Transcription-Austin最新文献

Transcription termination is a highly regulated step which sets boundaries between genes and maintains genome integrity. Defects in transcription termination will cause unexpected expression of downstream genes and traffic-jam of RNA polymerases with protein machineries. Termination occurs mainly in two types of mechanisms regarding whether it depends on molecular motor action, i.e. factor-dependent termination, or is induced solely by nucleic acid signals, i.e. intrinsic termination. In recent years, great efforts have been devoted to, and significant advances have been achieved in understanding the mechanisms of transcription termination. This review focuses on the topic of factor-dependent termination and intrinsic termination and highlights the recent progress in the structural and functional studies of RNA polymerases that are critical for transcription termination.

CGGBP1, a 20 kDa protein, has several functions associated with its DNA-binding through a C2H2 zinc finger. A range of studies have shown that GC richness, inter-strand G/C-skew and low cytosine methylation are associated with CGGBP1 occupancy. The non-preference of any sequence motif as CGGBP1 binding site suggests widespread association of CGGBP1 with DNA including at potent transcription factor-binding sites (TFBSs) in promoter regions. The evolutionary advantage of such a design remains unclear. The regulatory interference by human CGGBP1 at TFBSs is supported by purifying selection in the DNA-binding domain of CGGBP1 and its requirement for gene repression as well as restriction of cytosine methylation at GC-rich TFBSs. Here, we describe an evolutionary trajectory of this property of CGGBP1 by combining global gene expression and cytosine methylation analyses on human cells expressing CGGBPs from four different vertebrates (representatives of coelacanth, reptiles, aves and mammals). We discover a potent cytosine methylation restriction by human CGGBP1 at some GC-rich TFBSs in repressed promoters. Further, we combine a high-throughput analysis of GC compositional bias of these CGGBP-regulated TFBSs from available orthologous sequences from a pool of over 100 species. We show that cytosine methylation restriction by CGGBP1 is tightly linked to GC retention in a set of TFBSs. Our experiments using four representative and three consensus forms of CGGBPs and orthology analyses of target gene promoters indicate that this property of CGGBPs has most likely evolved in higher amniotes (aves and mammals) with lineage-specific heterogeneities in lower amniotes (reptiles). ChIP-seq and C-T transition analysis in MeDIP-seq suggest that occupancy of CGGBP1 at these target TFBSs plays a crucial role in their low methylation, GC-biased evolution and associated functions in gene repression.

TATA-box binding protein (TBP) is a core subunit of the transcription factor TFIID and plays a pivotal role in recognizing the TATA-box in protein-coding genes, facilitating the assembly of the transcription preinitiation complex. In Taenia solium, only one TBP isoform (TsTBP1) has been previously reported. Here, we identify and characterize a second isoform, TsTBP2, using a combination of molecular biology and bioinformatics approaches. TsTBP2 shares 42% primary sequence identity with TsTBP1 and exhibits distinct expression patterns between cysticerci and adult stages. To investigate the molecular determinants of DNA recognition, selectivity, and binding affinity, we performed molecular docking and molecular dynamics simulations for both TsTBPs with various TATA-box sequences. Our results reveal that TsTBP1 exhibits higher affinity for T. solium TATA-box sequences compared to the consensus AdML TATA-box (TATAAAAG), largely due to the specific interaction of critical phenylalanine residues with the DNA minor groove, which induces DNA bending and stabilizes the TBP-DNA complex. Furthermore, analysis of the Buckle parameter indicates that these Phe residues are the principal contributors to DNA distortion. To our knowledge, this study represents the first analysis of TBP selectivity and affinity in cestodes, providing insights into the molecular mechanisms underlying transcriptional regulation in T. solium.

Proper regulation of transcription involves not only quantitative control of RNA dosage but also ensuring the correct biochemical properties of transcripts. In all eukaryotes, the epigenetic landscape and the dynamic composition of the RNA Polymerase II complex (PolII) interact to control the transcription of translatable mRNA. Decades of research have described dogmatic rules for model organisms, such as the distribution of individual chromatin marks along the transcription unit or the hierarchical phosphorylation pattern in the C-terminal domain (CTD) of the largest PolII subunit RPB1. Besides this canonical mRNA transcription, there are exceptions; on the one hand, not all genes in a species follow the dogma, and on the other hand, there are species that show general divergence from the models, both in the epigenomic landscape and in the genetically encoded PolII. In the recent literature, protists in particular have shifted their attention as they show considerable differences in chromatin structure and PolII complex composition. Here, we aim to enlighten the transcription machinery of the unicellular ciliate Paramecium as an exciting model to study a divergent transcriptional machinery for vegetative mRNA and developmental ncRNA transcription.

Human Immunodeficiency Virus 1 (HIV-1) is the causative agent for acquired immunodeficiency syndrome (AIDS). Antiretroviral therapy has turned HIV-1 from a lethal disease to a chronic condition but is not curative due to the persistence of a small reservoir of latently infected cells. The molecular mechanisms driving HIV-1 latency have been extensively studied, thus far largely focusing on transcriptional regulation. Here, we summarize well established and newly discovered mechanisms of HIV-1 latency, as well as how studies of the HIV-1 promoter have informed the broader transcription field. As a strategy toward HIV-1 cure, latency reversal agents (LRAs) have been developed to pharmacologically target blocks in HIV-1 transcription to achieve reactivation of viral gene expression. However, clinical studies indicate that LRAs have largely failed to sufficiently activate the reservoir such that viral protein is produced, and there was no reduction in the size of the viral reservoir. Indeed it has become clear that co- and post-transcriptional mechanisms are also at play to regulate HIV-1 gene expression and may also serve as attractive targetable blocks. We also outline recent developments in technologies allowing the ex vivo characterization of the HIV-1 reservoir in people living with HIV (PWH). These novel technologies enable us to interrogate the different molecular compartments such as integrated intact and defective proviral HIV-1 DNA, unspliced and spliced RNA, and protein levels that provide unprecedented new insight into latency mechanisms. Lastly, the potential of different transcription-targeting cure strategies is discussed in light of the contributions of co- and posttranscriptional blocks and the advent of Long Acting (LA)-ART.

Epstein-Barr Virus (EBV) establishes life-long latent infection in >90% of adults and is a causal agent for diverse cancers and autoimmune diseases. EBV has a complex life cycle in multiple different tissue types that involve dynamic variations in viral gene expression. These gene expression changes account for the success of the virus in long-term persistence and evading host immune control, as well as its potential for driving cancer evolution and autoimmune disease. Here, we review some of the salient features of EBV gene regulation highlighting the many variations of viral transcription. We review recent advances in our understanding of the factors that bind and regulate EBV gene expression. Based on this diversity of viral transcription patterns, we propose that EBV genome consists of gene modules regulated by local promoter-proximal transcription factor combinations that are further regulated by distal regulatory interactions among the various modules that interact through architectural factors, such as CTCF and cohesion. These modules are likely to represent chromatin architectural domains, and can also interact with host chromosome domains that further regulate viral and host gene expression. We propose that this gene regulatory hierarchy provides EBV with necessary plasticity for viral persistence, as well as a strong potentiator for cancer and autoimmune disease.

Eukaryotic transcription of mRNAs and some non-coding RNAs is governed by RNA Polymerase II (RNA pol II). The full progression of RNA pol II across a gene - from promoter clearance through transcript elongation and termination - is dependent upon the post-translational modifications (PTMs) of its carboxy-terminal domain (CTD) and the dynamic recruitment of numerous trans-acting factors. Rtr1 in yeast and its human orthologue, RPAP2, have emerged as multifunctional regulators of RNA pol II. Despite evidence supporting their role as Ser5-specific CTD phosphatases, structural and biochemical studies have raised doubts about whether they are bona fide phosphatases or instead function as cofactors that influence the activity of established CTD phosphatases. Furthermore, both proteins have been implicated in processes ranging from RNA pol II biogenesis and nuclear transport to transcriptional elongation and termination. Notably, Rtr1's influence also extends to post-transcriptional events like mRNA stability. In this review, we describe the main functions attributed to Rtr1 and RPAP2, and discuss the role of the human homologue in various diseases.

Background: Transcription factor (TF) proteins play a critical role in the regulation of eukaryotic gene expression via sequence-specific binding to genomic locations known as transcription factor binding sites (TFBSs). Accurate prediction of TFBSs is essential for understanding gene regulation, disease mechanisms, and drug discovery. These studies are therefore relevant not only in humans but also in model organisms and domesticated and wild animals. However, current tools for the automatic analysis of TFBSs in gene promoter regions are limited in their usability across multiple species. To our knowledge, no tools currently exist that allow for automatic analysis of TFBSs in gene promoter regions for many species.

Methodology and findings: The TFBSFootprinter tool combines multiomic transcription-relevant data for more accurate prediction of functional TFBSs in 317 vertebrate species. In humans, this includes vertebrate sequence conservation (GERP), proximity to transcription start sites (FANTOM5), correlation of expression between target genes and TFs predicted to bind promoters (FANTOM5), overlap with ChIP-Seq TF metaclusters (GTRD), overlap with ATAC-Seq peaks (ENCODE), eQTLs (GTEx), and the observed/expected CpG ratio (Ensembl). In non-human vertebrates, this includes GERP, proximity to transcription start sites, and CpG ratio.TFBSFootprinter analyses are based on the Ensembl transcript ID for simplicity of use and require minimal setup steps. Benchmarking of the TFBSFootprinter on a manually curated and experimentally verified dataset of TFBSs produced superior results when using all multiomic data (average area under the receiver operating characteristic curve, 0.881), compared with DeepBind (0.798), DeepSEA (0.682), FIMO (0.817) and traditional PWM (0.854). The results were further improved by selecting the best overall combination of multiomic data (0.910). Additionally, we determined combinations of multiomic data that provide the best model of binding for each TF. TFBSFootprinter is available as Conda and Python packages.

The lncRNAs have deepened our understanding of crop domestication and improvement. These regulators influence key traits like yield, germination, and stress response. Future research should identify functional lncRNAs, explore their interactions, and use CRISPR for targeted improvements. Understanding their roles in polyploid crops may enhance resilience and productivity.

The regulation of transcription is a major control point in the flow of information from the genome to the phenome. Central to this regulation are transcription factors (TFs), which bind specific DNA motifs in gene regulatory regions. In both metazoans and plants, 5-7% of all genes encode TFs. Although individual TFs can recognize and regulate thousands of target genes, an important question remains: how many TFs are required to precisely control the expression of a single gene? In this review, we compare the regulation of gene expression in plants and metazoans, outline key methodologies for identifying genes recognized or regulated by TFs, and explore what is currently known about the number of TFs needed to define the expression of any given plant gene. As the volume of high-throughput sequencing data continues to grow exponentially, it becomes increasingly clear that transcriptional regulatory networks exhibit remarkable complexity, characterized by many targets influenced by each TF; and that many TFs, often several dozens, contribute to the regulation of individual genes.