifiable. Expand the claim to see per-atom verdicts.

    Experimental — accuracy not yet measured

Cites

Flagged first, then by citations

4 of the 143 references couldn’t be matched to a known paper.

Research works printed but not linked: 1

  1. 10.1210/me.9.11.1610 · DOI

Cited by

Sorted by citations

Related

Authors
Presnell, J. S., Schnitzler, C. E., & Browne, W. E.
Affiliations
  • University of Miami (US)
  • National Institutes of Health (US)
Corresponding author
Browne, William E
ORCID
Venue
Genome Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2015-07-30
Volume
7
Issue
8
Pages
2289-2309
ISSN
1759-6653 (ISSN-L)
DOI
10.1093/gbe/evv141
PMC
PMC4558859
OpenAlex
W2287717772
Semantic Scholar
eb0e67270a69e53c295c9d7fdf2c6b50199f8754
Cited by
119
References
143
Citations by year
2026: 8 · 2025: 15 · 2024: 15 · 2023: 14 · 2022: 20 · 2021: 12 · 2020: 10 · 2019: 7 · 2018: 6 · 2017: 8 · 2016: 3 · 2014: 1
FWCI
2.45
Type
journal article
Language
en
Open access
Licence
cc-by-nc
Locations
  • Genome Biology and Evolution (publishedVersion, cc-by-nc)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
Funders
  • University of Miami
  • National Institutes of Health
  • National Human Genome Research Institute
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Kruppel-like factors research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
Krüppel-like factors, specificity proteins, gene family evolution, gene family expansion, transactivation domain, repression domain, metazoan origin, eukaryotic phylogeny
MeSH terms
Animals, Multigene Family, Molecular Sequence Data, Phylogeny, Repressor Proteins, Trans-Activators, Zinc Fingers, Protein Structure, Tertiary, Evolution, Molecular, Sp Transcription Factors, Kruppel-Like Transcription Factors, Eukaryota

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-07.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-07.

Statistics and arithmetic are recomputed, not judged.

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