245. Genome-Wide Specificity of DNA-Binding, Gene Regulation, and Chromatin Remodeling by TALE- and CRISPR/Cas9-Based Transcription Factors

AbstractEctopic DNA binding by transcription factors and other DNA binding proteins can be detrimental to cellular functions and ultimately to organismal fitness. The frequency of protein-DNA binding at non-functional sites depends on the global composition of a genome with respect to all possible short motifs, or k-mer words. To determine whether weak yet ubiquitous protein-DNA interactions could exert significant evolutionary pressures on genomes, we correlate in vitro measurements of binding strengths on all 8-mer words from a large collection of transcription factors, in several different species, against their relative genomic frequencies. Our analysis reveals a clear signal of purifying selection to reduce the large number of weak binding sites genome-wide. This evolutionary process, which we call global selection, has a detectable hallmark in that similar words experience similar evolutionary pressure, a consequence of the biophysics of protein-DNA binding. By analyzing a large collection of genomes, we show that global selection exists in all domains of life, and operates through tiny selective steps, maintaining genomic binding landscapes over long evolutionary timescales.

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A GO catalogue of human DNA-binding transcription factors

10.1101/2020.10.28.359232 ◽

2020 ◽

Cited By ~ 1

Author(s):

Ruth C. Lovering ◽

Pascale Gaudet ◽

Marcio L. Acencio ◽

Alex Ignatchenko ◽

Arttu Jolma ◽

...

Keyword(s):

Gene Regulation ◽

Transcription Factors ◽

Dna Binding ◽

Regulation Of Transcription ◽

Sequence Motifs ◽

Specific Sequence ◽

Go Annotation ◽

Human Dna ◽

Gene Regulatory ◽

The Many

AbstractDNA-binding transcription factors recognise genomic addresses, specific sequence motifs in gene regulatory regions, to control gene transcription. A complete and reliable catalogue of all DNA-binding transcription factors is key to investigating the delicate balance of gene regulation in response to environmental and developmental stimuli. The need for such a catalogue of proteins is demonstrated by the many lists of DNA-binding transcription factors that have been produced over the past decade.The COST Action Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC) Consortium brought together experts in the field of transcription with the aim of providing high quality and interoperable gene regulatory data. The Gene Ontology (GO) Consortium provides strict definitions for gene product function, including factors that regulate transcription. The collaboration between the GREEKC and GO Consortia has enabled the application of those definitions to produce a new curated catalogue of human DNA-binding transcription factors, that can be accessed at https://www.ebi.ac.uk/QuickGO/targetset/dbTF.In addition, this curation effort has led to the GO annotation of almost sixty thousand DNA-binding transcription factors in over a hundred species. Thus, this work will aid researchers investigating the regulation of transcription in both biomedical and basic science.

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Comprehensive genome-wide transcription factor analysis reveals that a combination of high affinity and low affinity DNA binding is needed for human gene regulation

BMC Genomics ◽

10.1186/1471-2164-16-s7-s12 ◽

2015 ◽

Vol 16 (S7) ◽

Cited By ~ 13

Author(s):

Junbai Wang ◽

Agnieszka Malecka ◽

Gunhild Trøen ◽

Jan Delabie

Keyword(s):

Gene Regulation ◽

Factor Analysis ◽

Transcription Factor ◽

Dna Binding ◽

Human Gene ◽

High Affinity ◽

Genome Wide

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Mechanisms of DNA-binding specificity and functional gene regulation by transcription factors

Current Opinion in Structural Biology ◽

10.1016/j.sbi.2016.05.006 ◽

2016 ◽

Vol 38 ◽

pp. 68-74 ◽

Cited By ~ 27

Author(s):

Ngaio C Smith ◽

Jacqueline M Matthews

Keyword(s):

Gene Regulation ◽

Transcription Factors ◽

Dna Binding ◽

Binding Specificity ◽

Functional Gene ◽

Dna Binding Specificity

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Transcription factors: specific DNA binding and specific gene regulation

Trends in Genetics ◽

10.1016/j.tig.2014.04.002 ◽

2014 ◽

Vol 30 (6) ◽

pp. 211-219 ◽

Cited By ~ 87

Author(s):

Anne-Laure Todeschini ◽

Adrien Georges ◽

Reiner A. Veitia

Keyword(s):

Gene Regulation ◽

Transcription Factors ◽

Dna Binding ◽

Specific Gene

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Genome-Wide Analysis of Estrogen Receptor α DNA Binding and Tethering Mechanisms Identifies Runx1 as a Novel Tethering Factor in Receptor-Mediated Transcriptional Activation

Molecular and Cellular Biology ◽

10.1128/mcb.00118-10 ◽

2010 ◽

Vol 30 (16) ◽

pp. 3943-3955 ◽

Cited By ~ 141

Author(s):

Joshua D. Stender ◽

Kyuri Kim ◽

Tze Howe Charn ◽

Barry Komm ◽

Ken C. N. Chang ◽

...

Keyword(s):

Gene Regulation ◽

Estrogen Receptor ◽

Dna Binding ◽

Transcriptional Activation ◽

Estrogen Receptor Alpha ◽

High Throughput Sequencing ◽

De Novo ◽

Motif Analysis ◽

Phenotypic Properties ◽

Genome Wide

ABSTRACT Nuclear receptor estrogen receptor alpha (ERα) controls the expression of hundreds of genes responsible for target cell phenotypic properties, but the relative importance of direct versus tethering mechanisms of DNA binding has not been established. In this first report, we examine the genome-wide chromatin localization of an altered-specificity mutant ER with a DNA binding domain deficient in binding to estrogen response element (ERE)-containing DNA (DBDmut ER) versus wild-type ERα. Using high-throughput sequencing of ER chromatin immunoprecipitations (ChIP-Seq) and mRNA transcriptional profiling, we show that direct ERE binding is required for most of (75%) estrogen-dependent gene regulation and 90% of hormone-dependent recruitment of ER to genomic binding sites. De novo motif analysis of the chromatin binding regions in MDA-MB-231 human breast cancer cells defined unique transcription factor profiles responsible for genes regulated through tethering versus direct ERE binding, with Runx motifs enriched in ER-tethered sites. We confirmed a role for Runx1 in mediating ERα genomic recruitment and regulation of tethering genes. Our findings delineate the contributions of direct receptor ERE binding versus binding through response elements for other transcription factors in chromatin localization and ER-dependent gene regulation, paradigms likely to underlie the gene regulatory actions of other nuclear receptors as well.

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Single-molecule dynamics and genome-wide transcriptomics reveal that NF-κB (p65)-DNA binding times can be decoupled from transcriptional activation

10.1101/255380 ◽

2018 ◽

Author(s):

Andrea Callegari ◽

Christian Sieben ◽

Alexander Benke ◽

David M. Suter ◽

Beat Fierz ◽

...

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Single Molecule ◽

Protein Interaction ◽

Transcriptional Activation ◽

Dna Binding Domain ◽

Protein Protein Interaction ◽

Genome Wide ◽

Binding Time ◽

Transcriptional Output

AbstractTranscription factors (TFs) regulate gene expression in both prokaryotes and eukaryotes by recognizing and binding to specific DNA promoter sequences. In higher eukaryotes, it remains unclear how the duration of TF binding to DNA relates to downstream transcriptional output. Here, we address this question for the transcriptional activator NF-κB (p65), by live-cell single molecule imaging of TF-DNA binding kinetics and genome-wide quantification of p65-mediated transcription. We used mutants of p65, perturbing either the DNA binding domain (DBD) or the protein-protein transactivation domain (TAD). We found that p65-DNA binding time was predominantly determined by its DBD and directly correlated with its transcriptional output as long as the TAD is intact. Surprisingly, mutation or deletion of the TAD did not modify p65-DNA binding stability, suggesting that the p65 TAD generally contributes neither to the assembly of an “enhanceosome,” nor to the active removal of p65 from putative specific binding sites. However, TAD removal did reduce p65-mediated transcriptional activation, indicating that protein-protein interactions act to translate the long-lived p65-DNA binding into productive transcription.Author SummaryTo control transcription of a certain gene or a group of genes, both eukaryotes and prokaryotes express specialized proteins, transcription factors (TFs). During gene activation, TFs bind gene promotor sequences to recruit the transcriptional machinery including DNA polymerase II. TFs are often multi-subunit proteins containing a DNA-binding domain (DBD) as well as a protein-protein interaction interface. It was suggested that the duration of a TF-DNA binding event 1) depends on these two subunits and 2) dictates the outcome, i.e. the amount of mRNA produced from an activated gene. We set out to address these hypotheses using the transcriptional activator NF-κB (p65) as well as a number of mutants affecting different functional subunits. Using a combination of live-cell microscopy and RNA sequencing, we show that p65 DNA-binding time indeed correlates with the transcriptional output, but that this relationship depends on, and hence can be uncoupled by altering, the protein-protein interaction capacity. Our results suggest that, while p65 DNA binding times are dominated by the DBD, a transcriptional output can only be achieved with a functional protein-protein interaction subunit.

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Abstract MP142: Genome-wide Studies Reveal the Essential and Opposite Roles of Arid1a in Controlling Human Cardiogenesis and Neurogenesis From Pluripotent Stem Cells

Circulation Research ◽

10.1161/res.127.suppl_1.mp142 ◽

2020 ◽

Vol 127 (Suppl_1) ◽

Author(s):

Juli Liu ◽

Sheng Liu ◽

Hongyu Gao ◽

Lei Han ◽

Xiaona Chu ◽

...

Keyword(s):

Stem Cells ◽

Dna Binding ◽

Brain Development ◽

Chromatin Remodeling ◽

Neural Development ◽

Human Heart ◽

Chromatin Accessibility ◽

Neurogenic Genes ◽

Genome Wide ◽

Early Human

Background: Early human heart and brain development simultaneously occur during embryogenesis. Notably, in human newborns, congenital heart defects strongly associate with neurodevelopmental abnormalities, suggesting a common gene/complex underlying both cardiogenesis and neurogenesis. However, due to lack of in vivo studies, the molecular mechanisms that govern both early human heart and brain development remain elusive. The evolutionarily conserved ATP-dependent SWI/SNF complex is one of the largest chromatin remodeling complexes, consisting of ~15 subunits, including SMARCA2 (also known as BRM) or SMARCA4 (also known as BRG1) as the ATPase catalytic subunit. Several BRG1-associated factors (BAFs), such as ARID1A (Baf250a), have DNA binding capacity and assemble with either BRM or BRG1 to form a functional chromatin-remodeling complex. A single amino acid mutation (Arid1aV 1068G/V1068G ), impaired Arid1a-DNA interactions and resulted in both cardiac neural defects. Mutations in 4 different SWI/SNF subunits including ARID1A/B were identified in human congenital syndromes that include both neural and cardiac defects. Results: Here, we report ARID1A, which is a DNA-binding-subunit of the SWI/SNF epigenetic complex, controls both neurogenesis and cardiogenesis from human embryonic stem cells (hESCs) via employing distinct mechanisms. CRISPR/Cas-9 knockout of ARID1A (ARID1A -/- ) led to spontaneous differentiation of neural cells together with globally enhanced expression of neurogenic genes in undifferentiated hESCs. Additionally, when compared with WT hESCs, cardiac differentiation from ARID1A -/- hESCs was prominently suppressed, whereas neural differentiation was significantly promoted. Whole genome-wide ChIP-seq and ATAC-seq analyses revealed that ARID1A was required to open chromatin accessibility on promoters of essential cardiogenic genes, and temporally associated with key cardiogenic transcriptional factors T and MEF2C during early cardiac development. However, during neural development, transcription of most essential neurogenic genes was dependent on ARID1A and ARID1A could interact with REST, which is a known transcriptional repressor. Conclusions: We uncovered the key and opposite roles by ARID1A to govern both early human cardiac and neural development and characterized the mechanisms. We found global chromatin accessibility on cardiogenic genes was dependent on ARID1A, whereas transcriptional activity of neurogenic genes was regulated by ARID1A, possibly through ARID1A-REST interaction.

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