DNA microarray chips: Fabrication and cutting-edge applications

Chemical Engineering Journal, Год журнала: 2024, Номер unknown, С. 155937 - 155937

Опубликована: Сен. 1, 2024

Язык: Английский

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Structural variation, selection, and diversification of theNPIPgene family from the human pangenome

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Фев. 5, 2025

ABSTRACT The NPIP (nuclear pore interacting protein) gene family has expanded to high copy number in humans and African apes where it been subject an excess of amino acid replacement consistent with positive selection (1). Due the limitations short-read sequencing, human genetic diversity poorly understood. Using highly accurate assemblies generated from long-read sequencing as part pangenome, we completely characterize 169 haplotypes (4,665 paralogs alleles). Of 28 paralogs, just three ( NPIPB2 , B11 B14 ) are fixed at a single copy, only locus, B2 shows no structural variation. Four map large segmental duplication blocks that mediate polymorphic inversions (355 kbp–1.6 Mbp) corresponding microdeletions associated developmental delay autism. Haplotype-based tests selective sweeps identify two B9 B15 within top percentile for both tests. full-length cDNA data 101 tissue/cell types, construct paralog-specific models show 56% (31/55 most abundant isoforms) have not previously described RefSeq. We define six distinct translation start sites other protein features distinguish including variable tandem repeat encodes beta helix size emerged ∼3.1 million years ago evolution. Among tissue patterns expression few maintaining ancestral testis-enriched expression. A subset NPIPA1 A5 A6-9 B3-5 B12/B13 increased brain Our results suggest ongoing population rapid diversification models.

Язык: Английский

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Exploring the connection between RNA splicing and intellectual disability

Current Opinion in Genetics & Development, Год журнала: 2025, Номер 91, С. 102322 - 102322

Опубликована: Фев. 8, 2025

Intellectual disability (ID) is a broad diagnostic category that encompasses individuals with impaired cognitive ability. While these disorders have heterogeneous causes, recent developments in next-generation sequencing (NGS) are revealing the prevalence of genetic etiologies. In particular, germline mutations genes affect RNA splicing increasingly common causes ID disorders. Research to elucidate functional relationship between and neurodevelopment critical since molecular therapeutics require nuanced understanding pathological mechanism. this review, we first summarize trends led discovery splicing-ID relationship, then discuss progress future directions for research surrounding neurodevelopment. Finally, speak on how results may serve as foundation burgeoning therapies.

Язык: Английский

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Discovery of Novel Protein-Coding and Long Non-coding Transcripts in Distinct Regions of the Human Brain

Journal of Molecular Neuroscience, Год журнала: 2025, Номер 75(1)

Опубликована: Март 6, 2025

Recent improvements in the accuracy of long-read sequencing (LRS) technologies have expanded scope for novel transcriptional isoform discovery. Additionally, these advancements improved precision transcript quantification, enabling a more accurate reconstruction complex splicing patterns and transcriptomes. Thus, this project aims to take advantage analytical developments discovery analysis RNA isoforms human brain. A set was compiled using three bioinformatic tools, quantifying their expression across eight replicates cerebellar hemisphere, five frontal cortex, six putamen. By taking subset consistent all methods, 170 highly confident curated downstream analysis. This consisted 104 messenger RNAs (mRNAs) 66 long non-coding (lncRNAs) isoforms. The detailed structure, expression, potential encoded proteins mRNA BambuTx321 been further described as an exemplary representative. tissue-specific [mean counts per million (CPM) 5.979] lncRNA, BambuTx1299, hemisphere observed. Overall, has identified annotated several diverse tissues brain, providing insights into investigating functional roles. contributed comprehensive understanding brain's transcriptomic landscape applications basic research.

Язык: Английский

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Transcriptional determinism and stochasticity contribute to the complexity of autism-associated SHANK family genes

Cell Reports, Год журнала: 2024, Номер 43(7), С. 114376 - 114376

Опубликована: Июнь 19, 2024

Precision of transcription is critical because transcriptional dysregulation disease causing. Traditional methods profiling are inadequate to elucidate the full spectrum transcriptome, particularly for longer and less abundant mRNAs. SHANK3 one most common autism causative genes. Twenty-four Shank3-mutant animal lines have been developed modeling. However, their preclinical validity has questioned due incomplete Shank3 transcript structure. We apply an integrative approach combining cDNA-capture long-read sequencing profile transcriptome in humans mice. unexpectedly discover extremely complex transcriptome. Specific transcripts altered mice postmortem brain tissues from individuals with disorder. The enhanced significantly improves detection rate potential deleterious variants genomics studies neuropsychiatric disorders. Our findings suggest that both deterministic stochastic genome associated SHANK family

Язык: Английский

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Iso-Seq enables discovery of novel isoform variants in human retina at single cell resolution

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Авг. 9, 2024

Abstract Recent single cell transcriptomic profiling of the human retina provided important insights into genetic signals in heterogeneous retinal populations that enable vision. However, conventional RNAseq with 3’ short-read sequencing is not suitable to identify isoform variants. Here we utilized Iso-Seq full-length profile at resolution for discovery. We generated a transcriptome dataset consisting 25,302 nuclei from three donor retina, and detected 49,710 known transcripts 241,949 novel across major types. surveyed use alternative promoters drive transcript variant expression, showed 1-8% genes multiple Also, our results enabled gene expression variants inherited disease (IRD) genes, identified differential usage exon splicing Altogether, sequencing. Our study highlighted potential map diversity providing an expanded view complex landscape retina.

Язык: Английский

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Sex-specific gene expression differences in the prefrontal cortex of major depressive disorder individuals

Neuroscience, Год журнала: 2024, Номер 559, С. 272 - 282

Опубликована: Сен. 14, 2024

Язык: Английский

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Human-derived monoclonal autoantibodies as interrogators of cellular proteotypes in the brain

Trends in Neurosciences, Год журнала: 2024, Номер unknown

Опубликована: Сен. 1, 2024

Язык: Английский

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