Biology subjects

Her, H.-L.

Publications and source records attributed to Her, H.-L..

6 recordsLinked to original sources

bioRxiv2025

KIF5A binds RNA to orchestrate synaptic mRNA localization and stress granules in ALS

Neuronal health depends on the precise transport and local translation of mRNAs to maintain synaptic function across highly polarized cellular architecture. While kinesin motor proteins are known to mediate mRNA transport, the specificity and direct involvement of individual kinesins as RNA-binding proteins (RBPs) remain unclear. Here, we demonstrate that KIF5A, a neuron-specific kinesin implicated in amyotrophic lateral sclerosis (ALS), functions as an RBP. We show that KIF5A directly binds mRNAs encoding synaptic ribosomal proteins and is required for their synaptic localization and for maintaining normal synaptic composition and function. Additionally, we show ALS-linked KIF5A mutations confer gain-of-function properties, enhancing mRNA binding, increasing synaptic ribosomal protein accumulation, inducing neuronal hyperexcitability, and impairing stress responses. These findings reveal a previously unrecognized mechanism by which mutant KIF5A disrupts synaptic homeostasis. Our work positions a kinesin motor protein as an RBP with critical roles in mRNA transport, local translation, and stress response. HighlightsO_LIKIF5A interacts with mRNA encoding synaptic ribosomal proteins C_LIO_LIKIF5A is required for normal synaptic composition and function C_LIO_LIKIF5A binds to G3BP1 and G3BP1 stress granule associated proteins C_LIO_LIKIF5A mutant ALS patient-derived motor neurons have abnormal synaptic function and stress response C_LI

neuroscience↗

bioRxiv2022

LARP4 Is an RNA-Binding Protein That Binds Nuclear-Encoded Mitochondrial mRNAs To Promote Mitochondrial Function

Mitochondrial associated RNA-binding proteins (RBPs) have emerged as key contributors to mitochondrial biogenesis and homeostasis. With few examples described, we set out to identify RBPs that regulate nuclear-encoded mitochondrial mRNAs (NEMmRNAs). Our systematic analysis of RNA-targets of 150 RBPs identified RBPs with a preference for binding NEMmRNAs, including LARP4, a La RBP family member. We show that LARP4s targets are particularly enriched in mRNAs that encode respiratory chain complex proteins (RCCPs) and mitochondrial ribosome proteins (MRPs) across multiple human cell lines. Quantitative proteomics of cells lacking LARP4 show that protein levels of RCCPs and MRPs are significantly reduced. Furthermore, we show that LARP4 depletion reduces mitochondrial function, and that this phenotype is rescued by LARP4 re-expression. Our findings shed light onto a novel function for LARP4 as an RBP that binds to NEMmRNAs to promote mitochondrial respiratory function. HighlightsO_LIAnalysis of CLIP data reveals RBPs with a preference for mitochondrial mRNA targets C_LIO_LILARP4s RNA-target set is enriched for OXPHOS and mitochondrial ribosomal proteins C_LIO_LILoss of LARP4 reduces protein levels of these two groups of mitochondrial proteins C_LIO_LILARP4 is required for normal proliferation, translation, and OXPHOS function C_LI

cell biology↗

bioRxiv2022

Skipper analysis of RNA-protein interactions highlights depletion of genetic variation in translation factor binding sites

Technology for crosslinking and immunoprecipitation followed by sequencing (CLIP-seq) has identified the transcriptomic targets of hundreds of RNA-binding proteins in cells. To increase the power of existing and future CLIP-seq datasets, we introduce Skipper, an end-to-end workflow that converts unprocessed reads into annotated binding sites using an improved statistical framework. Compared to existing methods, Skipper on average calls 3.1-4.2 times more transcriptomic binding sites and sometimes >10 times more sites, providing deeper insight into post-transcriptional gene regulation. Skipper also calls binding to annotated repetitive elements and identifies bound elements for 99% of enhanced CLIP experiments. We perform nine translation factor enhanced CLIPs and apply Skipper to learn determinants of translation factor occupancy including transcript region, sequence, and subcellular localization. Furthermore, we observe depletion of genetic variation in occupied sites and nominate transcripts subject to selective constraint because of translation factor occupancy. Skipper offers fast, easy, customizable analysis of CLIP-seq data.

genomics↗

bioRxiv2022

Multiplexed transcriptome discovery of RNA binding protein binding sites by antibody-barcode eCLIP

UV cross-linking and immunoprecipitation (CLIP) methodologies enable the identification of RNA binding sites of RNA-binding proteins (RBPs). Despite improvements in the library preparation of RNA fragments, the current enhanced CLIP (eCLIP) protocol requires 4 days of hands-on time and lacks the ability to process many RBPs in parallel. We present a new method termed antibody-barcode eCLIP (ABC) that utilizes DNA-barcoded antibodies and proximity ligation of the DNA oligonucleotides to RBP-protected RNA fragments to interrogate multiple RBPs simultaneously. We observe performance comparable to eCLIP with the advantage of a reduced hands-on time of 2 days and dramatically increased scaling while minimizing sample-to-sample variation and maintaining the same material requirement of a single eCLIP experiment.

genomics↗

bioRxiv2022

Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions

The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The betacoronvirus has a positive sense RNA genome which encodes for several RNA binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral and host RNAs in authentic virus-infected cells. SARS-CoV-2 proteins, NSP8, NSP12, and nucleocapsid display distinct preferences to specific regions in the RNA viral genome, providing evidence for their shared and separate roles in replication, transcription, and viral packaging. SARS-CoV-2 proteins expressed in human lung epithelial cells bind to 4773 unique host coding RNAs. Nine SARS-CoV-2 proteins upregulate target gene expression, including NSP12 and ORF9c, whose RNA substrates are associated with pathways in protein N-linked glycosylation ER processing and mitochondrial processes. Furthermore, siRNA knockdown of host genes targeted by viral proteins in human lung organoid cells identify potential antiviral host targets across different SARS-CoV-2 variants. Conversely, NSP9 inhibits host gene expression by blocking mRNA export and dampens cytokine productions, including interleukin-1/{beta}. Our viral protein-RNA interactome provides a catalog of potential therapeutic targets and offers insight into the etiology of COVID-19 as a safeguard against future pandemics.

molecular biology↗

bioRxiv2020

Inferring the spatial code of cell-cell interactions and communication across a whole animal body

Cell-cell interactions shape cellular function and ultimately organismal phenotype. However, the code embedded in the molecular interactions driving and sustaining the spatial organization of cells remains to be elucidated. Here we present a computational framework to infer the spatial code underlying cell-cell interactions from the transcriptomes of the cell types across the whole body of a multicellular organism. As core of this framework, we introduce our tool cell2cell, which uses the coexpression of ligand-receptor pairs to compute the potential for intercellular interactions, and we test it across the Caenorhabditis elegans body. Leveraging a 3D atlas of C. elegans cells, we also implement a genetic algorithm to identify the ligand-receptor pairs most informative of the spatial organization of cells. Validating the spatial code extracted with this strategy, the resulting intercellular distances are negatively correlated with the inferred cell-cell interactions. Furthermore, for selected cell-cell and ligand-receptor pairs, we experimentally confirm the communicatory behavior inferred with cell2cell and the genetic algorithm. Thus, our framework helps identify a code that predicts the spatial organization of cells across a whole-animal body.

bioinformatics↗