Copies Of Sequence Research Articles

EPSPS target site mechanisms confer glyphosate resistance in Arctotheca calendula.

The first case of glyphosate resistance was reported in a capeweed population from Western Australia in our previous study. This current study investigates the resistance mechanisms in the population. Target-site EPSPS gene sequencing revealed two partial sequences of the EPSPS transcripts (1001 bp and 998 bp), and the full-length sequence (1551 bp) containing the 1001-bp transcript was cloned as it was found in the resistant plants. A known resistance-endowing target-site mutation in the 1551-bp transcript was identified in the resistant plants, resulting in the Pro-106-Ser substitution. The subpopulation derived from these mutant plants exhibited >10-fold resistance to glyphosate compared to the susceptible population. Additionally, the EPSPS gene (1551 bp) was constitutively expressed at a higher level (4.3-fold) in the resistant than in the susceptible populations. However, 14C-glyphosate foliar uptake was similar with no visual difference in 14C-glyphosate translocation from leaves to other parts of a plant, between the resistant and susceptible population. Glyphosate resistance in the studied population is associated with both a target-site mutation (Pro-106-Ser) and increased EPSPS gene expression. © 2025 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Characterization of novel human endogenous retrovirus structures on chromosomes 6 and 7

Human endogenous retroviruses (HERV) represent nearly 8% of the human genome. Of these, HERV-K subtype HML-2 is a transposable element that plays a critical role in embryonic development and in the pathogenesis of several diseases. Quantification and characterization of these multiple HML-2 insertions in the human chromosome has been challenging due to their size, sequence homology with each other, and their repetitive nature. We examined a cohort of 222 individuals for HML-2 proviruses 6q14.1 and 7p22.1a, two loci that are capable of producing full-length viral proteins and have been previously implicated in several cancers, autoimmune disorders and neurodegenerative diseases, using long-read DNA sequencing. While the reference genome for both regions suggests these two loci are structurally dissimilar, we found that for both loci about 5% of individuals have a unique tandem repeat-like sequence (three long terminal repeat sequences sandwiching two internal, potentially protein coding sequences), while most individuals have a standard proviral structure (one internal region sandwiched by two long terminal repeats). Moreover, both proviruses can make full-length, or nearly full-length, HERV-K proteins in multiple transcription orientations. The amino acid sequences from different loci in the same transcriptional orientation share sequence homology with each other. These results demonstrate a clear, previously unreported, relationship between HML-2 loci 6q14.1 and 7p22.1a and highlight the utility of long-read sequencing to study repetitive elements. Future studies need to determine if these polymorphisms determine genetic susceptibility to diseases that are associated with them.

PlantReg: the reconstruction of links between transcription factor regulatory networks and biological processes under their control

The description of the path from a gene to a trait, as the main task of many areas in biology, is currently being equipped with new methods affecting not only experimental techniques, but also analysis of the results. The pleiotropic effect of a gene is due to its participation in numerous biological processes involved in different traits. A widespread use of genome-wide sequencing of transcripts and transcription factor (TF) binding regions has made the following tasks relevant: unveiling pleiotropic effects of TFs based on the functions of their target genes; compiling the lists of TFs that regulate biological processes of interest; and describing the ways of TF functioning (their primary and secondary targets, higher order targets, TF interactions in the process under study). We have previously developed a method for the reconstruction of TF regulatory networks and proposed an approach that allows identifying which biological processes are controlled by these networks and how this control is exerted. In this paper, we have implemented the approach as PlantReg, a program available as a web service. The paper describes how the program works. The input consists of a list of genes and a list of TFs – known or putative transcriptional regulators of these genes. As an output, the program provides a list of biological processes enriched for these genes, as well as information about by which TFs and through which genes these processes are controlled. We illustrated the use of PlantReg deciphering transcriptional regulation of processes initiated at the early salt stress response in Arabidopsis thaliana L. With PlantReg, we identified biological processes stimulated by the stress, and specific sets of TFs that activate each process. With one of these processes (response to abscisic acid) as an example, we showed that salt stress mainly affects abscisic acid signaling and identified key TFs in this regulation. Thus, PlantReg is a convenient tool for generating hypotheses about the molecular mechanisms that control plant traits.

Reimagining André Rey's method for recording the copy process of the Rey Complex Figure Test: A commentary.

In 1941, André Rey published the Rey Complex Figure, a widely used test for assessing visual-constructional ability and visual memory. It consists of two parts: copy and recall. Evaluating the copy portion presents challenges, as it requires the administrator to focus on both the process and outcome. The assessor must systematically track how the patient copies the figure in real-time to evaluate their planning, organisation and executive abilities. This 'clinician's copy' serves as a record of the patient's approach, aiding later judgements about their cognitive skills. To ensure accuracy, clinicians need a method to record this process for later review or colleague consultation. This paper revisits Rey's suggestion of using different coloured pencils to observe the copy sequence, proposing an alternative. Instead of providing coloured pencils to the patient, we recommend that the administrator use them to record the copy sequence. This method aligns with test norms, reducing potential distractions for the patient while enabling both experienced and novice administrators to easily track and document the sequence of copying.

Assessing Human Ribosomal DNA Variation and Its Association With Phenotypic Outcomes.

Although genome-scale analyses have provided insights into the connection between genetic variability and complex human phenotypes, much trait variation is still not fully understood. Genetic variation within repetitive elements, such as the multi-copy, multi-locus ribosomal DNA (rDNA), has emerged as a potential contributor to trait variation. Whereas rDNA was long believed to be largely uniform within a species, recent studies have revealed substantial variability in the locus, both within and across individuals. This variation, which takes the form of copy number, structural arrangement, and sequence differences, has been found to be associated with human phenotypes. This review summarizes what is currently known about human rDNA variation, its causes, and its association with phenotypic outcomes, highlighting the technical challenges the field faces and the solutions proposed to address them. Finally, we suggest experimental approaches that can help clarify the elusive mechanisms underlying the phenotypic consequences of rDNA variation.

Development and Application of Transcript Sequencing

Transcriptome sequencing has become one of the mainstream methods for detecting gene expression after the development of high-throughput sequencing technology. We present the trajectory of the technological evolution of sequencing technologies between three generations and discuss their technical implementations, advantages, and disadvantages. Next, we show examples of this technology through the current mainstream NGS technology-based RNA-seq sequencing and analysis. We also look forward to the progress of the third-generation sequencing technology in read length and variable splicing detection.

Expression Cloning of Antibodies from Single Human B Cells.

The majority of lymphomas originate from B cells at the germinal center stage. Preferential selection of B-cell clones by a limited set of antigens has been suggested to drive lymphoma development. While recent studies in B-cell chronic lymphocytic leukemia (CLL) have shown that self-reactive B-cell receptors (BCR) can generate cell-autonomous signaling and proliferation, our knowledge about the role of BCRs for the development or survival of other lymphomas remains limited. Here, we describe a strategy to characterize the antibody reactivity of human B cells. The approach allows for unbiased characterization of the human antibody repertoire on single-cell level through the generation of recombinant monoclonal antibodies from primary human B cells of defined origin. This protocol offers a detailed description of the method starting from the flow cytometric isolation of single human B cells to the RT-PCR-based amplification of the expressed immunoglobulin (Ig) transcripts (IGH, IGK, and IGL) and their subsequent cloning into expression vectors for the in vitro production of recombinant monoclonal antibodies. The strategy may be used to obtain information about the clonal evolution of B-cell lymphomas by single-cell sequencing of Ig transcripts and on the antibody reactivity of human lymphoma B cells.

An Open-Label Phase II Trial of Pembrolizumab, an Immune Checkpoint Inhibitor Alone or in Combination With Oral Azacitidine as Second-Line Therapy for Advanced Head and Neck Squamous Cell Cancers.

Sensitivity to immune checkpoint inhibitor (ICI) therapy depends in part on the genetic and epigenetic makeup of cancer cells, and CD8 T-lymphocytes that mediate immune responses. Epigenetics are heritable reversible changes in gene expression that occur without any changes in the nuclear DNA sequence or DNA copy number. i. To determine if non-cytotoxic oral azacytidine when combined with pembrolizumab can improve ORRs of ICI treatment in patients with recurrent/metastatic tumors of head and neck region. i. To evaluate the clinical effectiveness endpoints and toxicity of oral azacytidine when combined with pembrolizumab. ii. To assess the induction of a T-cell response among the study subjects. iii. To examine the hypotheses on the predictive biomarkers of response to pembrolizumab, and the mechanisms of resistance. Our trial is a Phase 2 randomized study of immunotherapy drug pembrolizumab given in combination with azacitidine (HMA). The intervention model includes "Parallel assignment," with the primary purpose of the trial being treatment. The primary effectiveness endpoint is overall RECIST-defined response. To accomplish this goal, 232 patients will be randomized 1:1 (116 in each arm), respectively, to azacitidine plus pembrolizumab or pembrolizumab only groups. In this trial, molecular profiling of tumor and peripheral blood samples will be conducted which will enable in gaining biological insights for survival benefit. The expected primary outcome assessed at a time frame of 2 years includes the objective response rate of patients measured as per RECIST 1.1 criteria. The secondary outcomes assessed at 2 years include progression-free survival, time to progression, overall survival, and incidence of treatment-emergent adverse events. The findings of this trial will have translational implications, in terms of immune reprogramming induced by epigenetic therapy among a subset of advanced H & N cancer patients in a clinical setting.

Systematic Analysis of E3 Ligase-Related Genes Identified UBE2L3 as a Prognostic Biomarker Associated With Drug Resistance in Acute Myeloid Leukemia.

Acute Myeloid Leukemia (AML) is a prevalent neoplastic disorder. The roles of E3 ubiquitin ligases and related genes in AML drug resistance and prognosis remain unclear. Genes were identified from GeneCards and UniProt databases, differentially expressed genes were selected based on transcriptional sequencing data from wild-type and Adriamycin-resistant HL60 (HL60/WT & HL60/ADR) cell lines, and the intersection of these three sources was taken. We then constructed a prognostic model comprising five genes (HBP1, RNF130, RMND5B, TRIM32, and UBE2L3) through univariate Cox and LASSO regression analyses in the TCGA cohort and validated it in the BeatAML2.0 cohort. Finally, the expression of UBE2L3 was verified in cell lines and clinical case specimens. The model accurately predicted AML prognosis and identified the UBE2L3 gene within the model as a high-risk biomarker associated with drug resistance, significantly influencing AML outcomes. The high expression of UBE2L3 is a reliable biomarker for drug resistance and poor prognosis of acute myeloid leukemia.

Combining Short- and Long-Read Transcriptomes for Targeted Enzyme Discovery.

The discovery of genes that code for a specific enzymatic activity is important in various fields of life science and provides valuable biotechnological tools. Many genes that contribute to the production of secondary metabolites and specialized metabolic pathways are still not identified. Due to the great diversity of metabolic functions found in nature and their rapid evolutionary adaptation, we need precise but high-throughput approaches for a targeted search based on minimal prior knowledge. In this chapter, we describe a transcriptomics pipeline that was used to search for candidate genes coding for a specific enzymatic activity in a nonmodel species. We generated and combined short- and long-read transcriptomic data to obtain reliable full-length transcript sequences along with information on allelic variation, isoform expression, and condition-specific expression. Based on protein domain annotations of coding sequences and transcriptomic data, we selected candidate genes for activity assays. We provide detailed instructions for analysis and quality control steps in our pipeline that can be applied to other biological questions.

Identification of the Mitf gene mutation causing congenital deafness and pigmentation disorders in porcupines using BSA-Seq

Worldwide, congenital deafness and pigmentation disorders impact millions with their diverse manifestations, and among these genetic conditions, mutations in the Microphthalmia-associated transcription factor (MITF: OMIM#156845) gene are notable for their profound effects on melanocyte development and auditory functions. This study reports a novel porcupine model exhibiting spontaneous deafness and pigmentation abnormalities reminiscent of human Waardenburg Syndrome Type 2 (WS2: OMIM#193510). Through phenotypic characterization, including coat color, skin, eye morphology, and auditory brainstem response (ABR) assessments, we identified hypopigmentation and complete deafness in mutant porcupines. To pinpoint the genetic basis, a breeding program was established, and Bulk Segregant Analysis (BSA) combined with RNA sequencing was conducted. Primers based on the identified candidate genes were designed for PCR amplification, followed by verification through Sanger sequencing. Through BSA analysis, we identified a total of 88 SNP and 336 InDel candidate sites. By annotating the Mitf gene, we obtained four unique transcript sequences. The SNP and InDel sites within the porcupine Mitf gene sequence, identified through BSA screening, were analyzed in conjunction with the gene’s annotation results. This analysis revealed a specific mutation site, Mitf c.875_877delGAA p. (Arg217del), which was subsequently verified by Sanger sequencing. This naturally occurring Mitf mutation in porcupines provides a valuable model for studying the mechanisms underlying WS2 and exploring potential therapeutic strategies for deafness and pigmentation-related disorders.

Genetic characterization of diagnostic epitopes of cardiac troponin I in African rhinoceros.

African rhinoceros undergo chemical immobilization and prolonged transport during translocations for conservation purposes and, hence, experience several pathophysiologic changes, including skeletal muscle injury. Potential concurrent myocardial injury has not been investigated due to a lack of validated immunoassays. We aimed to use inferred cardiac troponin I (cTnI) amino acid sequences of southern white (Ceratotherium simum simum) and southern-central black (Diceros bicornis minor) rhinoceros to assess the potential usefulness of several commercial cTnI immunoassays for detecting cTnI in African rhinoceros. We extracted RNA from the myocardium of deceased rhinoceros (2 white, 1 black rhinoceros) followed by primer design, cDNA synthesis via RT-PCR, and Sanger sequencing. The inferred cTnI amino acid sequences were obtained from the mRNA transcript sequences. The homology of epitope binding sites recognized by capture and detection antibodies in 6 human immunoassays was visually evaluated using aligned inferred rhinoceros cTnI amino acid sequences. Percentage identity between white and black rhinoceros cDNA nucleotide sequences was 99%; inferred amino acid sequences were identical. There were 5 amino acid differences between humans and rhinoceros in the epitope binding sites of immunoassay antibodies; 5 assays contained antibodies against epitopes that were not conserved. For one assay, the single capture antibody targeted a short heterologous epitope (residue 87-91), and cross-reactivity with rhinoceros cTnI was deemed unlikely. For the other 5 assays, complete antibody-epitope homology, or the inclusion of multiple detection or capture antibodies, or targeting of long epitopes, indicated that these assays could be suitable for further investigation of cTnI measurement in African rhinoceros.

Effect of copper and nickel exposure on ribosomal DNA variation in Daphnia pulex mutation accumulation lines.

The release of heavy metals from industrial, agricultural, and mining activities poses significant risks to aquatic ecosystems by degrading water quality and generating reactive oxygen species (ROS) that can damage DNA in aquatic organisms. Daphnia is a widespread keystone species in freshwater ecosystems that is routinely exposed to a range of anthropogenic and natural stressors. With a fully sequenced genome, a well-understood life history and ecology, and an extensive library of responses to toxicity, Daphnia serves as an ideal model organism for studying the impact of environmental stressors on genomic stability. Ribosomal DNA (rDNA) encodes ribosomal RNA, which is essential for protein synthesis, and the spacers that separate the rRNA genes contain regulatory elements. However, the effects of heavy metals on this region of the genome are not well documented. We used short-read whole-genome sequences to analyze copy number and sequence variation in Daphnia pulex mutation accumulation lines exposed to nickel and copper, both individually and in combination, at concentrations that mimic levels often found at contaminated sites. We found no significant direct effect of chronic exposure to either metal on rDNA copy number or sequence variation. However, the results suggest that nickel and copper exposure may indirectly influence rDNA by altering recombination rates. We also emphasize the importance of interval length between generational samples for accurately assessing the frequency and magnitude of rDNA copy number changes. In addition, we observed differential expansion of rDNA haplotypes, suggesting that they may be clustered within the rDNA array.

Engineering a live-attenuated porcine reproductive and respiratory syndrome virus vaccine to prevent RNA recombination by rewiring transcriptional regulatory sequences.

Porcine reproductive and respiratory syndrome viruses (PRRSVs) are genetically diverse, and this is due in part to their extensive recombination. Live vaccines are widely used to prevent and control PRRS in China. However, owing to the wide variety of live vaccines, non-standard use, and the wild viruses prevalent on pig farms, new strains, generated via RNA recombination, are continuously emerging. Vaccine strains are also involved in PRRSV recombination, which leads to the emergence of new variants and alterations in virulence and pathogenesis. A recombination-resistant genome was engineered by rewiring the entire transcriptional regulatory sequence (TRS) circuit of the live PRRSV vaccine strain. Theoretically, after clinical application, once the virus recombines with the genome of the epidemic strain, the base pairing between the two sets of TRS circuits should be disrupted, resulting in a fatal genetic trap for the generation of an RNA recombinant progeny virus. Therefore, the remodeled PRRSV TRS mutant generated in this study can serve as a recombination-resistant platform for the rational design of safe PRRS vaccines in the future.

Exosomal ANXA2 facilitates ovarian cancer peritoneal metastasis by activating peritoneal mesothelial cells through binding with TLR2

BackgroundPeritoneal dissemination of ovarian cancer (OvCa) can be largely attributed to the formation of a metastatic microenvironment driven by tumoral exosomes. Here, we aimed to elucidate the mechanisms through which exosomal annexin A2 (ANXA2) derived from OvCa cells induces an HPMC phenotypic shift in favour of peritoneal metastasis.MethodsImmunohistochemistry and orthotopic and intraperitoneal OvCa xenograft mouse models were used to clarify the relationship between tumour ANXA2 expression and peritoneal metastasis. Exosomes were isolated from OvCa cell lines via ultracentrifugation. Functional experiments on cell proliferation and motility, and western blot were performed to investigate the activation of HPMCs and its impact on tumour cell in vitro. High-throughput transcriptional sequencing and rescue experiments in which ANXA2 inhibitor (LCKLSL) or the toll-like receptor 2 (TLR2) inhibitor (C29) was used to co-culture the HPMCs with exosome were employed to identify the crucial functional molecules through which exosomal ANXA2 activates HPMCs. The impact of exosomal ANXA2-activated HPMCs on tumour progression was assessed via functional experiments.ResultsPrimary OvCa samples with high ANXA2 expression exhibited a stronger tendency to metastasize to the abdominal cavity. Tumoral ANXA2 promoted OvCa peritoneal metastasis through the secretion of exosomes carrying ANXA2. ANXA2-loaded exosomes activated HPMCs through exosomal ANXA2 binding to TLR2, shifting the phenotype of HPMCs towards mesenchymal cells, increasing their migration and invasion capacities, and elevating the expression of lipocalin 2 (LCN2). High LCN2 expression in HPMCs promoted OvCa cell adhesion, proliferation, motility, and lipid metabolism reprogramming.ConclusionExosomal ANXA2 secreted by tumour cells activates HPMCs and induces the expression of LCN2, which in turn promotes the peritoneal metastasis of OvCa.Graphical

NcRNA Editing: Functional Characterization and Computational Resources.

Non-coding RNAs (ncRNAs) play crucial roles in gene expression regulation, translation, and disease development, including cancer. They are classified by size in short and long non-coding RNAs. This chapter focuses on the functional implications of adenosine-to-inosine (A-to-I) RNA editing in both short (e.g., miRNAs) and long ncRNAs. RNA editing dynamically alters the sequence and structure of primary transcripts, impacting ncRNA biogenesis and function. Notable findings include the role of miRNA editing in promoting glioblastoma invasiveness, characterizing RNA editing hotspots across cancers, and its implications in thyroid cancer and ischemia. This chapter also highlights bioinformatics resources and next-generation sequencing (NGS) technologies that enable comprehensive ncRNAome studies and genome-wide RNA editing detection. Dysregulation of RNA editing machinery has been linked to various human diseases, emphasizing the potential of RNA editing as a biomarker and therapeutic target. This overview integrates current knowledge and computational tools for studying ncRNA editing, providing insights into its biological significance and clinical applications.

Exosome-delivered NR2F1-AS1 and NR2F1 drive phenotypic transition from dormancy to proliferation in treatment-resistant prostate cancer via stabilizing hormonal receptors

Cancer cells acquire the ability to reprogram their phenotype in response to targeted therapies, yet the transition from dormancy to proliferation in drug-resistant cancers remains poorly understood. In prostate cancer, we utilized high-plasticity mouse models and enzalutamide-resistant (ENZ-R) cellular models to elucidate NR2F1 as a key factor in lineage transition and ENZ resistance. Depletion of NR2F1 drives ENZ-R cells into a relative dormancy state, characterized by reduced proliferation and heightened drug resistance, while NR2F1 overexpression yields contrasting outcomes. Transcriptional sequencing analysis of NR2F1-silenced prostate cancer cells and tissues from the Cancer Genome Atlas-prostate cancer and SU2C cohorts indicated exosomes as the most enriched cell component, with pathways implicated in steroid hormone biosynthesis and drug metabolism. Moreover, NR2F1-AS1 forms a complex with SRSF1 to upregulate NR2F1 expression, facilitating its binding with ESR1 to sustain hormonal receptor expression and enhance proliferation in ENZ-R cells. Furthermore, HnRNPA2B1 interacts with NR2F1 and NR2F1-AS1, assisting their packaging into exosomes, wherein exosomal NR2F1 and NR2F1-AS1 promote the proliferation of dormant ENZ-R cells. Our works offer novel insights into the reawaking of dormant drug-resistant cancer cells governed by NR2F1 upregulation triggered by exosome-derived NR2F1-AS1 and NR2F1, suggesting therapeutic potential for phenotype reversal.Graphical

Evolutionary analysis of anthocyanin biosynthetic genes: insights into abiotic stress adaptation.

Anthocyanin regulation can be fruitfully explored from a diverse perspective by studying distantly related model organisms. Land plants pioneers faced a huge evolutionary leap, involving substantial physiological and genetic changes. Anthocyanins have evolved alongside these changes, becoming versatile compounds capable of mitigating terrestrial challenges such as drought, salinity, extreme temperatures and high radiation. With the accessibility of whole-genome sequences from ancient plant lineages, deeper insights into the evolution of key metabolic pathways like phenylpropanoids have emerged. Despite understanding the function of anthocyanins under stress, gaps remain in uncovering the precise metabolic and regulatory mechanisms driving their overproduction under stressful conditions. For example, the regulatory effect of reactive oxygen species (ROS) on well-known transcription factors like MYBs is not fully elucidated. This manuscript presents an evolutionary analysis of the anthocyanin biosynthetic pathway to elucidate key genes. CINNAMATE 4-HYDROXYLASE (C4H) and CHALCONE ISOMERASE (CHI2) received particular attention. C4H exposes remarkable differences between aquatic and land plants, while CHI2 demonstrates substantial variation in gene copy number and sequence similarity across species. The role of transcription factors, such as MYB, and the involvement of ROS in the regulation of anthocyanin biosynthesis are discussed. Complementary gene expression analyses under abiotic stress in Arabidopsis thaliana, Selaginella moellendorffii, and Marchantia polymorpha reveal intriguing gene-stress relationships. This study highlights evolutionary trends and the regulatory complexity of anthocyanin production under abiotic stress, providing insights and opening avenues for future research.

Landscape of alternative splicing and polyadenylation during growth and development of muscles in pigs

Alternative polyadenylation (APA) is emerging as a post-transcriptional regulatory mechanism, similar as that of alternative splicing (AS), and plays a prominent role in regulating gene expression and increasing the complexity of the transcriptome and proteome. We use polyadenylation selected long-read isoform sequencing to obtain full-length transcript sequences in porcine muscles at five developmental stages. We identify numerous novel transcripts unannotated in the existing pig genome, including transcripts mapping to known and unknown gene loci, and widespread transcript diversity in porcine muscles. The top 100 most isoformic genes are mainly enriched in Gene Ontology terms related to muscle growth and development. It is revealed that intron retention/exon inclusion and the usage of distal polyadenylation site (PAS) are associated with ageing through analyzing changes of AS and PAS during muscle development. We also identify developmental changes in major transcripts and major PASs. Furthermore, genes/transcripts important for muscle development are identified. The results confirm the importance of AS and APA in pig muscles, substantially increasing transcriptional diversity and showing an important mechanism underlying gene regulation in muscles.

Long‐read transcript sequencing identifies differential isoform expression in the entorhinal cortex in a transgenic model of tau pathology

AbstractBackgroundIncreasing evidence suggests that alternative splicing plays an important role in Alzheimer’s disease (AD), a devastating neurodegenerative disorder involving the intracellular aggregation of hyperphosphorylated tau.MethodWe used whole transcriptome and targeted long‐read cDNA sequencing to profile transcript diversity in the entorhinal cortex of wild‐type (WT) and transgenic (TG) mice harbouring a mutant form of human tau.ResultWhole transcriptome profiling showed that previously reported gene‐level expression differences between WT and TG mice reflect changes in the abundance of specific transcripts. Ultradeep targeted long‐read cDNA sequencing of genes implicated in AD revealed hundreds of novel isoforms and identified specific transcripts associated with the development of tau pathology.ConclusionOur results highlight the importance of differential transcript usage, even in the absence of gene‐level expression alterations, as a mechanism underpinning gene regulation in the development of neuropathology. Our transcript annotations and a novel informatics pipeline for the analysis of long‐read transcript sequencing data are provided as a resource to the community.