Biology subjects

Lin, Q.

Publications and source records attributed to Lin, Q..

6 recordsLinked to original sources

bioRxiv2018

N4-acetylcytidine and 5-formylcytidine are present in Saccharomyces cerevisiae mRNAs

Post-transcriptional nucleoside modifications have long been recognized as key modulators of non-coding RNA structure and function. There is an emerging appreciation that the chemical modification of protein-coding messenger RNAs (mRNAs) also plays critical roles in the cell. Although there are over 100 known RNA modifications found in biology only a handful have been identified in mRNAs. We sought to identify and quantify modifications present in the mRNAs of yeast cells using a high throughput ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method that measures the levels of 36 types of RNA nucleosides in parallel. We detected the presence of six modified nucleosides in mRNAs at relatively high abundances: N7-methylguanosine, N6-methyladenosine, 2-O-methylguanosine, 2-O-methylcytosine, N4-acetylcytidine and 5-formylcytidine. Additionally, we investigated how the levels of mRNA modifications vary in response to cellular stress. We find that the concentrations of mRNA modifications including N6-methyladenosine and N4-acetylcytidine change in response to heat stress, glucose starvation and/or oxidative stress. This work expands the repertoire of potential chemical modifications in mRNAs, and utilizes a high-throughput approach to search for modifications that highlights the value of integrating mass-spectrometry tools in the mRNA modification discovery and characterization pipeline.

biochemistry↗

bioRxiv2018

Localization and protein-protein interaction of protein kinase CK2 suggest a chaperone-like activity is integral to its function in M. oryzae.

Magnaporthe oryzae (Mo) is a model pathogen causing rice blast resulting in yield and economic losses world-wide. CK2 is a constitutively active, serine/threonine kinase in eukaryotes, having a wide array of known substrates and involved in many cellular processes. We investigated the localization and role of MoCK2 during growth and infection. BLAST search for MoCK2 components and targeted deletion of subunits was combined with protein-GFP fusions to investigate localization. We found one CKa and two CKb subunits of the CK2 holoenzyme. Deletion of the catalytic subunit CKa was not possible and might indicate that such deletions are lethal. The CKb subunits could be deleted but they were both necessary for normal growth and pathogenicity. Localization studies showed that the CK2 holoenzyme needed to be intact for normal localization at septal pores and at appressorium penetration pores. Nuclear localization of CKa was however not dependent on the intact CK2 holoenzyme. In appressoria, CK2 formed a large ring perpendicular to the penetration pore and the ring formation was dependent on the presence of all CK2 subunits. The effects on growth and pathogenicity of deletion of the b subunits combined with the localization indicate that CK2 can have important regulatory functions not only in the nucleus/nucleolus but also at fungal specific structures as septa and appressorial pores.

cell biology↗

bioRxiv2018

Developmental genetics of corolla tube formation: role of the tasiRNA-ARF pathway

More than 80,000 angiosperm species produce flowers with petals fused into a corolla tube. As an important element of the tremendous diversity of flower morphology, the corolla tube plays a critical role in many specialized interactions between plants and animal pollinators (e.g., beeflies, hawkmoths, hummingbirds, nectar bats), which in turn drives rapid plant speciation. Despite its clear significance in plant reproduction and evolution, the corolla tube remains one of the least understood plant structures from a developmental genetics perspective. Through mutant analyses and transgenic experiments, here we show that the tasiRNA-ARF pathway is required for corolla tube formation in the monkeyflower species Mimulus lewisii. Loss-of-function mutations in the M. lewisii orthologs of ARGONAUTE7 and SUPPRESSOR OF GENE SILENCING 3 cause a dramatic decrease in abundance of TAS3-derived small RNAs and a moderate up-regulation of AUXIN RESPONSE FACTOR 3 (ARF3) and ARF4, which lead to inhibition of lateral expansion of the bases of petal primordia and complete arrest of the upward growth of the inter-primordial regions, resulting in unfused corollas. By using an auxin reporter construct, we discovered that auxin distribution is continuous along the petal primordium base and the inter-primordial region during the critical stage of corolla tube formation in the wild-type, and that this auxin distribution is much weaker and more restricted in the mutant. Together, these results suggest a new conceptual model highlighting the central role of auxin directed synchronized growth of the petal primordium base and the inter-primordial region in corolla tube formation.

plant biology↗

bioRxiv2017

Discovering the Interactions between Circular RNAs and RNA-binding Proteins from CLIP-seq Data using circScan

Although tens of thousands of circular RNAs (circRNAs) have been identified in mammalian genomes, only few of them have been characterized with biological functions. Here, we report a new approach, circScan, to identify regulatory interactions between circRNAs and RNA-binding proteins (RBPs) by discovering back-splicing reads from Cross-Linking and Immunoprecipitation followed by high-throughput sequencing (CLIP-seq) data. By using our method, we have systematically scanned ~1500 CLIP-seq datasets, and identified ~12540 and ~1090 novel circRNA-RBP interactions in human and mouse genomes, respectively, which include all known interactions between circRNAs and Argonaute (AGO) proteins. More than twenty novel interactions were further experimentally confirmed by RNA Immunoprecipitation quantitative PCR (RIP-qPCR). Importantly, we uncovered that some natural circRNAs interacted with cap-independent translation factors eukaryotic initiation factor 3 (eIF3) and N6-Methyladenosine (m6A), indicating they can be translated into proteins. These findings demonstrate that circRNAs are regulated by various RBPs, suggesting they may play important roles in diverse biological processes.

molecular biology↗

bioRxiv2017

A novel method for large-scale identification of polymorphic microsatellites through comparative transcriptome analysis

Microsatellite (SSR) is one of the most popular markers for applied genetic research, but generally the current methods to develop SSRs are relatively time-consuming and expensive. Although high-throughput sequencing (HTS) approach has become a practical and relatively inexpensive option so far, only a small percentage of SSR markers turn out to be polymorphic. Here, we designed a new method to enrich polymorphic SSRs through the comparative transcriptome analysis. This program contains five main steps: 1) transcriptome data downloading or RNA-seq; 2) sequence assembly; 3) SSR mining and enrichment of sequences containing SSRs; 4) sequence alignment; 5) enrichment of sequences containing polymorphic SSRs. A validation experiment was performed and the results showed almost all markers (> 90%) that were indicated as putatively polymorphic by this method were indeed polymorphic. The frequency of polymorphic SSRs was significantly higher (P < 0.05) but the cost and running time were much lower than those of traditional and HTS approaches. The method has a practical value for polymorphic SSRs development and might be widely used for genetic analyses in any species.

bioinformatics↗

bioRxiv2017

Masking of a circadian behavior in larval zebrafish involves the thalamo-habenula pathway

Light has the ability to disrupt or mask behavior that is normally controlled by the circadian clock. In mammals, masking requires melanopsin-expressing retinal ganglion cells that detect blue light and project to the thalamus. It is not known whether masking is wavelength-dependent in other vertebrates, nor is it clear what higher circuits are involved. Here, we address these questions in zebrafish. We find that diel vertical migration, a circadian behavior in larval zebrafish, is effectively masked by blue, but not by red light. Two-photon calcium imaging reveals that a retino-recipient thalamic nucleus and a downstream structure, the habenula, are tuned to blue light. Lesioning the habenula inhibits light-evoked climbing. These data suggest that a thalamo-habenula pathway may be involved in the ability of blue light to mask circadian behavior.

neuroscience↗