Biology subjects

Mattick, J. S.

Publications and source records attributed to Mattick, J. S..

14 recordsLinked to original sources

bioRxiv2026

The long noncoding RNA Dory is required for female but not male spatial learning and memory

Large numbers of long noncoding RNAs (lncRNAs) exhibit region- or cell-specific expression and subcellular locations in the mammalian brain. We analyzed the expression and function of the mouse lncRNA 2700046G09Rik (also called Sgms1os1), which we have named Dory due to sex-specific disruption of spatial memory in rodent gene knockout and RNA knockdown. We show that Dory is predominantly expressed in a punctate pattern in nuclei of excitatory neurons in the hippocampus, and in both neuronal and non-neuronal cells in the cerebellum. We show by high resolution RNA sequencing that Dory brain transcripts are composed of 1-3 exons with multiple isoforms. Deletion of the constitutive first exon of Dory by CRISPR-Cas9 genome editing resulted in the impairment of spatial memory and some aspects of balance in female but not male mice. Dory-null mice presented without overt changes in brain morphology. Knockdown of the rat homolog of Dory in dorsal hippocampus using antisense oligonucleotides confirmed inhibition of spatial memory in females only. RNA sequencing and mass spectrometry revealed differential hippocampal gene and protein expression profiles, notably of prolactin, growth hormone and pro-opiomelanocortin, between male and female Dory knockout mice.

neuroscience↗

bioRxiv2025

Specificity of the stabilising interaction between intrinsically disordered protein sequences and G-quadruplexes in RNA

Intrinsically disordered regions (IDRs) are present in and essential for the function of nearly all the proteins involved in the regulation, cell and developmental processes. The RGG domain in IDRs binds promiscuously to RNA G-quadruplexes (rG4s), a non-canonical 4-stranded secondary structure that occurs in many transcripts involved in gene regulation. Here we show, using weak binding interactions between a minimal RGG-rich peptide and rG4s, that the IDR selectively templates and stabilises the structure of the human telomeric TERRA rG4, providing a unique pathway to RNA folding that does not rely on high-affinity binding or monovalent cations. Multidimensional NMR and circular dichroism analyses reveal individual nucleotide and amino acid identities determine the specificity of the interaction between RGG peptides and rG4s, explaining how IDRs can selectively recognise RNA over DNA G4s, the high specificity of such interactions in vivo, and the high frequency of monogenic mutations observed in IDRs. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=64 SRC="FIGDIR/small/683336v2_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@71fdeborg.highwire.dtl.DTLVardef@1d55ff1org.highwire.dtl.DTLVardef@18dd57dorg.highwire.dtl.DTLVardef@bb2d6c_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Long-read transcriptome-wide RNA structure maps using DMS-FIRST-seq

RNA modifications induce reverse transcription (RT) errors in an enzyme- and context-dependent manner, enabling transcriptome-wide mapping and RNA structure probing. We present FIRST-seq, a flexible, cost-effective nanopore cDNA method that avoids second-strand synthesis and PCR, making it compatible with any RT enzyme and enabling single-nucleotide resolution RT signature analysis. Benchmarking multiple RT enzymes and buffers identified conditions that reduce premature termination and enhance error detection. Coupled with DMS probing, FIRST-seq accurately detects m1A and m3C at unpaired sites, recapitulating known RNA structures in vitro and in vivo. FIRST-seq offers a versatile platform for profiling chemical-induced and natural RNA modifications using long-read sequencing.

molecular biology↗

bioRxiv2024

ECSFinder: Optimized prediction of evolutionarily conserved RNA secondary structures from genome sequences

Accurate prediction of RNA secondary structures is essential for understanding the evolutionary conservation and functional roles of long noncoding RNAs (lncRNAs) across diverse species. In this study, we benchmarked two leading tools for predicting evolutionarily conserved RNA secondary structures (ECSs)--SISSIz and R-scape-- using two distinct experimental frameworks: one focusing on well-characterized mitochondrial RNA structures and the other on experimentally validated Rfam structures embedded within simulated genome alignments. While both tools performed comparably overall, each displayed subtle preferences in detecting ECSs. To address these limitations, we evaluated two interpretable machine learning approaches that integrate the strengths of both methods. By balancing thermodynamic stability features from RNALalifold and SISSIz with robust covariation metrics from R-scape, a random forest classifier significantly outperformed both conventional tools. This classifier was implemented in ECSfinder, a new tool that provides a robust, interpretable solution for genome-wide identification of conserved RNA structures, offering valuable insights into lncRNA function and evolutionary conservation. ECSfinder is designed for large-scale comparative genomics applications and promises to facilitate the discovery of novel functional RNA elements.

bioinformatics↗

bioRxiv2021

Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore sequencing

RNA polyadenylation plays a central role in RNA maturation, fate, and stability. In response to developmental cues, polyA tail lengths can vary, affecting the translation efficiency and stability of mRNAs. Here, we develop Nanopore 3 end-capture sequencing (Nano3P-seq), a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance, tail composition and tail length dynamics at per-read resolution. By employing a template switching-based sequencing protocol, Nano3P-seq can sequence any given RNA molecule from its 3 end, regardless of its polyadenylation status, without the need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P-seq captures a wide diversity of RNA biotypes, providing quantitative estimates of RNA abundance and tail lengths in mRNA, lncRNA, sn/snoRNA, scaRNA, and rRNA molecules. We find that, in addition to mRNA and lncRNA, polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover, we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform-specific level, correlating with mRNA decay. Finally, we identify non-A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis. Overall, Nano3P-seq is a simple and robust method for accurately estimating transcript levels, tail lengths, and tail composition heterogeneity in individual reads, with minimal library preparation biases, both in the coding and non-coding transcriptome.

molecular biology↗

bioRxiv2020

Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation

RNA modifications are dynamic chemical entities that regulate RNA fate, and an avenue for environmental response in neuronal function. However, which RNA modifications may be playing a role in neuronal plasticity and environmental responses is largely unknown. Here we characterize the biochemical function and cellular dynamics of two human RNA methyltransferases previously associated with neurological dysfunction, TRMT1 and its homolog, TRMT1-like (TRMT1L). Using a combination of next-generation sequencing, LC-MS/MS, patient-derived cell lines and knockout mouse models, we confirm the previously reported dimethylguanosine (m 2,2 G) activity of TRMT1 in tRNAs, as well as reveal that TRMT1L, whose activity was unknown, is responsible for methylating a subset of cytosolic tRNA Ala (AGC) isoacceptors at position 26. Using a cellular in vitro model that mimics neuronal activation and long term potentiation, we find that both TRMT1 and TRMT1L change their subcellular localization upon neuronal activation. Specifically, we observe a major subcellular relocalization from mitochondria and other cytoplasmic domains (TRMT1) and nucleoli (TRMT1L) to different small punctate compartments in the nucleus, which are as yet uncharacterized. This phenomenon does not occur upon heat shock, suggesting that the relocalization of TRMT1 and TRMT1L is not a general reaction to stress, but rather a specific response to neuronal activation. Our results suggest that subcellular relocalization of RNA modification enzymes play a role in neuronal plasticity and transmission of information, presumably by addressing new targets.

molecular biology↗

bioRxiv2020

Decoding ribosomal RNA modification dynamics at single molecule resolution

A broad diversity of modifications decorate RNA molecules. Originally conceived as static components, evidence is accumulating that some RNA modifications may be dynamic, contributing to cellular responses to external signals and environmental circumstances. A major difficulty in studying these modifications, however, is the need of tailored protocols to map each modification type individually. Here, we present a new approach that uses direct RNA nanopore sequencing to identify and quantify RNA modifications present in native RNA molecules. First, we show that each RNA modification type results in a distinct and characteristic base-calling error signature, which we validate using a battery of genetic strains lacking either pseudouridine (Y) or 2-O-methylation (Nm) modifications. We then demonstrate the value of these signatures for de novo prediction of Y modifications transcriptome-wide, confirming known Y-modified sites as well as uncovering novel Y sites in mRNAs, ncRNAs and rRNAs, including a previously unreported Pus4-dependent Y modification in yeast mitochondrial rRNA, which we validate using orthogonal methods. To explore the dynamics of pseudouridylation across environmental stresses, we treat the cells with oxidative, cold and heat stresses, finding that yeast ribosomal rRNA modifications do not change upon environmental exposures, contrary to the general belief. By contrast, our method reveals many novel heat-sensitive Y-modified sites in snRNAs, snoRNAs and mRNAs, in addition to recovering previously reported sites. Finally, we develop a novel software, nanoRMS, which we show can estimate per-site modification stoichiometries from individual RNA molecules by identifying the reads with altered current intensity and trace profiles, and quantify the RNA modification stoichiometry changes between two conditions. Our work demonstrates that Y RNA modifications can be predicted de novo and in a quantitative manner using native RNA nanopore sequencing.

molecular biology↗

bioRxiv2019

Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

BackgroundRNA modifications play central roles in cellular fate and differentiation. These features have placed the epitranscriptome in the forefront of developmental biology and cancer research. However, the machinery responsible for placing, removing and recognizing more than 170 RNA modifications remains largely uncharacterized and poorly annotated, and we currently lack integrative studies that identify which RNA modification-related proteins (RMPs) may be dysregulated in each cancer type. ResultsHere we have performed a comprehensive annotation and evolutionary analysis of human RMPs as well as an integrative analysis of their expression patterns across 32 tissues, 10 species and 13,358 paired tumor-normal human samples. Our analysis reveals an unanticipated heterogeneity of RMP expression patterns across mammalian tissues, with a vast proportion of duplicated enzymes displaying testis-specific expression, suggesting a key role for RNA modifications in sperm formation and possibly intergenerational inheritance. Moreover, through the analysis of paired tumor-normal human samples we uncover many RMPs that are dysregulated in various types of cancer, and whose expression levels are predictive of cancer progression. Surprisingly, we find that several commonly studied RNA modification enzymes such as METTL3 or FTO, are not significantly up-regulated in most cancer types, once the sample is properly scaled and normalized to the full dataset, whereas several less-characterized RMPs, such as LAGE3 and HENMT1, are dysregulated in many cancers. ConclusionsOur analyses reveal an unanticipated heterogeneity in the expression patterns of RMPs across mammalian tissues, and uncover a large proportion of dysregulated RMPs in multiple cancer types. We provide novel targets for future cancer research studies targeting the human epitranscriptome, as well as foundations to understand cell type-specific behaviours that are orchestrated by RNA modifications.

molecular biology↗

bioRxiv2019

Targeted, High-Resolution RNA Sequencing Of Non-Coding Genomic Regions Associated With Neuropsychiatric Functions

The human brain is one of the last frontiers of biomedical research. Genome-wide association studies (GWAS) have succeeded in identifying thousands of haplotype blocks associated with a range of neuropsychiatric traits, including disorders such as schizophrenia, Alzheimers and Parkinsons disease. However, the majority of single nucleotide polymorphisms (SNPs) that mark these haplotype blocks fall within non-coding regions of the genome, hindering their functional validation. While some of these GWAS loci may contain cis-acting regulatory DNA elements such as enhancers, we hypothesized that many are also transcribed into non-coding RNAs that are missing from publicly available transcriptome annotations. Here, we use targeted RNA capture ( RNA CaptureSeq) in combination with nanopore long-read cDNA sequencing to transcriptionally profile 1,023 haplotype blocks across the genome containing non-coding GWAS SNPs associated with neuropsychiatric traits, using post-mortem human brain tissue from three neurologically healthy donors. We find that the majority (62%) of targeted haplotype blocks, including 13% of intergenic blocks, are transcribed into novel, multi-exonic RNAs, most of which are not yet recorded in GENCODE annotations. We validated our findings with short-read RNA-seq, providing orthogonal confirmation of novel splice junctions and enabling a quantitative assessment of the long-read assemblies. Many novel transcripts are supported by independent evidence of transcription including cap analysis of gene expression (CAGE) data and epigenetic marks, and some show signs of potential functional roles. We present these transcriptomes as a preliminary atlas of non-coding transcription in human brain that can be used to connect neurological phenotypes with gene expression.

genomics↗

bioRxiv2019

Accurate detection of m6A RNA modifications in native RNA sequences

The field of epitranscriptomics has undergone an enormous expansion in the last few years; however, a major limitation is the lack of generic methods to map RNA modifications transcriptome-wide. Here we show that using Oxford Nanopore Technologies, N6-methyladenosine (m6A) RNA modifications can be detected with high accuracy, in the form of systematic errors and decreased base-calling qualities. Our results open new avenues to investigate the universe of RNA modifications with single nucleotide resolution, in individual RNA molecules.

molecular biology↗

bioRxiv2018

Structural venomics: evolution of a complex chemical arsenal by massive duplication and neofunctionalization of a single ancestral fold

Spiders are the most successful venomous animals on the planet, with more than 47,000 extant species. Most spider venoms are dominated by disulfide-rich peptides (DRPs) with a diverse range of pharmacological activities. Although some venoms contain thousands of unique peptides, little is known about the mechanisms used to generate such complex chemical arsenals. We used a combined transcriptomic, proteomic and structural biology approach to demonstrate that the lethal Australian funnel-web spider produces 33 superfamilies of venom peptides and proteins, more than described for any other arachnid. We show that 15 of the 26 DRP superfamilies form an ultra-stable inhibitor cystine knot motif, and that these DRPs are the major contributor to the diversity of the venom peptidome. NMR data reveal that most of these DRPs are structurally related and range in complexity from simple to highly elaborated knottin domains that likely evolved from a single ancestral fold.

biochemistry↗

bioRxiv2018

Transcription initiation RNAs are associated with chromatin activation mark H3K4me3

Transcription initiation RNAs (tiRNAs) are small, predominantly 18 nt, RNAs whose biogenesis is associated with nucleosomes adjacent to active transcription initiation sites. These loci usually contain modified histones associated with transcription initiation, including histone H3 trimethylated at lysine 4 (H3K4me3). To further characterize the relationship of tiRNAs and H3K4me3 marked nucleosomes, H3K4me3-targeted RNA:chromatin immunoprecipitations were performed in a murine macrophage cell line, and small RNA sequence libraries were constructed and subjected to deep sequencing. The H3K4me3 libraries exhibited a distinct profile of read lengths with a noticeable enrichment of sequences 17-26 nt in length, with a peak at [~]18nt that included tiRNAs. These RNAs show clear enrichment of sequences that map to genomic features known to be associated with transcription initiation, including CAGE transcription initiation sites (TSSs), sites of RNAPII occupancy, and H3K4me3 sites. The distribution of sequences that map in the vicinity of TSSs is consistent with previous descriptions of tiRNAs; viz. a major peak at approximately 40 nt downstream of the TSS, and a minor broader peak approximately 150-200 nt upstream of, and on the opposite strand to, the TSS. These results show that tiRNAs are physically associated with H3K4me3-marked chromatin. tiRNAs may be markers of RNAPII pausing and it remains a possibility that their association with H3K4me3 is part of an epigenetic signaling system.

genomics↗

bioRxiv2017

Best practices for genome-wide RNA structure analysis: combination of mutational profiles and drop-off information

Genome-wide RNA structure maps have recently become available through the coupling of in vivo chemical probing reagents with next-generation sequencing. Initial analyses relied on the identification of truncated reverse transcription reads to identify the chemically modified nucleotides, but recent studies have shown that mutational signatures can also be used. While these two methods have been employed interchangeably, here we show that they actually provide complementary information. Consequently, analyses using exclusively one of the two methodologies may disregard a significant portion of the structural information. We also show that the identity and sequence environment of the modified nucleotide greatly affect the odds of introducing a mismatch or causing reverse transcriptase drop-off. Finally, we identify specific mismatch signatures generated by dimethyl sulfate probing that can be exploited to remove false positives typically produced in RNA structurome analyses, and how these signatures vary depending on the reverse transcription enzyme used.

bioinformatics↗

bioRxiv2017

Universal Alternative Splicing Of Noncoding Exons

The human transcriptome is so large, diverse and dynamic that, even after a decade of investigation by RNA sequencing (RNA-Seq), we are yet to resolve its true dimensions. RNA-Seq suffers from an expression-dependent bias that impedes characterization of low-abundance transcripts. We performed targeted single-molecule and short-read RNA-Seq to survey the transcriptional landscape of a single human chromosome (Hsa21) at unprecedented resolution. Our analysis reaches the lower limits of the transcriptome, identifying a fundamental distinction between protein-coding and noncoding gene content: almost every noncoding exon undergoes alternative splicing, producing a seemingly limitless variety of isoforms. Analysis of syntenic regions of the mouse genome shows that few noncoding exons are shared between human and mouse, yet human splicing profiles are recapitulated on Hsa21 in mouse cells, indicative of regulation by a deeply conserved splicing code. We propose that noncoding exons are functionally modular, with alternative splicing generating an enormous repertoire of potential regulatory RNAs and a rich transcriptional reservoir for gene evolution.

genomics↗