Motif Scanning Research Articles

Genome-wide identification, characterization and expression pattern analysis of TIFY family members in Artemisia argyi

BackgroundPlant-specific TIFY proteins play crucial roles in regulating plant growth, development, and various stress responses. However, there is no information available about this family in Artemisia argyi, a well-known traditional medicinal plant with great economic value.ResultsA total of 34 AaTIFY genes were identified, including 4 TIFY, 22 JAZ, 5 PPD, and 3 ZML genes. Structural, motif scanning, and phylogenetic relationships analysis of these genes revealed that members within the same group or subgroup exhibit similar exon-intron structures and conserved motif compositions. The TIFY genes were unevenly distributed across the 15 chromosomes. Tandem duplication events and segmental duplication events have been identified in the TIFY family in A. argyi. These events have played a crucial role in the gene multiplication and compression of different subfamilies within the TIFY family. Promoter analysis revealed that most AaTIFY genes contain multiple cis-elements associated with stress response, phytohormone signal transduction, and plant growth and development. Expression analysis of roots and leaves using RNA-seq data revealed that certain AaTIFY genes showed tissue-specific expression patterns, and some AaTIFY genes, such as AaTIFY19/29, were found to be involved in regulating salt and saline-alkali stresses. In addition, RT-qPCR analysis showed that TIFY genes, especially AaTIFY19/23/27/29, respond to a variety of hormonal treatments, such as MeJA, ABA, SA, and IAA. This suggested that TIFY genes in A. argyi regulate plant growth and respond to different stresses by following different hormone signaling pathways.ConclusionTaken together, our study conducted a comprehensive identification and analysis of the TIFY gene family in A. argyi. These findings suggested that TIFY might play an important role in plant development and stress responses, which laid a valuable foundation for further understanding the function of TIFY genes in multiple stress responses and phytohormone crosstalk in A. argyi.

Virome-wide analysis of histone modification mimicry motifs carried by viral proteins

Histone mimicry (HM) refers to the presence of short linear motifs in viral proteins that mimic critical regions of host histone proteins. These motifs have the potential to interfere with host cell epigenome and counteract antiviral response. Recent research shows that HM is critical for the pathogenesis and transmissibility of influenza virus and coronavirus. However, the distribution, characteristics, and functions of HM in eukaryotic viruses remain obscure. Herein, we developed a bioinformatic pipeline, Histone Motif Scan (HiScan), to identify HM motifs in viral proteins and predict their functions in silico. By analyzing 592,643 viral proteins using HiScan, we found that putative HM motifs were widely distributed in most viral proteins. Among animal viruses, the ratio of HM motifs between DNA viruses and RNA viruses was approximately 1.9:1, and viruses with smaller genomes had a higher density of HM motifs. Notably, coronaviruses exhibited an uneven distribution of HM motifs, with betacoronaviruses (including most human pathogenic coronaviruses) harboring more HM motifs than other coronaviruses, primarily in the NSP3, S, and N proteins. In summary, our virome-wide screening of HM motifs using HiScan revealed extensive but uneven distribution of HM motifs in most viral proteins, with a preference in DNA viruses. Viral HM may play an important role in modulating viral pathogenicity and virus-host interactions, making it an attractive area of research in virology and antiviral medication.

Abstract We139: 3D Chromatin Architectures and Transcription Regulation in Diabetic Endothelial Dysfunction

Cardiovascular disease is the major cause of mortality in people with type 2 diabetes, primarily due to endothelial dysfunction. Recent studies have suggested that transcriptional reprogramming plays a central role in endothelial dysfunction, but its regulation in the context of diabetes remains poorly understood. In this study, we utilized 3D chromatin mapping analysis (H3K27ac HiChIP) to investigate the transcriptional regulation in aortic endothelial cells (db/db mice) and HUVEC cells treated with high glucose (HUVEC high-glu ). We found that these cells were characterized by a massive loss of enhancer-promoter loops, which was associated with transcriptional downregulation. Through transcription factor motif scan, ChIP-seq and ATAC-seq analysis, we uncovered that the lost loop anchors are demarcated by reduced JUNB (transcription factor) binding while their chromatin accessibility remains unchanged. Moreover, we demonstrated that overexpression of JUNB significantly restored enhancer-promoter loops lost in HUVEC high-glu and ameliorated endothelial dysfunctions both in vitro (cell scratch, Transwell), ex vivo (aorta relaxation/contraction) and in vivo (hindlimb ischemia) assays. We further showed that JUNB protein (but not RNA) expression is reduced in aortic endothelial cells (db/db), HUVEC high-glu and primary endothelial cells from diabetic patients. Through RIME (Rapid immunoprecipitation mass spectrometry of endogenous protein) assay, we identified that RBBP6 (RB Binding Protein 6, Ubiquitin Ligase) is a JUNB interacting protein in HUVEC high-glu . We further showed that overexpression of RBBP6 downregulated JUNB expression while proteasome inhibitor MG132 treatment largely abolished the inhibitory effect of RBBP6 on JUNB protein levels in normal HUVEC cells, suggesting that RPPB6 promoted JUNB degradation through ubiquitination. Notably, knockdown of RBBP6 in HUVEC high-glu significantly upregulated JUNB expression, enhancer-promoter loopings and improved endothelial dysfunction. Overall, our findings provide novel 3D chromatin insights into diabetic endothelial dysfunction and illustrate a model whereby RBBP6-mediated JUNB degradation leads to global loss of enhancer-promoter looping and transcriptional inhibition in diabetic endothelial dysfunction.

Dynamic Changes in Histone Modifications Are Associated with Differential Chromatin Interactions.

Eukaryotic genomes are organized into chromatin domains through long-range chromatin interactions which are mediated by the binding of architectural proteins, such as CTCF and cohesin, and histone modifications. Based on the published Hi-C and ChIP-seq datasets in human monocyte-derived macrophages, we identified 206 and 127 differential chromatin interactions (DCIs) that were not located within transcription readthrough regions in influenza A virus- and interferon β-treated cells, respectively, and found that the binding positions of CTCF and RAD21 within more than half of the DCI sites did not change. However, five histone modifications, H3K4me3, H3K27ac, H3K36me3, H3K9me3, and H3K27me3, showed significantly more dramatic changes than CTCF and RAD21 within the DCI sites. For H3K4me3, H3K27ac, H3K36me3, and H3K27me3, significantly more dramatic changes were observed outside than within the DCI sites. We further applied a motif scanning approach to discover proteins that might correlate with changes in histone modifications and chromatin interactions and found that PRDM9, ZNF384, and STAT2 frequently bound to DNA sequences corresponding to 1 kb genomic intervals with gains or losses of a histone modification within the DCI sites. This study explores the dynamic regulation of chromatin interactions and extends the current knowledge of the relationship between histone modifications and chromatin interactions.

Physiological Roles of an Acinetobacter-specific σ Factor.

The Gram-negative pathogen Acinetobacter baumannii is considered an "urgent threat" to human health due to its propensity to become antibiotic resistant. Understanding the distinct regulatory paradigms used by A. baumannii to mitigate cellular stresses may uncover new therapeutic targets. Many γ-proteobacteria use the extracytoplasmic function (ECF) σ factor, RpoE, to invoke envelope homeostasis networks in response to stress. Acinetobacter species contain the poorly characterized ECF "SigAb;" however, it is unclear if SigAb has the same physiological role as RpoE. Here, we show that SigAb is a metal stress-responsive ECF that appears unique to Acinetobacter species and distinct from RpoE. We combine promoter mutagenesis, motif scanning, and ChIP-seq to define the direct SigAb regulon, which consists of sigAb itself, the stringent response mediator, relA, and the uncharacterized small RNA, "sabS." However, RNA-seq of strains overexpressing SigAb revealed a large, indirect regulon containing hundreds of genes. Metal resistance genes are key elements of the indirect regulon, as CRISPRi knockdown of sigAb or sabS resulted in increased copper sensitivity and excess copper induced SigAb-dependent transcription. Further, we found that two uncharacterized genes in the sigAb operon, "aabA" and "aabB", have anti-SigAb activity. Finally, employing a targeted Tn-seq approach that uses CRISPR-associated transposons, we show that sigAb, aabA, and aabB are important for fitness even during optimal growth conditions. Our work reveals new physiological roles for SigAb and SabS, provides a novel approach for assessing gene fitness, and highlights the distinct regulatory architecture of A. baumannii.

REUNION: transcription factor binding prediction and regulatory association inference from single-cell multi-omics data.

Profiling of gene expression and chromatin accessibility by single-cell multi-omics approaches can help to systematically decipher how transcription factors (TFs) regulate target gene expression via cis-region interactions. However, integrating information from different modalities to discover regulatory associations is challenging, in part because motif scanning approaches miss many likely TF binding sites. We develop REUNION, a framework for predicting genome-wide TF binding and cis-region-TF-gene "triplet" regulatory associations using single-cell multi-omics data. The first component of REUNION, Unify, utilizes information theory-inspired complementary score functions that incorporate TF expression, chromatin accessibility, and target gene expression to identify regulatory associations. The second component, Rediscover, takes Unify estimates as input for pseudo semi-supervised learning to predict TF binding in accessible genomic regions that may or may not include detected TF motifs. Rediscover leverages latent chromatin accessibility and sequence feature spaces of the genomic regions, without requiring chromatin immunoprecipitation data for model training. Applied to peripheral blood mononuclear cell data, REUNION outperforms alternative methods in TF binding prediction on average performance. In particular, it recovers missing region-TF associations from regions lacking detected motifs, which circumvents the reliance on motif scanning and facilitates discovery of novel associations involving potential co-binding transcriptional regulators. Newly identified region-TF associations, even in regions lacking a detected motif, improve the prediction of target gene expression in regulatory triplets, and are thus likely to genuinely participate in the regulation. All source code is available at https://github.com/yangymargaret/REUNION.

Identification of the New GmJAG1 Transcription Factor Binding Motifs Using DAP-Seq.

Interaction between transcription factors (TFs) and motifs is essential for gene regulation and the subsequent phenotype formation. Soybean (Glycine max) JAGGEED 1 (GmJAG1) is a key TF that controls leaf shape, seed number and flower size. To understand the GmJAG1 binding motifs, in this study, we performed the GmJAG1 DNA affinity purification sequencing (DAP-seq) experiment, which is a powerful tool for the de novo motif prediction method. Two new significant GmJAG1 binding motifs were predicted and the EMSA experiments further verified the ability of GmJAG1 bound to these motifs. The potential binding sites in the downstream gene promoter were identified through motif scanning and a potential regulatory network mediated by GmJAG1 was constructed. These results served as important genomic resources for further understanding the regulatory mechanism of GmJAG1.

Bioinformatics approach for structure modeling, vaccine design, and molecular docking of Brucella candidate proteins BvrR, OMP25, and OMP31

Brucellosis is a zoonotic disease with significant economic and healthcare costs. Despite the eradication efforts, the disease persists. Vaccines prevent disease in animals while antibiotics cure humans with limitations. This study aims to design vaccines and drugs for brucellosis in animals and humans, using protein modeling, epitope prediction, and molecular docking of the target proteins (BvrR, OMP25, and OMP31). Tertiary structure models of three target proteins were constructed and assessed using RMSD, TM-score, C-score, Z-score, and ERRAT. The best models selected from AlphaFold and I-TASSER due to their superior performance according to CASP 12 – CASP 15 were chosen for further analysis. The motif analysis of best models using MotifFinder revealed two, five, and five protein binding motifs, however, the Motif Scan identified seven, six, and eight Post-Translational Modification sites (PTMs) in the BvrR, OMP25, and OMP31 proteins, respectively. Dominant B cell epitopes were predicted at (44–63, 85–93, 126–137, 193–205, and 208–237), (26–46, 52–71, 98–114, 142–155, and 183–200), and (29–45, 58–82, 119–142, 177–198, and 222–251) for the three target proteins. Additionally, cytotoxic T lymphocyte epitopes were detected at (173–181, 189–197, and 202–210), (61–69, 91–99, 159–167, and 181–189), and (3–11, 24–32, 167–175, and 216–224), while T helper lymphocyte epitopes were displayed at (39–53, 57–65, 150–158, 163–171), (79–87, 95–108, 115–123, 128–142, and 189–197), and (39–47, 109–123, 216–224, and 245–253), for the respective target protein. Furthermore, structure-based virtual screening of the ZINC and DrugBank databases using the docking MOE program was followed by ADMET analysis. The best five compounds of the ZINC database revealed docking scores ranged from (− 16.8744 to − 15.1922), (− 16.0424 to − 14.1645), and (− 14.7566 to − 13.3222) for the BvrR, OMP25, and OMP31, respectively. These compounds had good ADMET parameters and no cytotoxicity, while DrugBank compounds didn't meet Lipinski's rule criteria. Therefore, the five selected compounds from the ZINC20 databases may fulfill the pharmacokinetics and could be considered lead molecules for potentially inhibiting Brucella’s proteins.

A non-coding SCN5A variant that reduces sodium channel function in hiPSC-derived cardiomyocytes is significantly enriched in Brugada syndrome patients from Thailand

Abstract Background/Introduction Brugada syndrome (BrS) is an inherited arrhythmia condition that can cause sudden cardiac death. Rare coding and common non-coding genetic variation in the Nav1.5 cardiac sodium channel-encoding SCN5A gene is robustly associated with BrS, but the role of rare and low frequency non-coding variants remains unexplored. BrS is several times more prevalent in Southeast Asia compared to other populations, indicating ancestry-specific genetic risk factors remain to be discovered. Purpose To identify and characterise novel genetic risk factors in BrS patients from Southeast Asia. Methods We performed genome sequencing in 231 BrS probands from Thailand and 500 population-matched controls to identify novel disease associated variants across the entire SCN5A locus. The candidate variant was engineered into human induced pluripotent stem cells (hiPSCs) by CRISPR-Cas9 and its effect was evaluated by single cell electrophysiology analysis on hiPSC-derived cardiomyocytes. Results We identified a rare (absent in gnomAD), non-coding variant in a regulatory element of the SCN5A gene (GRCh38:3-38580380-A-C) that was significantly enriched in cases (3.9%) vs controls (0.2%) (OR=20.2[2.5-160.6], p=2e-04). Transcription factor motif scanning analysis suggested the variant is likely to disrupt a Mef2 site that is conserved across species (Figure 1) – the MEF2 family of transcription factors play a critical role in cardiac transcriptional regulation. In hiPSC-derived cardiomyocytes, a significant reduction of peak Nav1.5-mediated sodium-current (INa) density (30% decrease at -20mV, p=8e-03), without changes in gating properties, was observed in cardiomyocytes carrying the variant in heterozygosity compared to isogenic controls (Figure 2). The variant also significantly reduced luciferase activity of the candidate regulatory element in HEK cells in the presence of cardiac transcription factors (Tbx5, Gata4, Mef2A, Mef2D). Conclusion A novel, non-coding variant in an SCN5A enhancer region is associated with BrS and was functionally validated using single cell electrophysiology in hiPSC-derived cardiomyocytes. This variant is found in ∼1 in every 25 BrS patients from Thailand and therefore may at least partially explain the increased prevalence of BrS in this region. Our study highlights the importance of research in understudied populations to understand the genetic aetiology of disease in diverse ancestries and to identify novel disease risk factors.

The Adr1 transcription factor directs regulation of the ergosterol pathway and azole resistance in Candida albicans.

Research often relies on well-studied orthologs within related species, with researchers using a well-studied gene or protein to allow prediction of the function of the ortholog. In the opportunistic pathogen Candida albicans, orthologs are usually compared with Saccharomyces cerevisiae, and this approach has been very fruitful. Many transcription factors (TFs) do similar jobs in the two species, but many do not, and typically changes in function are driven not by modifications in the structures of the TFs themselves but in the connections between the transcription factors and their regulated genes. This strategy of changing TF function has been termed transcription factor rewiring. In this study, we specifically looked for rewired transcription factors, or Candida-specific TFs, that might play a role in drug resistance. We investigated 30 transcription factors that were potentially rewired or were specific to the Candida clade. We found that the Adr1 transcription factor conferred resistance to drugs like fluconazole, amphotericin B, and terbinafine when activated. Adr1 is known for fatty acid and glycerol utilization in Saccharomyces, but our study reveals that it has been rewired and is connected to ergosterol biosynthesis in Candida albicans.

Comparative Studies on Duplicated foxl2 Paralogs in Spotted Knifejaw Oplegnathus punctatus Show Functional Diversification.

As a member of the forkhead box L gene family, foxl2 plays a significant role in gonadal development and the regulation of reproduction. During the evolution of deuterostome, whole genome duplication (WGD)-enriched lineage diversifications and regulation mechanisms occurs. However, only limited research exists on foxl2 duplication in teleost or other vertebrate species. In this study, two foxl2 paralogs, foxl2 and foxl2l, were identified in the transcriptome of spotted knifejaw (Oplegnathus punctatus), which had varying expressions in the gonads. The foxl2 was expressed higher in the ovary, while foxl2l was expressed higher in the testis. Phylogenetic reconstruction, synteny analysis, and the molecular evolution test confirmed that foxl2 and foxl2l likely originated from the first two WGD. The expression patterns test using qRT-PCR and ISH as well as motif scan analysis revealed evidence of potentially functional divergence between the foxl2 and foxl2l paralogs in spotted knifejaw. Our results indicate that foxl2 and foxl2l may originate from the first two WGD, be active in transcription, and have undergone functional divergence. These results shed new light on the evolutionary trajectories of foxl2 and foxl2l and highlights the need for further detailed functional analysis of these two duplicated paralogs.

Analysis of genetic variants in the exon 2 and 3 of autosomal DAZLA gene among infertile South Indian men

BackgroundBoule, DAZLA, and DAZ are members of the Deleted in Azoospermia family of genes, which play significant roles in gametogenesis and are important fertility factors in humans. In a few studies, deletion of the Y chromosomal DAZ cluster and single nucleotide polymorphisms in the DAZLA gene were reported to affect male fertility, although this is paradoxical because they were found in both control and fertile men. As a result, the goal of this study was to check if Y chromosomal DAZ cluster deletion and SNPs in the DAZLA gene on chromosome 3 of humans are associated to male infertility in the population. For computational analysis, different bioinformatics tools such as SIFT, PolyPhen2, Mutation Taster, FATHMM, and PROVEAN were used to analyse mutations.ResultsWithin the studied population, we found no association between DAZ deletion and the most prevalent DAZLA SNPs A260G (rs11710967) and A386G (rs1219183446). We also discovered two new deleterious genetic variations in exon 3 of the DAZLA gene, one nonsynonymous mutation that replaced Valine with Glutamate at the 66 codon position and the other a stop gain mutation at the 74 amino acid position. These genetic changes are found in the RRM domain of the DAZLA gene, which is confirmed by Motif scan analysis and results in a change in the DAZLA protein's secondary structure. The RRM domain is a highly conserved regulatory domain for mRNA transport and translation. Azoospermia and necrospermia infertility phenotypes were shown in infertile male samples with these genotypes.ConclusionWe can conclude that further investigation of the aforesaid new mutations in the DAZLA gene may be valuable in understanding their significance in male infertility in different populations due to the multifactorial nature of male infertility and arrays of gene expression required at every stage of spermatogenesis.

1197 Validation of the MoTiF scanning method for multiplexed cell phenotyping and spatial profiling in melanoma samples

1197 Validation of the MoTiF scanning method for multiplexed cell phenotyping and spatial profiling in melanoma samples

Abstract 4757: Loss of KDM5A supports KRAS-driven pancreatic cancer

Abstract Objective: Mutant KRAS is a primary driver of pancreatic ductal adenocarcinoma (PDAC), which exhibits marked hypoxia. Despite the strong association of hypoxia and PDAC, the relationship between KRAS and hypoxia is still poorly understood. The oxygen-sensitive histone lysine demethylase, KDM5A, was recently reported to mediate epigenetic responses to hypoxia independent of the hypoxia-inducible factors. KDM5A epigenetically represses transcription via two mechanisms: by its demethylase activity on activating H3K4me3 marks, and through its interaction with deacetylase complexes containing HDAC1/2, which deacetylates activating H3K9ac and H4K16ac histone marks. Under hypoxic conditions, KDM5A loses its activity, leading to restoration of these H3K4me3 marks, thereby activating KDM5A target genes. The purpose of this study is to understand how KDM5A loss of function contributes to pathogenesis of mutant KRAS-driven pancreatic cancer. Methods: Cell lines derived from mice with pancreas-specific p53 deletion and doxycycline-inducible expression of KrasG12D (iKPC). Protein lysates were prepared using RIPA buffer. Histones were purified by acid extraction. Immunoblotting was used to probe for protein levels of Kdm5a, H3K4me3, H3K9ac, and H4K16ac. Genetic ablation of KrasG12D was performed by culturing iKPCs in tetracycline-free medium. Kras was induced by adding doxycycline to the culture medium. Pharmaceutical inhibition of MEK, proteasome, and Kdm5a were performed by treating iKPCs with mirdametinib, MG-132, and CPI-455, respectively. Knockdown of β-TrCP and FBXW7 were performed by stable expression of shRNA in iKPCs. Protein motif scanning was performed using the Eukaryotic Linear Motif (ELM) Prediction online software. Results: We discovered that Kdm5a protein levels were abrogated by induction of KrasG12D and stabilized by genetic ablation of Kras. Pharmaceutical inhibition of MEK or proteasome function stabilized Kdm5a, indicating that Kras induces Kdm5a proteasomal degradation through the MEK/ERK pathway. H3K4me3, H3K9ac, and H4K16ac histone marks were increased in Kras-on iKPC compared to Kras-off iKPC, consistent the expected effect of Kras-induced Kdm5a degradation. Pharmaceutical inhibition Kdm5a in the Kras-off setting restored H3K4me3, suggesting that Kdm5a contributes to demethylation of H3K4me3 in iKPC. We identified two phosphodegron sites corresponding to β-TrCP and FBXW7 of the ubiquitin ligase complex within the Kdm5a protein sequence. Knockdown of either β-TrCP or FBXW7 in iKPC both stabilized Kdm5a despite induction of Kras. Conclusion: We conclude that Kdm5a plays a tumor suppressor role in pancreatic cancer by epigenetically repressing transcriptional programs necessary for KRAS-driven oncogenesis. Citation Format: Jasper R. Chen, Jincheng Han, Cullen M. Taniguchi, Ronald A. DePinho. Loss of KDM5A supports KRAS-driven pancreatic cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4757.

The transcript interactome of skeletal muscle RNA binding protein motif 3 (RBM3).

Post-transcriptional regulation of gene expression represents a critical regulatory step in the production of a functional proteome. Elevated expression of post-transcriptional regulator RNA binding motif protein 3 (RBM3), an RNA binding protein in the cold-shock family, is positively correlated with skeletal muscle growth in adult mice. However, mechanisms through which RBM3 exerts its effects are largely unknown. The purpose of this study was to perform RNA immunoprecipitation followed by RNA sequencing (RIP-seq) and apply a network science approach to understand biological processes (BPs) most associated with RBM3-bound mRNAs. In addition, through nucleotide-sequence-scanning of enriched transcripts, we predicted the motif for skeletal muscle RBM3 binding. Gene set enrichment analysis followed by enrichment mapping of RBM3-bound transcripts (fold change >3; p.adj <0.01) revealed significant enrichment of BPs associated with "Contractile apparatus," "Translation initiation," and "Proteosome complex." Clusters were driven largely by enrichment of Myh1 (FC: 4.43), Eif4b (FC: 5.03), and Trim63 (FC: 5.84), respectively. Motif scanning of enriched sequences revealed a discrete 14 nucleotide-wide motif found most prominently at the junction between the protein coding region's termination sequence and the start of the 3' untranslated region (UTR; E-Value: 1.1 e-015 ). Proof of concept investigation of motif location along enriched transcripts Myh1 and Myl4 revealed 3' UTR binding, suggesting RBM3 involvement in transcript half-life regulation. Together, these results demonstrate the potential influence of RBM3 in reshaping the skeletal muscle proteome through post-transcriptional regulation of mRNAs crucial to muscle adaptations.

MaxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.

Transcription factors read the genome, fundamentally connecting DNA sequence to gene expression across diverse cell types. Determining how, where, and when TFs bind chromatin will advance our understanding of gene regulatory networks and cellular behavior. The 2017 ENCODE-DREAM in vivo Transcription-Factor Binding Site (TFBS) Prediction Challenge highlighted the value of chromatin accessibility data to TFBS prediction, establishing state-of-the-art methods for TFBS prediction from DNase-seq. However, the more recent Assay-for-Transposase-Accessible-Chromatin (ATAC)-seq has surpassed DNase-seq as the most widely-used chromatin accessibility profiling method. Furthermore, ATAC-seq is the only such technique available at single-cell resolution from standard commercial platforms. While ATAC-seq datasets grow exponentially, suboptimal motif scanning is unfortunately the most common method for TFBS prediction from ATAC-seq. To enable community access to state-of-the-art TFBS prediction from ATAC-seq, we (1) curated an extensive benchmark dataset (127 TFs) for ATAC-seq model training and (2) built "maxATAC", a suite of user-friendly, deep neural network models for genome-wide TFBS prediction from ATAC-seq in any cell type. With models available for 127 human TFs, maxATAC is the largest collection of high-performance TFBS prediction models for ATAC-seq. maxATAC performance extends to primary cells and single-cell ATAC-seq, enabling improved TFBS prediction in vivo. We demonstrate maxATAC's capabilities by identifying TFBS associated with allele-dependent chromatin accessibility at atopic dermatitis genetic risk loci.

Identification of upstream transcription factor binding sites in orthologous genes using mixed Student’s t-test statistics

Transcription factor (TF) regulates the transcription of DNA to messenger RNA by binding to upstream sequence motifs. Identifying the locations of known motifs in whole genomes is computationally intensive. This study presents a computational tool, named "Grit", for screening TF-binding sites (TFBS) by coordinating transcription factors to their promoter sequences in orthologous genes. This tool employs a newly developed mixed Student's t-test statistical method that detects high-scoring binding sites utilizing conservation information among species. The program performs sequence scanning at a rate of 3.2 Mbp/s on a quad-core Amazon server and has been benchmarked by the well-established ChIP-Seq datasets, putting Grit amongst the top-ranked TFBS predictors. It significantly outperforms the well-known transcription factor motif scanning tools, Pscan (4.8%) and FIMO (17.8%), in analyzing well-documented ChIP-Atlas human genome Chip-Seq datasets. Grit is a good alternative to current available motif scanning tools.

Characterization of Three cDNAs Obtained by Spliced Leader-PCR Screening of a Taenia solium cDNA Library

Cysticerci or metacestodes of Taenia solium cause cysticercosis, being the neurocysticercosis (NCC) the main pathology. The characterization of genes is essential for the knowledge of parasite biology, the understanding of the parasite-host relationship, and the identification of possible targets for diagnosis, treatment, and protection. The objective of this work was the molecular and bioinformatic characterization of three news cDNAs (TsTF10, TsAAP8, and TsrGAP8), obtained by spliced leader-PCR screening of a Taenia solium cDNA library. The sequences of the three cDNA were compared with the sequences in the nucleic acid and protein databases (GenBank, EMBL) and analyzed by bioinformatic programs (CDD-Search of the National Center for Biotechnology Information, Interpro of the European Bioinformatics Institute, Motif scan and Expert Protein Analysis System of the Proteomics Server from Swiss Institute of Bioinformatics). Considering the high identities with similar molecules of related helminths (Taenia asiatica, Echinococcus granulosus, Echinococcus multilocularis, and Hymenolepis diminuta) and the functional domains found, the TsTF10, TsAAP8, and TsrGAP8 genes of Taenia could act as a nuclear transcription factor gamma, a putative vacuolar ATPase membrane sector associated protein and a Rho GTPase activating protein, respectively. Although few B epitopes could be predicted in the sequences, it could be relevant to evaluate them as possible candidates for diagnosis and protection in cysticercosis. The characterization and analysis of these sequences and the prediction of their possible usefulness as antigens, vaccines, or therapeutic targets contribute to the designing and planning of future studies.

RSAT 2022: regulatory sequence analysis tools.

RSAT (Regulatory Sequence Analysis Tools) enables the detection and the analysis of cis-regulatory elements in genomic sequences. This software suite performs (i) de novo motif discovery (including from genome-wide datasets like ChIP-seq/ATAC-seq) (ii) genomic sequences scanning with known motifs, (iii) motif analysis (quality assessment, comparisons and clustering), (iv) analysis of regulatory variations and (v) comparative genomics. RSAT comprises 50 tools. Six public Web servers (including a teaching server) are offered to meet the needs of different biological communities. RSAT philosophy and originality are: (i) a multi-modal access depending on the user needs, through web forms, command-line for local installation and programmatic web services, (ii) a support for virtually any genome (animals, bacteria, plants, totalizing over 10 000 genomes directly accessible). Since the 2018 NAR Web Software Issue, we have developed a large REST API, extended the support for additional genomes and external motif collections, enhanced some tools and Web forms, and developed a novel tool that builds or refine gene regulatory networks using motif scanning (network-interactions). The RSAT website provides extensive documentation, tutorials and published protocols. RSAT code is under open-source license and now hosted in GitHub. RSAT is available at http://www.rsat.eu/.

A de Novo ZMIZ1 Pathogenic Variant for Neurodevelopmental Disorder With Dysmorphic Facies and Distal Skeletal Anomalies

Background: Neurodevelopmental disorder with dysmorphic facies and distal skeletal anomalies (NEDDFSA) is a rare syndromic disorder characterized by global neurodevelopmental delay, early-onset hypotonia, poor overall growth, poor speech/language ability, and additional common phenotypes such as eye anomalies, joint hypermobility, and skeletal anomalies of the hands and feet. NEDDFSA is caused by heterozygous pathogenic variants in the ZMIZ1 gene on chromosome 10q22.3 with autosomal dominant (AD) mode of inheritance. All the 32 reported cases with variants in ZMIZ1 gene had a genetic background in Caucasian, Hispanic, North African, and Southeastern Asian. Until now, there are no reports of Chinese patients with ZMIZ1 pathogenic variants. Methods: A 5-year-old girl was found to have the characteristic phenotypes of NEDDFSA. Array-Comparative Genomic Hybridization (array-CGH) and whole exome sequencing (WES) were applied for the trio of this female patient. Sanger sequencing was used to verify the selected variants. A comprehensive molecular analysis was carried out by protein structure prediction, evolutionary conservation, motif scanning, tissue-specific expression, and protein interaction network to elucidate pathogenicity of the identified ZMIZ1 variants. Results: The karyotype was 46, XX with no micro-chromosomal abnormalities identified by array-CGH. There were 20 variants detected in the female patient by WES. A de novo heterozygous missense variant (c.2330G > A, p.Gly777Glu, G777E) was identified in the exon 20 of ZMIZ1. No variants of ZMIZ1 were identified in the non-consanguineous parents and her healthy elder sister. It was predicted that G777E was pathogenic and detrimental to the spatial conformation of the MIZ/SP-RING zinc finger domain of ZMIZ1. Conclusion: Thus far, only four scientific articles reported deleterious variants in ZMIZ1 and most of the cases were from Western countries. This is the first report about a Chinese patient with ZMIZ1 variant. It will broaden the current knowledge of ZMIZ1 variants and variable clinical presentations for clinicians and genetic counselors.