Biology subjects

Nam, K.

Publications and source records attributed to Nam, K..

18 recordsLinked to original sources

bioRxiv2026

Proficiency-Dependent Reorganisation of Language and Control Networks during Second Language Processing: An fMRI Study of Korean-English Bilinguals

Second language (L2) processing engages both language-specific and domain-general control systems, yet how these systems vary with L2 proficiency remains unclear. We used functional magnetic resonance imaging (fMRI) to examine neural activity during L2 English processing in Korean-English (K-E) bilinguals across three proficiency levels (beginner, intermediate, advanced). Participants performed rhyme and spelling judgement tasks manipulating orthographic-phonological conflict. Behaviourally, conflict conditions reduced accuracy, with proficiency effects observed selectively in the rhyme task. fMRI results showed that conflict processing recruited frontoparietal control regions, including inferior frontal and parietal cortices, accompanied by deactivation in default mode network regions. Critically, proficiency-related effects differed by task. During rhyme judgement, advanced bilinguals showed greater activation in the left supramarginal gyrus (SMG) and cerebellum, whereas intermediate bilinguals exhibited greater recruitment of the left middle orbital gyrus and dorsomedial prefrontal cortex. During spelling judgement, advanced bilinguals showed greater thalamic activation alongside greater deactivation of the right dorsolateral prefrontal cortex. Activity in the left SMG and cerebellum was positively associated with L2 reading score, and cerebellar activity was also associated with rhyme-task performance, whereas right DLPFC activity was negatively associated with the scores. These findings suggest that increasing L2 proficiency is associated less with altered recruitment of core reading regions than with task-specific shifts in the balance between phonological-specialized, subcortical attentional, and domain-general control systems supporting L2 processing.

neuroscience↗

bioRxiv2026

Rapid Orthographic and Delayed Phonological Processing: ERP and Oscillatory Evidence from Masked Priming in Korean

A central question in visual word recognition concerns whether orthographic and phonological codes are coordinated sequentially or in parallel during lexical access. Korean Hangul, an alpha-syllabic writing system with morphophonemic spelling principles, allows independent manipulation of orthographic and phonological syllable overlap. In a masked priming lexical decision task with EEG (N = 30), we contrasted orthographically identical primes (e.g., -), phonologically overlapping primes (e.g., -), and unrelated primes. Event-related potentials and time-frequency representations (theta: 4-8 Hz, lower beta: 13-20 Hz, upper beta: 20-30 Hz) were analyzed to capture both evoked and oscillatory neural dynamics. Orthographic priming produced a cascade of facilitative effects: early fronto-central P200 enhancement (150-250 ms) with upper beta synchronization (30-290 ms), followed by centro-parietal N400 reduction (350-550 ms) with frontal theta suppression (400-730 ms), and behavioral facilitation. Phonological priming, by contrast, elicited an inhibitory behavioral effect and sustained lower beta activity over central regions (310-590 ms) but produced no early electrophysiological modulation, consistent with lexical competition. This spatiotemporal dissociation suggests that orthographic syllable processing can emerge at early stages and cascades into later lexical-level processing, whereas phonological syllable effects are confined to later processing stages. These findings provide support for a sequential or cascaded account of orthographic-phonological coordination, as predicted by dual-route models, while challenging strong forms of parallel activation, and suggest that the alpha-syllabic structure of Korean may enable a processing strategy in which orthographic parsing serves as an efficient entry route to the lexicon.

neuroscience↗

bioRxiv2025

Sensitizing tumor response to topoisomerase I antibody drug conjugate by selective CDK7 inhibition

This study investigates the transcriptional impact of Q901, a highly selective CDK7 inhibitor in clinical development. Q901 primarily disrupted MYC and E2F-dependent transcription program, downregulating cell cycle control and DNA damage repair pathways. CDK7 binding at the promoter-proximal regions was dramatically stabilized by Q901, leading to reduced occupancy of MYC, E2F, and RNA Polymerase II (RNAPII). These findings offered a novel therapeutic strategy to enhance cancer susceptibility to TOP1-DNA protein crosslinks (TOP1-DPCs) induced by TOP1 inhibitors. Resistance to TOP1 inhibitors arises through activation of DNA repair pathway when elongating RNAPII encounters TOP1-DPCs. By suppressing RNAPII transition from initiation to elongation and DNA repair pathways, Q901 stabilizes TOP1-DPCs and sensitizes tumor to TOP1 inhibitors. Preclinical studies demonstrated enhanced tumor suppression when combining Q901 with TOP1 inhibitor-based antibody-drug conjugates (TOP1i-ADCs), highlighting its potential as a therapeutic option for cancers resistant to TOP1i-ADC therapy. TeaserOvercoming ADC cross-resistance through combination approach.

cancer biology↗

bioRxiv2025

Neural Sensitivity to Word Frequency Modulated by Morphological Structure: Univariate and Multivariate fMRI Evidence from Korean

A central question in psycholinguistics in visual word recognition is whether morphologically complex words are obligatorily decomposed into stems and affixes during visual word recognition or whether whole- word access can occur when forms are frequent and familiar. The present study investigated how morphological complexity and lexical frequency jointly shape neural responses by leveraging Korean nominal inflection, whose transparent stem-suffix structure permits a clean dissociation between base (stem) frequency and surface (whole- word) frequency. Twenty-five native Korean speakers completed a rapid event-related fMRI lexical decision task involving simple and inflected nouns that varied parametrically in both frequency measures. Representational similarity analysis (RSA) revealed robust encoding of surface frequency--but not base frequency--in the inferior frontal gyrus (IFG) pars opercularis and supramarginal gyrus (SMG), with significantly stronger correlations for inflected than simple nouns. Univariate analyses converged with this result: surface frequency selectively increased activation for inflected nouns in inferior parietal regions, whereas base frequency showed no reliable effects in any ROI. These findings challenge models positing obligatory pre-lexical decomposition, instead supporting accounts in which morphological processing is shaped by post-lexical, usage-driven lexical statistics. Taken together, our findings shed light on a distributed perspective on morphological processing, suggesting that structural and statistical factors jointly constrain access to morphologically complex forms.

neuroscience↗

bioRxiv2025

A characterization of piARNs, their biogenesis and their targets in Spodoptera frugiperda (Lepidoptera, Noctuidae)

PIWI-interacting RNAs (piRNAs) and PIWI proteins were initially described as involved in gametogenesis and preservation of genome integrity through the control of transposable elements (TE). Expressed also in the soma and able to regulate protein coding gene expression, they are involved in multiple biological pathways including host-pathogens interaction, sex determination, reproductive isolation. Spodoptera frugiperda is a major invasive insect pest species consisting of two strains with different host-plant ranges. In this paper, we characterized proteins and genomic regions involved in their biogenesis as well as TE and gene transcripts regulated by piRNAs. By phylogenetic analysis, we identified two new Piwi genes conserved in the genus Spodoptera, compared to the Lepidopteran model Bombyx mori, one more than in Drosophila. One of them, more expressed in gonads then soma could be a functional homolog of Drosophila PIWI or replace AGO3. A pool of 11 sRNA-Seq libraries was used to annotate piRNA clusters with Shortstack in the genomes of the two strains of Spodoptera frugiperda. Identification of TE targeted by piRNAs revealed that active transposons differ between the two strains of S. frugiperda despite of a similar TE content, as putative cause or consequence of reproductive isolation. GO analysis of genes targeted by piRNAs shows that some are involved in protein translation initiation. A piRNA cluster in the Masc gene suggests that sex determination is regulated by piRNAs in Spodoptera frugiperda. Our analysis supports that piRNAs have additional roles than silencing of transposable elements and contributes to functional annotation of the two strains genomes of Spodoptera frugiperda.

genomics↗

bioRxiv2025

Simple 3D-Printed Stirred Bioreactor Enhances Retinal Organoid Production Via Improved Oxygenation

Retinal organoids (ROs), derived from human pluripotent stem cells (hPSCs), simulate in vivo development and retinal morphology, providing a platform to study retinal development and diseases. However, current differentiation protocols often yield inconsistent results with substantial cell line and batch variability. These protocols utilize static culture methods that rely on passive oxygen diffusion to reach the vessel bottom, where adherent hPSCs initially differentiate. Static culture is standard for adherent monolayer cells and is presumed suitable for RO differentiation. We questioned this assumption given that, during differentiation, the monolayer hPSCs become highly structured and multi-layered, first as neural rosettes and then as optic vesicles (OVs). We hypothesized that the cellular oxygen consumption rate would exceed the rate of delivery via passive diffusion, particularly to inner regions of emerging OVs. To test this hypothesis, we measured dissolved oxygen concentrations at the vessel bottom and found that within hours of media change, oxygen dropped to < 1 %, a level considered non-physiologically hypoxic, which imperils cell viability. This non-physiological hypoxia caused OV degeneration, hypoxic marker expression, and necrosis. To address this problem, we developed a novel 3D-printed stirred bioreactor (SBR) that maintains physiological oxygen levels between [~]4-6%. This approach significantly improved organoid yield, quality, and reproducibility while being easily adaptable to typical laboratory cell culture workflows. We conclude that non-physiological hypoxia, a previously unappreciated condition, is a limiting factor underlying inconsistent yield and quality in RO production. Physiological oxygenation levels can be restored by the SBR platform, resulting in greater consistency and improved production outcomes.

bioengineering↗

bioRxiv2024

The sperm hook in house mice: a functional adaptation for migration and self-organised behaviour

In most murine species, spermatozoa exhibit a falciform apical hook at the head end. The function of the sperm hook is not yet clearly understood. In this study, we investigate the role of the sperm hook in the migration of spermatozoa through the female reproductive tract in Mus musculus (C57BL/6), using a deep tissue imaging custom-built two-photon microscope. Through live reproductive tract imaging, we found evidence indicating that the sperm hook aids in the attachment of spermatozoa to the epithelium and facilitates interactions between spermatozoa and the epithelium during migration in the uterus and oviduct. We also observed synchronised sperm beating, which resulted from the spontaneous unidirectional rearrangement of spermatozoa in the uterus. Based on live imaging of spermatozoa-epithelium interaction dynamics, we propose that the sperm hook plays a crucial role in successful migration through the female reproductive tract by providing anchor-like mechanical support and facilitating interactions between spermatozoa and the female reproductive tract in the house mouse.

cell biology↗

bioRxiv2021

H3K9me2 genome-wide distribution in the holocentric insect Spodoptera frugiperda (Lepidoptera: Noctuidae)

BackgroundEukaryotic genomes are packaged by Histone proteins in a structure called chromatin. There are different chromatin types. Euchromatin is typically associated with decondensed, transcriptionally active regions and heterochromatin to more condensed regions of the chromosomes. Methylation of Lysine 9 of Histone H3 (H3K9me) is a conserved biochemical marker of heterochromatin. In many organisms, heterochromatin is usually localized at telomeric as well as pericentromeric regions but can also be found at interstitial chromosomal loci. This distribution may vary in different species depending on their general chromosomal organization. Holocentric species such as Spodoptera frugiperda (Lepidoptera: Noctuidae) possess dispersed centromeres instead of a monocentric one and thus no observable pericentromeric compartment. To identify the localization of heterochromatin in such species we performed ChIP-Seq experiments and analyzed the distribution of the heterochromatin marker H3K9me2 in the Sf9 cell line and whole 4th instar larvae (L4) in relation to RNA-Seq data. ResultsIn both samples we measured an enrichment of H3K9me2 at the (sub) telomeres, rDNA loci, and satellite DNA sequences, which could represent dispersed centromeric regions. We also observed that density of H3K9me2 is positively correlated with transposable elements and protein-coding genes. But contrary to most model organisms, H3K9me2 density is not correlated with transcriptional repression. ConclusionThis is the first genome-wide ChIP-Seq analysis conducted in S. frugiperda for H3K9me2. Compared to model organisms, this mark is found in expected chromosomal compartments such as rDNA and telomeres. However, it is also localized at numerous dispersed regions, instead of the well described large pericentromeric domains, indicating that H3K9me2 might not represent a classical heterochromatin marker in Lepidoptera.

genomics↗

bioRxiv2020

Identifying genes and cell types with dynamic alternative polyadenylation in multi-cluster single-cell transcriptomics data

Alternative polyadenylation (APA) causes shortening or lengthening of the 3-untranslated region (3-UTR) of genes across multiple cell types. Bioinformatic tools have been developed to identify genes that are affected by APA (APA genes) in single-cell RNA-Seq (scRNA-Seq) data. However, they suffer from low power, and they cannot identify APA genes specific to each cell type (cell-type-specific APA) when multiple cell types are analyzed. To address these limitations, we developed scMAPA that systematically integrates two novel steps. First, scMAPA quantifies 3-UTR long and short isoforms without requiring assumptions on the read density shape of input data. Second, scMAPA estimates the significance of the APA genes for each cell type while controlling confounders. In the analyses on our novel simulation data and human peripheral blood mono cellular data, scMAPA showed enhanced power in identifying APA genes. Further, in mouse brain data, scMAPA identifies cell-type-specific APA genes, improving interpretability for the cell-type-specific function of APA. We further showed that this improved interpretability helps to understand a novel role of APA on the interaction between neurons and blood vessels, which is critical to maintaining the operational condition of brains. With high sensitivity and interpretability, scMAPA shed novel insights into the function of dynamic APA in complex tissues. Key PointsO_LIWe developed a bioinformatic tool, scMAPA, that identifies dynamic APA across multiple cell types and a novel simulation pipeline to assess performance of such tools in APA calling. C_LIO_LIIn simulation data of various scenarios from our novel simulation pipeline, scMAPA achieves sensitivity with a minimal loss of specificity. C_LIO_LIIn human peripheral blood monocellular data, scMAPA identifies APA genes accurately and robustly, finding unique associations of APA with hematological processes. C_LIO_LIscMAPA identifies APA genes specific to each cell type in mouse brain data while controlling confounders that sheds novel insights into the complex molecular processes. C_LI

bioinformatics↗

bioRxiv2020

Genomic balancing selection is key to the invasive success of the fall armyworm

A successful biological invasion involves survival in a newly occupied environment. If a population bottleneck occurs during an invasion, the resulting depletion of genetic variants could cause increased inbreeding depression and decreased adaptive potential, which may result in a fitness reduction. How invasive populations survive in the newly occupied environment despite reduced heterozygosity and how, in many cases, they maintain moderate levels of heterozygosity are still contentious issues1. The Fall armyworm (FAW; Lepidoptera: Spodoptera frugiperda), a polyphagous pest, is native to the Western hemisphere. Its invasion in the Old World was first reported from West Africa in early 2016, and in less than four years, it swept sub-Saharan Africa and Asia, finally reaching Australia. We used population genomics approaches to investigate the factors that may explain the invasive success of the FAW. Here we show that genomic balancing selection played a key role in invasive success by restoring heterozygosity before the global invasion. We observe a drastic loss of mitochondrial polymorphism in invasive populations, whereas nuclear heterozygosity exhibits a mild reduction. The population from Benin in West Africa has the lowest length of linkage disequilibrium amongst all invasive and native populations despite its reduced population size. This result indicates that balancing selection increased heterozygosity by facilitating the admixture of invasive populations from distinct origins and that, once heterozygosity was sufficiently high, FAW started spreading globally in the Old World. As comparable heterozygosity levels between invasive and native populations are commonly observed1, we postulate that the restoration of heterozygosity through balancing selection could be widespread among successful cases of biological invasions.

evolutionary biology↗

bioRxiv2020

Whole genome sequencing of global Spodoptera frugiperda populations: evidence for complex, multiple introductions across the Old World

Native to the Americas, the invasive Spodoptera frugiperda (fall armyworm; FAW) was reported in West Africa in 2016, followed by chronological order of detections across the Old World and the hypothesis of an eastward Asia expansion. We explored population genomic signatures of American and Old World FAW and identified 12 maternal mitochondrial DNA genome lineages across the invasive range, while from 870 high-quality nuclear single nucleotide polymorphic DNA markers five distinct New World population clusters were identified, broadly reflected their native geographical ranges and absence of host-plant preferences. We identified unique admixed Old World populations, and admixed and non-admixed Asian FAW individuals, all of which suggested multiple introductions underpinned the pests global spread. Directional gene flow from the East into eastern Africa was also detected, in contrast to the west-to-east spread hypothesis. Our study demonstrated population genomic approaches via international partnership to address global emerging pest threats and biosecurity challenges.

genomics↗

bioRxiv2020

Resetting proteostasis with ISRIB prevents pulmonary fibrosis

Aging is among the most important risk factors for the development of pulmonary fibrosis. We found that a small molecule that specifically inhibits translational inhibition induced by activation of the integrated stress response (ISRIB) attenuated the severity of pulmonary fibrosis in young and old mice. The more severe fibrosis in old compared to young mice was associated with increased recruitment of pathogenic monocyte-derived alveolar macrophages. Using genetic lineage tracing and transcriptomic profiling we found that ISRIB modulates stress response signaling in alveolar epithelial cells resulting in decreased apoptosis and decreased recruitment of pathogenic monocyte-derived alveolar macrophages. These data support multicellular model of fibrosis involving epithelial cells, pathogenic monocyte-derived alveolar macrophages and fibroblasts. Inhibition of the integrated stress response in the aging lung epithelium ameliorates pulmonary fibrosis by preventing the prolonged recruitment of monocyte-derived alveolar macrophages.

immunology↗

bioRxiv2019

Impaired phagocytic function in CX3CR1+ tissue-resident skeletal muscle macrophages prevents muscle recovery after influenza A virus-induced pneumonia in aged mice

Skeletal muscle dysfunction in survivors of pneumonia is a major cause of lasting morbidity that disproportionately affects older individuals. We found that skeletal muscle recovery was impaired in aged compared with young mice after influenza A virus-induced pneumonia. In young mice, recovery of muscle loss was associated with expansion of tissue-resident skeletal muscle macrophages and downregulation of MHC II expression, followed by a proliferation of muscle satellite cells. These findings were absent in aged mice and in mice deficient in Cx3cr1. Transcriptomic profiling of tissue-resident skeletal muscle macrophages from aged compared with young mice showed downregulation of pathways associated with phagocytosis and proteostasis, and persistent upregulation of inflammatory pathways. Consistently, skeletal muscle macrophages from aged mice failed to downregulate MHCII expression during recovery from influenza A virus induced pneumonia and showed impaired phagocytic function in vitro. Like aged animals, mice deficient in the phagocytic receptor Mertk showed no macrophage expansion, MHCII downregulation or satellite cell proliferation and failed to recover skeletal muscle function after influenza A pneumonia. Our data suggest that a loss of phagocytic function in a CX3CR1+ tissue-resident skeletal muscle macrophage population in aged mice precludes satellite cell proliferation and recovery of skeletal muscle function after influenza A pneumonia.

immunology↗

bioRxiv2019

High-depth resequencing reveals hybrid population and insecticide resistance characteristics of fall armyworm (Spodoptera frugiperda) invading China

The rapid wide-scale spread of fall armyworm (Spodoptera frugiperda) has caused serious crop losses globally. However, differences in the genetic background of subpopulations and the mechanisms of rapid adaptation behind the invasion are still not well understood. Here we report a 393.25-M chromosome-level genome assembly of fall armyworm with scaffold N50 of 13.3 M consisting of 23281 annotated protein-coding genes. Genome-wide resequencing of 105 samples from 16 provinces in China revealed that the fall armyworm population comprises a complex inter-strain hybrid, mainly with the corn-strain genetic background and less of the rice-strain genetic background, which highlights the inaccuracy of strain identification using mitochondrial or Tpi genes. An analysis of genes related to pesticide- and Bt-resistance showed that the risk of fall armyworm developing resistance to conventional pesticides is very high, while remaining currently susceptible to Bt toxins. Laboratory bioassay results showed that insects invading China carry resistance to organophosphate and pyrethroid pesticides, but are sensitive to genetically modified maize expressing Cry1Ab in field experiments. Additionally, we found that two mitochondrial fragments are inserted into the nuclear genome, and the insertion event occurred after the differentiation of the two strains. This study represents a valuable advancement toward the analysis of genetic differences among subpopulations and improving management strategies for fall armyworm.

genomics↗

bioRxiv2019

The Aging Microenvironment Shapes Alveolar Macrophage Identity in Aging

A dysfunctional response to inhaled pathogens and toxins drives a substantial portion of the susceptibility to acute and chronic lung disease in the elderly. We used transcriptomic profiling combined with genetic lineage tracing, heterochronic adoptive transfer, parabiosis and treatment with metformin to show that the lung microenvironment defines the phenotype of long-lived alveolar macrophages during aging. While tissue-resident alveolar macrophages persist in the lung without input from monocytes over the lifespan, severe lung injury results in their replacement with monocyte-derived alveolar macrophages. These monocyte-derived alveolar macrophages are also shaped by the microenvironment both during aging and in response to a subsequent environmental challenge to become transcriptionally and functionally similar to tissue-resident alveolar macrophages. These findings show that changes in alveolar macrophage phenotypes during injury and aging are not cell autonomous but instead are shaped by changes in the aging lung microenvironment.

immunology↗

bioRxiv2018

Single-Cell Transcriptomic Analysis of Human Lung Reveals Complex Multicellular Changes During Pulmonary Fibrosis

Pulmonary fibrosis is a devastating disorder that results in the progressive replacement of normal lung tissue with fibrotic scar. Available therapies slow disease progression, but most patients go on to die or require lung transplantation. Single-cell RNA-seq is a powerful tool that can reveal cellular identity via analysis of the transcriptome, but its ability to provide biologically or clinically meaningful insights in a disease context is largely unexplored. Accordingly, we performed single-cell RNA-seq on lung tissue obtained from eight transplant donors and eight recipients with pulmonary fibrosis and one bronchoscopic cryobiospy sample. Integrated single-cell transcriptomic analysis of donors and patients with pulmonary fibrosis identified the emergence of distinct populations of epithelial cells and macrophages that were common to all patients with lung fibrosis. Analysis of transcripts in the Wnt pathway suggested that within the same cell type, Wnt secretion and response are restricted to distinct non-overlapping cells, which was confirmed using in situ RNA hybridization. Single-cell RNA-seq revealed heterogeneity within alveolar macrophages from individual patients, which was confirmed by immunohistochemistry. These results support the feasibility of discovery-based approaches applying next generation sequencing technologies to clinically obtained samples with a goal of developing personalized therapies.\n\nOne Sentence SummarySingle-cell RNA-seq applied to tissue from diseased and donor lungs and a living patient with pulmonary fibrosis identifies cell type-specific disease-associated molecular pathways.

systems biology↗

bioRxiv2017

Whole genome hybrid assembly and protein-coding gene annotation of the entirely black native Korean chicken breed Yeonsan Ogye

Yeonsan Ogye (YO), an indigenous Korean chicken breed (gallus gallus domesticus), has entirely black external features and internal organs. In this study, the draft genome of YO was assembled using a hybrid de novo assembly method that takes advantage of high-depth Illumina short-reads (232.2X) and low-depth PacBio long-reads (11.5X). Although the contig and scaffold N50s (defined as the shortest contig or scaffold length at 50% of the entire assembly) of the initial de novo assembly were 53.6Kbp and 10.7Mbp, respectively, additional and pseudo-reference-assisted assemblies extended the assembly to 504.8Kbp for contig N50 (pseudo-contig) and 21.2Mbp for scaffold N50, which included 551 structural variations including the Fibromelanosis (FM) locus duplication, compared to galGal4 and 5. The completeness (97.6%) of the draft genome (Ogye_1) was evaluated with single copy orthologous genes using BUSCO, and found to be comparable to the current chicken reference genome (galGal5; 97.4%), which was assembled with a long read-only method, and superior to other avian genomes (92~93%), assembled with short read-only and hybrid methods. To comprehensively reconstruct transcriptome maps, RNA sequencing (RNA-seq) and representation bisulfite sequencing (RRBS) data were analyzed from twenty different tissues, including black tissues. The maps included 15,766 protein-coding and 6,900 long non-coding RNA genes, many of which were expressed in the tissue-specific manner, closely related with the DNA methylation pattern in the promoter regions.

genomics↗

bioRxiv2017

Non-coding Transcriptome Maps Across Twenty Tissues of the Korean Black Chicken, Yeonsan Ogye

The Yeonsan Ogye (Ogye) is a rare Korean domestic chicken breed, the entire body of which, including its feathers and skin, has a unique black coloring. Although some protein-coding genes related to this unique feature have been examined, non-coding elements have not been globally investigated. In this study, high-throughput RNA sequencing and DNA methylation sequencing were performed to dissect the expression landscape of 14,264 Ogye protein-coding and 6900 long non-coding RNA (lncRNA) genes along with DNA methylation landscape in twenty different Ogye tissues. About 75% of Ogye lncRNAs showed tissue-specific expression whereas about 45% of protein-coding genes did. For some genes, the tissue-specific expression levels were inversely correlated with DNA methylation levels in their promoters. About 39% of the tissue-specific lncRNAs displayed functional association with proximal or distal protein-coding genes. In particular, heat shock transcription factor 2 (HSF2)-associated lncRNAs were discovered to be functionally linked to protein-coding genes that are specifically expressed in black skin tissues, tended to be more syntenically conserved in mammals, and were differentially expressed in black tissues relative to white tissues. Our results not only facilitate understanding how the non-coding genome regulates unique phenotypes but also should be of use for future genomic breeding of chickens.

bioinformatics↗