Ally Yang
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View article: Differential usage of two, distinct DNA-binding domains regulates tissue-specific occupancy of the pioneer factor Zelda
Differential usage of two, distinct DNA-binding domains regulates tissue-specific occupancy of the pioneer factor Zelda Open
Pioneer transcription factors act at the top of gene-regulatory networks by promoting accessible chromatin at the cis -regulatory regions that drive gene expression. Despite their ability to bind closed chromatin, pioneer factors occupy di…
View article: Modulation of Growth and Immunity in Carp by <i>Hermetia illucens</i> Larvae induced by <i>Aeromonas hydrophila</i>
Modulation of Growth and Immunity in Carp by <i>Hermetia illucens</i> Larvae induced by <i>Aeromonas hydrophila</i> Open
This experiment aimed to investigate the effects of Aeromonas hydrophila -induced treatment of black soldier fly ( Hermetia illucens ) larvae on the growth performance and immune function of the common carp. Aeromonas hydrophila -induced b…
View article: A TATA-box-binding protein binds single-stranded DNA in two modes: To poly(G) tracts and to flexible DNA regions
A TATA-box-binding protein binds single-stranded DNA in two modes: To poly(G) tracts and to flexible DNA regions Open
The TATA-box-binding protein (TBP) homolog from Giardia intestinalis (gTBP) is highly divergent, lacking key phenylalanine residues crucial for binding and unwinding double-stranded DNA. Surprisingly, we determined that gTBP exhibits uncon…
View article: GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors
GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors Open
SUMMARY Precise identification of transcription factor (TF) binding sites is a long standing challenge in human regulatory genomics: TF binding motifs are short and degenerate, while the genome is large. Motif scans, therefore, often produ…
View article: Extensive binding of uncharacterized human transcription factors to genomic dark matter
Extensive binding of uncharacterized human transcription factors to genomic dark matter Open
SUMMARY Most of the human genome is thought to be non-functional, and includes large segments often referred to as “dark matter” DNA. The genome also encodes hundreds of putative and poorly characterized transcription factors (TFs). We det…
View article: Identification of methylation-sensitive human transcription factors using meSMiLE-seq
Identification of methylation-sensitive human transcription factors using meSMiLE-seq Open
Transcription factors (TFs) are key players in eukaryotic gene regulation, but the DNA binding specificity of many TFs remains unknown. Here, we assayed 284 mostly poorly characterized, putative human TFs using selective microfluidics-base…
View article: Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors
Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors Open
SUMMARY We describe an effort (“Codebook”) to determine the sequence specificity of 332 putative and largely uncharacterized human transcription factors (TFs), as well as 61 control TFs. Nearly 5,000 independent experiments across multiple…
View article: Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors
Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors Open
A DNA sequence pattern, or “motif”, is an essential representation of DNA-binding specificity of a transcription factor (TF). Any particular motif model has potential flaws due to shortcomings of the underlying experimental data and comput…
View article: Transcription factor binding specificities of the oomycete Phytophthora infestans reflect conserved and divergent evolutionary patterns and predict function
Transcription factor binding specificities of the oomycete Phytophthora infestans reflect conserved and divergent evolutionary patterns and predict function Open
Background Identifying the DNA-binding specificities of transcription factors (TF) is central to understanding gene networks that regulate growth and development. Such knowledge is lacking in oomycetes, a microbial eukaryotic lineage withi…
View article: The human genome contains over a million autonomous exons
The human genome contains over a million autonomous exons Open
Mammalian mRNA and lncRNA exons are often small compared to introns. The exon definition model predicts that exons splice autonomously, dependent on proximal exon sequence features, explaining their delineation within large introns. This m…
View article: Structural insights into DNA recognition by the BEN domain of the transcription factor BANP
Structural insights into DNA recognition by the BEN domain of the transcription factor BANP Open
The BEN domain-containing transcription factors regulate transcription by recruiting chromatin-modifying factors to specific chromatin regions via their DNA-binding BEN domains. The BEN domain of BANP has been shown to bind to a CGCG DNA s…
View article: Supplementary Table 2 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus
Supplementary Table 2 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus Open
Genes selected for NanoString analysis. Contains the following tabs: (1) Nanostring gene set: final list for NanoString analysis. Gene Symbol, genes selected for nanostring analysis; Pathway, annotation from literature or from pathways in …
View article: Supplementary Table 1 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus
Supplementary Table 1 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus Open
Primers used in this study.
View article: Supplementary Table 5 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus
Supplementary Table 5 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus Open
eQTL Associations from GTEx (Release V7 (dbGaP Accession phs000424.v7.p2). Contains single gene eQTLs for BNC2, CNTLN, c9orf92 and SH3GL2 in all tissues and single SNP eQTL for all 40 SNPs in the credible candidate set.
View article: Supplementary Table 4 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus
Supplementary Table 4 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus Open
Fine mapping association results. Contains univariate and conditional (conditioning on rs3814113) analysis.
View article: Supplementary Table 1 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus
Supplementary Table 1 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus Open
Primers used in this study.
View article: Supplementary Table 2 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus
Supplementary Table 2 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus Open
Genes selected for NanoString analysis. Contains the following tabs: (1) Nanostring gene set: final list for NanoString analysis. Gene Symbol, genes selected for nanostring analysis; Pathway, annotation from literature or from pathways in …
View article: Supplementary Table 3 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus
Supplementary Table 3 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus Open
List of 134 SNPs in linkage disequilibrium (r2 {greater than or equal to} 0.3) with rs3814113 (based on 1000GP v3), selected for functional analysis.
View article: Data from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus
Data from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus Open
Genome-wide association studies have identified 40 ovarian cancer risk loci. However, the mechanisms underlying these associations remain elusive. In this study, we conducted a two-pronged approach to identify candidate causal SNPs and ass…
View article: Supplementary Table 4 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus
Supplementary Table 4 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus Open
Fine mapping association results. Contains univariate and conditional (conditioning on rs3814113) analysis.
View article: Supplementary Table 3 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus
Supplementary Table 3 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus Open
List of 134 SNPs in linkage disequilibrium (r2 {greater than or equal to} 0.3) with rs3814113 (based on 1000GP v3), selected for functional analysis.
View article: Supplementary Table 5 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus
Supplementary Table 5 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus Open
eQTL Associations from GTEx (Release V7 (dbGaP Accession phs000424.v7.p2). Contains single gene eQTLs for BNC2, CNTLN, c9orf92 and SH3GL2 in all tissues and single SNP eQTL for all 40 SNPs in the credible candidate set.
View article: Data from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus
Data from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus Open
Genome-wide association studies have identified 40 ovarian cancer risk loci. However, the mechanisms underlying these associations remain elusive. In this study, we conducted a two-pronged approach to identify candidate causal SNPs and ass…
View article: Supplementary Figures 1-4 and extended methods from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus
Supplementary Figures 1-4 and extended methods from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus Open
This file contains: Supplementary Figure 1 (Related to Figure 2): Haplotype frequency for tiles Enhancer Scanning times with multiple SNPs. Supplementary Figure 2 (Related to Figure 3): Conservation and S/MAR predicted sequences at the loc…
View article: A multimorphic mutation in IRF4 causes human autosomal dominant combined immunodeficiency
A multimorphic mutation in IRF4 causes human autosomal dominant combined immunodeficiency Open
Interferon regulatory factor 4 (IRF4) is a transcription factor (TF) and key regulator of immune cell development and function. We report a recurrent heterozygous mutation in IRF4, p.T95R, causing an autosomal dominant combined immunodefic…
View article: Chromatin accessibility is a two-tier process regulated by transcription factor pioneering and enhancer activation
Chromatin accessibility is a two-tier process regulated by transcription factor pioneering and enhancer activation Open
Summary Chromatin accessibility is integral to the process by which transcription factors (TFs) read out cis-regulatory DNA sequences, but it is difficult to differentiate between TFs that drive accessibility and those that do not. Deep le…
View article: Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins
Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins Open
The BEN domain is a recently recognized DNA binding module that is present in diverse metazoans and certain viruses. Several BEN domain factors are known as transcriptional repressors, but, overall, relatively little is known of how BEN fa…
View article: Diverse Eukaryotic CGG-Binding Proteins Produced by Independent Domestications of<i>hAT</i>Transposons
Diverse Eukaryotic CGG-Binding Proteins Produced by Independent Domestications of<i>hAT</i>Transposons Open
The human transcription factor (TF) CGGBP1 (CGG-binding protein) is conserved only in amniotes and is believed to derive from the zf-BED and Hermes transposase DNA-binding domains (DBDs) of a hAT DNA transposon. Here, we show that sequence…