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1.
Nat Commun ; 15(1): 3110, 2024 Apr 10.
Artigo em Inglês | MEDLINE | ID: mdl-38600112

RESUMO

Homeodomains (HDs) are the second largest class of DNA binding domains (DBDs) among eukaryotic sequence-specific transcription factors (TFs) and are the TF structural class with the largest number of disease-associated mutations in the Human Gene Mutation Database (HGMD). Despite numerous structural studies and large-scale analyses of HD DNA binding specificity, HD-DNA recognition is still not fully understood. Here, we analyze 92 human HD mutants, including disease-associated variants and variants of uncertain significance (VUS), for their effects on DNA binding activity. Many of the variants alter DNA binding affinity and/or specificity. Detailed biochemical analysis and structural modeling identifies 14 previously unknown specificity-determining positions, 5 of which do not contact DNA. The same missense substitution at analogous positions within different HDs often exhibits different effects on DNA binding activity. Variant effect prediction tools perform moderately well in distinguishing variants with altered DNA binding affinity, but poorly in identifying those with altered binding specificity. Our results highlight the need for biochemical assays of TF coding variants and prioritize dozens of variants for further investigations into their pathogenicity and the development of clinical diagnostics and precision therapies.


Assuntos
Proteínas de Homeodomínio , Fatores de Transcrição , Humanos , Proteínas de Homeodomínio/metabolismo , Fatores de Transcrição/metabolismo , DNA/metabolismo , Mutação , Modelos Moleculares
2.
Stem Cell Reports ; 18(6): 1325-1339, 2023 06 13.
Artigo em Inglês | MEDLINE | ID: mdl-37315524

RESUMO

Skeletal muscle function and regenerative capacity decline during aging, yet factors driving these changes are incompletely understood. Muscle regeneration requires temporally coordinated transcriptional programs to drive myogenic stem cells to activate, proliferate, fuse to form myofibers, and to mature as myonuclei, restoring muscle function after injury. We assessed global changes in myogenic transcription programs distinguishing muscle regeneration in aged mice from young mice by comparing pseudotime trajectories from single-nucleus RNA sequencing of myogenic nuclei. Aging-specific differences in coordinating myogenic transcription programs necessary for restoring muscle function occur following muscle injury, likely contributing to compromised regeneration in aged mice. Differences in pseudotime alignment of myogenic nuclei when comparing aged with young mice via dynamic time warping revealed pseudotemporal differences becoming progressively more severe as regeneration proceeds. Disruptions in timing of myogenic gene expression programs may contribute to incomplete skeletal muscle regeneration and declines in muscle function as organisms age.


Assuntos
Núcleo Celular , Células-Tronco , Animais , Camundongos , Envelhecimento/genética , Músculo Esquelético , Expressão Gênica
3.
Cell Rep ; 34(1): 108574, 2021 01 05.
Artigo em Inglês | MEDLINE | ID: mdl-33406418

RESUMO

The zinc finger transcription factor SALL4 is highly expressed in embryonic stem cells, downregulated in most adult tissues, but reactivated in many aggressive cancers. This unique expression pattern makes SALL4 an attractive therapeutic target. However, whether SALL4 binds DNA directly to regulate gene expression is unclear, and many of its targets in cancer cells remain elusive. Here, through an unbiased screen of protein binding microarray (PBM) and cleavage under targets and release using nuclease (CUT&RUN) experiments, we identify and validate the DNA binding domain of SALL4 and its consensus binding sequence. Combined with RNA sequencing (RNA-seq) analyses after SALL4 knockdown, we discover hundreds of new SALL4 target genes that it directly regulates in aggressive liver cancer cells, including genes encoding a family of histone 3 lysine 9-specific demethylases (KDMs). Taken together, these results elucidate the mechanism of SALL4 DNA binding and reveal pathways and molecules to target in SALL4-dependent tumors.


Assuntos
Carcinoma Hepatocelular/metabolismo , Proteínas de Ligação a DNA/metabolismo , Células-Tronco Embrionárias/metabolismo , Regulação Neoplásica da Expressão Gênica , Histona Desmetilases/metabolismo , Fatores de Transcrição/metabolismo , Dedos de Zinco , Motivos de Aminoácidos , Sequência de Aminoácidos , Carcinoma Hepatocelular/genética , Linhagem Celular Tumoral , Proteínas de Ligação a DNA/genética , Técnicas de Silenciamento de Genes , Células HEK293 , Células HeLa , Histona Desmetilases/genética , Humanos , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/metabolismo , Análise Serial de Proteínas , Ligação Proteica , Análise de Sequência de RNA , Fatores de Transcrição/genética
4.
Mol Cell ; 77(2): 324-337.e8, 2020 01 16.
Artigo em Inglês | MEDLINE | ID: mdl-31704182

RESUMO

A major challenge in biology is to understand how complex gene expression patterns are encoded in the genome. While transcriptional enhancers have been studied extensively, few transcriptional silencers have been identified, and they remain poorly understood. Here, we used a novel strategy to screen hundreds of sequences for tissue-specific silencer activity in whole Drosophila embryos. Almost all of the transcriptional silencers that we identified were also active enhancers in other cellular contexts. These elements are bound by more transcription factors than non-silencers. A subset of these silencers forms long-range contacts with promoters. Deletion of a silencer caused derepression of its target gene. Our results challenge the common practice of treating enhancers and silencers as separate classes of regulatory elements and suggest the possibility that thousands or more bifunctional CRMs remain to be discovered in Drosophila and 104-105 in humans.


Assuntos
Drosophila/genética , Elementos Facilitadores Genéticos/genética , Elementos Silenciadores Transcricionais/genética , Transcrição Gênica/genética , Animais , Animais Geneticamente Modificados/genética , Masculino
5.
Genes Dev ; 32(9-10): 723-736, 2018 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-29764918

RESUMO

The K50 (lysine at amino acid position 50) homeodomain (HD) protein Orthodenticle (Otd) is critical for anterior patterning and brain and eye development in most metazoans. In Drosophila melanogaster, another K50HD protein, Bicoid (Bcd), has evolved to replace Otd's ancestral function in embryo patterning. Bcd is distributed as a long-range maternal gradient and activates transcription of a large number of target genes, including otd Otd and Bcd bind similar DNA sequences in vitro, but how their transcriptional activities are integrated to pattern anterior regions of the embryo is unknown. Here we define three major classes of enhancers that are differentially sensitive to binding and transcriptional activation by Bcd and Otd. Class 1 enhancers are initially activated by Bcd, and activation is transferred to Otd via a feed-forward relay (FFR) that involves sequential binding of the two proteins to the same DNA motif. Class 2 enhancers are activated by Bcd and maintained by an Otd-independent mechanism. Class 3 enhancers are never bound by Bcd, but Otd binds and activates them in a second wave of zygotic transcription. The specific activities of enhancers in each class are mediated by DNA motif variants preferentially bound by Bcd or Otd and the presence or absence of sites for cofactors that interact with these proteins. Our results define specific patterning roles for Bcd and Otd and provide mechanisms for coordinating the precise timing of gene expression patterns during embryonic development.


Assuntos
Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/embriologia , Drosophila melanogaster/genética , Regulação da Expressão Gênica no Desenvolvimento , Proteínas de Homeodomínio/genética , Proteínas de Homeodomínio/metabolismo , Transativadores/genética , Transativadores/metabolismo , Motivos de Aminoácidos , Animais , Padronização Corporal/genética , Drosophila melanogaster/metabolismo , Desenvolvimento Embrionário/efeitos dos fármacos , Desenvolvimento Embrionário/genética , Elementos Facilitadores Genéticos/genética , Ligação Proteica
6.
Cell ; 173(2): 430-442.e17, 2018 04 05.
Artigo em Inglês | MEDLINE | ID: mdl-29606353

RESUMO

Fetal hemoglobin (HbF, α2γ2) level is genetically controlled and modifies severity of adult hemoglobin (HbA, α2ß2) disorders, sickle cell disease, and ß-thalassemia. Common genetic variation affects expression of BCL11A, a regulator of HbF silencing. To uncover how BCL11A supports the developmental switch from γ- to ß- globin, we use a functional assay and protein binding microarray to establish a requirement for a zinc-finger cluster in BCL11A in repression and identify a preferred DNA recognition sequence. This motif appears in embryonic and fetal-expressed globin promoters and is duplicated in γ-globin promoters. The more distal of the duplicated motifs is mutated in individuals with hereditary persistence of HbF. Using the CUT&RUN approach to map protein binding sites in erythroid cells, we demonstrate BCL11A occupancy preferentially at the distal motif, which can be disrupted by editing the promoter. Our findings reveal that direct γ-globin gene promoter repression by BCL11A underlies hemoglobin switching.


Assuntos
Proteínas de Transporte/metabolismo , Hemoglobina Fetal/genética , Proteínas Nucleares/metabolismo , Sequência de Bases , Sítios de Ligação , Proteínas de Transporte/genética , Linhagem Celular , Cromatina/metabolismo , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/genética , Células Eritroides/citologia , Células Eritroides/metabolismo , Edição de Genes , Humanos , Proteínas Nucleares/genética , Regiões Promotoras Genéticas , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Proteínas Repressoras , Dedos de Zinco/genética , Globinas beta/genética , Talassemia beta/genética , Talassemia beta/patologia , gama-Globinas/genética
7.
Cell Rep ; 22(12): 3227-3239, 2018 03 20.
Artigo em Inglês | MEDLINE | ID: mdl-29562179

RESUMO

Little is known about how variation in sequence composition alters transcription factor occupancy to precisely recruit large transcription complexes. A key model for understanding how transcription complexes are targeted is the Drosophila dosage compensation system in which the male-specific lethal (MSL) transcription complex specifically identifies and regulates the male X chromosome. The chromatin-linked adaptor for MSL proteins (CLAMP) zinc-finger protein targets MSL to the X chromosome but also binds to GA-rich sequence elements throughout the genome. Furthermore, the GAGA-associated factor (GAF) transcription factor also recognizes GA-rich sequences but does not associate with the MSL complex. Here, we demonstrate that MSL complex recruitment sites are optimal CLAMP targets. Specificity for CLAMP binding versus GAF binding is driven by variability in sequence composition within similar GA-rich motifs. Therefore, variation within seemingly similar cis elements drives the context-specific targeting of a large transcription complex.


Assuntos
Drosophila/genética , Drosophila/metabolismo , Animais , Feminino , Fator de Transcrição de Proteínas de Ligação GA/metabolismo , Masculino , Cromossomos Sexuais , Cromossomo X
8.
Nucleic Acids Res ; 46(5): 2509-2520, 2018 03 16.
Artigo em Inglês | MEDLINE | ID: mdl-29361124

RESUMO

Transcription factors IRF3, IRF5 and IRF7 (IRF3/5/7) have overlapping, yet distinct, roles in the mammalian response to pathogens. To examine the role that DNA-binding specificity plays in delineating IRF3/5/7-specific gene regulation we used protein-binding microarrays (PBMs) to characterize the DNA binding of IRF3/5/7 homodimers. We identified both common and dimer-specific DNA binding sites, and show that DNA-binding differences can translate into dimer-specific gene regulation. Central to the antiviral response, IRF3/5/7 regulate type I interferon (IFN) genes. We show that IRF3 and IRF7 bind to many interferon-stimulated response element (ISRE)-type sites in the virus-response elements (VREs) of IFN promoters. However, strikingly, IRF5 does not bind the VREs, suggesting evolutionary selection against IRF5 homodimer binding. Mutational analysis reveals a critical specificity-determining residue that inhibits IRF5 binding to the ISRE-variants present in the IFN gene promoters. Integrating PBM and reporter gene data we find that both DNA-binding affinity and affinity-independent mechanisms determine the function of DNA-bound IRF dimers, suggesting that DNA-based allostery plays a role in IRF binding site function. Our results provide new insights into the role and limitations of DNA-binding affinity in delineating IRF3/5/7-specific gene expression.


Assuntos
Fator Regulador 3 de Interferon/metabolismo , Fator Regulador 7 de Interferon/metabolismo , Fatores Reguladores de Interferon/metabolismo , Elementos de Resposta , Sítios de Ligação , DNA/metabolismo , Regulação da Expressão Gênica , Células HEK293 , Humanos , Fator Regulador 3 de Interferon/química , Fator Regulador 7 de Interferon/química , Fatores Reguladores de Interferon/química , Interferon Tipo I/genética , Análise Serial de Proteínas , Multimerização Proteica
9.
Nature ; 549(7671): 287-291, 2017 09 14.
Artigo em Inglês | MEDLINE | ID: mdl-28869966

RESUMO

The Polycomb repressive complex 2 (PRC2) mainly mediates transcriptional repression and has essential roles in various biological processes including the maintenance of cell identity and proper differentiation. Polycomb-like (PCL) proteins, such as PHF1, MTF2 and PHF19, are PRC2-associated factors that form sub-complexes with PRC2 core components, and have been proposed to modulate the enzymatic activity of PRC2 or the recruitment of PRC2 to specific genomic loci. Mammalian PRC2-binding sites are enriched in CG content, which correlates with CpG islands that display a low level of DNA methylation. However, the mechanism of PRC2 recruitment to CpG islands is not fully understood. Here we solve the crystal structures of the N-terminal domains of PHF1 and MTF2 with bound CpG-containing DNAs in the presence of H3K36me3-containing histone peptides. We show that the extended homologous regions of both proteins fold into a winged-helix structure, which specifically binds to the unmethylated CpG motif but in a completely different manner from the canonical winged-helix DNA recognition motif. We also show that the PCL extended homologous domains are required for efficient recruitment of PRC2 to CpG island-containing promoters in mouse embryonic stem cells. Our research provides the first, to our knowledge, direct evidence to demonstrate that PCL proteins are crucial for PRC2 recruitment to CpG islands, and further clarifies the roles of these proteins in transcriptional regulation in vivo.


Assuntos
Ilhas de CpG/genética , Complexo Repressor Polycomb 2/química , Complexo Repressor Polycomb 2/metabolismo , Animais , Sítios de Ligação , Cromatina/química , Cromatina/metabolismo , DNA/química , DNA/genética , DNA/metabolismo , Metilação de DNA , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , Células-Tronco Embrionárias/metabolismo , Histonas/química , Histonas/metabolismo , Humanos , Camundongos , Modelos Moleculares , Proteínas do Grupo Polycomb/química , Proteínas do Grupo Polycomb/metabolismo , Regiões Promotoras Genéticas/genética , Ligação Proteica , Domínios Proteicos , Fatores de Transcrição/química , Fatores de Transcrição/metabolismo , Transcrição Gênica
10.
Science ; 351(6280): 1450-1454, 2016 Mar 25.
Artigo em Inglês | MEDLINE | ID: mdl-27013732

RESUMO

Sequencing of exomes and genomes has revealed abundant genetic variation affecting the coding sequences of human transcription factors (TFs), but the consequences of such variation remain largely unexplored. We developed a computational, structure-based approach to evaluate TF variants for their impact on DNA binding activity and used universal protein-binding microarrays to assay sequence-specific DNA binding activity across 41 reference and 117 variant alleles found in individuals of diverse ancestries and families with Mendelian diseases. We found 77 variants in 28 genes that affect DNA binding affinity or specificity and identified thousands of rare alleles likely to alter the DNA binding activity of human sequence-specific TFs. Our results suggest that most individuals have unique repertoires of TF DNA binding activities, which may contribute to phenotypic variation.


Assuntos
Proteínas de Ligação a DNA/genética , DNA/metabolismo , Regulação da Expressão Gênica , Doenças Genéticas Inatas/genética , Fatores de Transcrição/genética , Sequência de Bases , Sítios de Ligação , Simulação por Computador , Proteínas de Ligação a DNA/metabolismo , Exoma/genética , Variação Genética , Genoma Humano , Humanos , Mutação , Polimorfismo de Nucleotídeo Único , Análise Serial de Proteínas , Ligação Proteica , Análise de Sequência de DNA , Fatores de Transcrição/metabolismo
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