Biology subjects

Anko, M.-L.

Publications and source records attributed to Anko, M.-L..

4 recordsLinked to original sources

bioRxiv2026

Profiling of HeLa nucleoplasmic and nucleolar RNAs by Halo-seq proximity labeling

Subcellular RNA localization is a key regulator of gene expression, but transcriptome wide characterization of RNAs enriched in specific cellular compartments has been hindered by methodological limitations in throughput and spatial resolution. Halo-seq is an RNA proximity-labeling approach that enables the extraction of RNAs located near virtually any Halo-tagged bait protein. However, its broader application has been restricted by the limited availability of the required Halo ligand. Here we present a Halo-seq dataset profiling the nucleoplasmic and nucleolar transcriptomes of HeLa cells. Through experimental and computational validation, we demonstrate that our optimized Halo-seq protocol achieves high spatial specificity, enabling robust mapping of compartment-enriched RNA populations.

molecular biology↗

bioRxiv2026

dirCLIP profiles variant-specific RNA-protein interactions via nanopore long-read sequencing

RNA binding proteins (RBPs) control gene expression through their activities in essentially all processing steps of coding and noncoding RNAs and are dysregulated in disease. With >95% of human multi-exon genes undergoing alternative splicing, the inability to assign RBP sites to distinct RNA variants fundamentally limits our understanding of RNA regulation. We present dirCLIP, a method combining UV crosslinking and immunoprecipitation (CLIP) with amplification-free direct nanopore long-read sequencing preserving full-length transcripts. dirCLIP employs two complementary strategies: direct RNA sequencing detecting amino acid adduct-induced perturbations in current signals and direct cDNA sequencing capturing binding sites as mutations. Benchmarking dirCLIP with SRSF3 demonstrated >75% concordance with short-read-based data, revealed isoform-selective RNA binding and enabled detection of co-occurring binding sites in single RNA molecules. Application to the noncanonical RBP HMGA1 uncovered new AT-hook mediated RNA variant-specific interactions. dirCLIP fundamentally transforms our ability to interrogate RNA regulation of distinct isoforms and transcript variants with direct implications to disease mechanisms and development of RNA therapeutics.

molecular biology↗

bioRxiv2019

SRSF3 confers selective processing of miR-17-92 cluster to promote tumorigenic properties in colorectal cancer

Almost a half of microRNAs (miRNAs) in mammalian cells are generated from polycistronic primary transcripts encoding more than one miRNA. Mature miRNAs from polycistronic clusters frequently regulate complementary sets of target mRNAs. How the processing of individual miRNAs within the clusters is controlled to give rise to distinct miRNA levels in vivo is not fully understood. Our investigation of SRSF3 (Serine-Arginine Rich Splicing Factor3) regulated noncoding RNAs in pluripotent cells identified miR-17-92 cluster as a key SRSF3 target, SRSF3 binding to the CNNC motif 17-18nt downstream of the miRNA stem loop. Here we show that SRSF3 binding site context, not merely the distance from the stem loop, within primary transcript is a critical determinant of the processing efficiency of distinct miRNAs derived from the miR-17-92 cluster. SRSF3 specifically enhanced the processing of two paralog miRNAs, miR-17 and miR-20a, targeting overlapping mRNAs including the cell cycle inhibitor CDKN1A/p21. Functional analysis demonstrated that SRSF3 inhibits CDKN1A expression and promotes cell cycle and self-renewal through the miRNA processing pathway both in normal pluripotent stem cells and cancer cells. Strikingly, analysis of colorectal cancer tumour-normal pairs demonstrated that the SRSF3-regulated miRNA processing pathway is present in a large proportion of colorectal cancer patients and distinguishes poorly differentiated high-grade tumours. Our research uncovers a critical role of SRSF3 in selective processing of miR-17-92 miRNAs, which mechanistically and functionally links SRSF3 to hallmark features of cancer.

cell biology↗

bioRxiv2019

Early migration of precursor neurons initiates cellular and functional regeneration after spinal cord injury in zebrafish.

Zebrafish have a remarkable capacity to regenerate following spinal cord (SC) injury but the responsible cellular events are not well understood. We used in vivo imaging and genetics to pin-point specific cellular processes controlling SC regeneration in zebrafish. We identified two temporally and mechanistically distinct phases of cellular regeneration in the SC. The initial phase relies on migration of precursor neurons to the injury, enabling rapid functional recovery, and activation of quiescent neural progenitor cells (NPCs). A second phase of regenerative neurogenesis compensates for both the lost tissue and cells depleted due to precursor neuron migration. We propose a critical role of precursor neurons recruitment in initiating neuronal circuit recovery and buying sufficient time for regenerative neurogenesis to take place. Taken together, our data suggests an unanticipated role of precursor cell recruitment in driving neural repair and functional recovery during the regenerative response. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/539940v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@12c5be9org.highwire.dtl.DTLVardef@1461e99org.highwire.dtl.DTLVardef@82d28aorg.highwire.dtl.DTLVardef@cc6870_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗