{"entity": "researcher", "timestamp": "2026-10-05T21:30:14.563Z", "family": "Churcher", "given": "Allison M", "initials": "AM", "orcid": "0000-0003-1902-3002", "affiliations": ["NBIS, Department of Molecular Biology, Ume\u00e5 University, Ume\u00e5, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/d97e6fb500a043f08d4f882e802cd91b.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/d97e6fb500a043f08d4f882e802cd91b"}}, "publications": [{"entity": "publication", "iuid": "e5d391bf60044ec28e46cbb0e9022320", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e5d391bf60044ec28e46cbb0e9022320.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e5d391bf60044ec28e46cbb0e9022320"}}, "title": "Conserved molecular signatures of hygrosensory neurons in two dipteran species.", "authors": [{"family": "Corthals", "given": "Kristina", "initials": "K", "orcid": "0000-0001-6106-4372", "researcher": {"href": "https://publications.scilifelab.se/researcher/e74699dee4534d95aaaa433361877c28.json"}}, {"family": "Giri", "given": "Ganesh", "initials": "G"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J", "orcid": "0000-0003-1518-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/db7ebacfd8764a988ee41f2e5ab23e50.json"}}, {"family": "Churcher", "given": "Allison", "initials": "A", "orcid": "0000-0003-1902-3002", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97e6fb500a043f08d4f882e802cd91b.json"}}, {"family": "Enjin", "given": "Anders", "initials": "A", "orcid": "0000-0001-7167-9434", "researcher": {"href": "https://publications.scilifelab.se/researcher/066263ac05e84d209e36550b439da505.json"}}], "type": "journal article", "published": "2026-04-28", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "21", "issue": "4", "pages": "e0347993", "issn-l": "1932-6203"}, "abstract": "Small poikilothermic animals like insects rely on environmental sensing for survival. The ability to detect humidity through specialized sensory neurons is particularly critical, allowing them to maintain water balance across diverse environments. While recent studies have identified key receptors associated with humidity sensing, our understanding of the underlying molecular architecture of these sensory systems remains incomplete. Here, we conducted a comparative analysis of single-nucleus transcriptomes of humidity receptor neurons (HRNs) between the vinegar fly Drosophila melanogaster and the yellow fever mosquito Aedes aegypti. We identified 21 shared genes that contribute to the molecular identity of HRNs in both species. These genes encode proteins involved in transcriptional regulation, cellular signalling, enzymatic pathways and cellular organization. Through behavioural analyses, we demonstrate that two of these genes, the serotonin receptor 5-HT7 and the kinesin motor protein Kif19A, are both necessary for humidity-guided behaviours in adult flies. The conservation of these genes between species separated by over 150 million years of evolution suggests shared functional requirements for humidity sensing in dipterans. Our findings provide insights into fundamental principles of sensory neuron organization and offer a framework for understanding how specialized sensory systems evolve and maintain their function.", "doi": "10.1371/journal.pone.0347993", "pmid": "42048343", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC13123972"}, {"db": "pii", "key": "PONE-D-25-60937"}], "notes": [], "created": "2026-08-13T11:52:23.963Z", "modified": "2026-08-13T11:52:24.552Z"}, {"entity": "publication", "iuid": "99d94470f07541c2b23fad1eefd0f74b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/99d94470f07541c2b23fad1eefd0f74b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/99d94470f07541c2b23fad1eefd0f74b"}}, "title": "Genomic studies in Linum shed light on the evolution of the distyly supergene and the molecular basis of convergent floral evolution.", "authors": [{"family": "Zervakis", "given": "Panagiotis-Ioannis", "initials": "PI", "orcid": "0000-0002-5197-3502", "researcher": {"href": "https://publications.scilifelab.se/researcher/295e9debf36c4641aa6c346e915b64ef.json"}}, {"family": "Postel", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0003-0502-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/0481ff1051564262af4e5384cbd17ac3.json"}}, {"family": "Losvik", "given": "Aleksandra", "initials": "A", "orcid": "0000-0001-7669-9266", "researcher": {"href": "https://publications.scilifelab.se/researcher/e85c35a0abd54a7087c94942290179be.json"}}, {"family": "Fracassetti", "given": "Marco", "initials": "M", "orcid": "0000-0002-2962-2669", "researcher": {"href": "https://publications.scilifelab.se/researcher/695213cdd1a645cbbf10d44122237b18.json"}}, {"family": "Sol\u00e9r", "given": "Lucile", "initials": "L", "orcid": "0000-0002-0121-2393", "researcher": {"href": "https://publications.scilifelab.se/researcher/f701059f90fe4c7c9b969079e74aac57.json"}}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E", "orcid": "0000-0003-3752-1806", "researcher": {"href": "https://publications.scilifelab.se/researcher/9257ccdfc6484cd9a95f9b2f17f9a8d1.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I", "orcid": "0009-0008-8375-0451", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2a9c139b7d64681a5712250d3cf63ff.json"}}, {"family": "Churcher", "given": "Allison", "initials": "A", "orcid": "0000-0003-1902-3002", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97e6fb500a043f08d4f882e802cd91b.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "issn-l": "0028-646X", "volume": "247", "issue": "6", "pages": "2964-2981"}, "abstract": "Distyly, an example of convergent evolution, is governed by a supergene, the S-locus, in several species. Recent studies highlight similar genomic architectures of independently evolved S-loci, but its mode of origin and whether similar regulatory pathways underlie the convergent evolution of distyly remains unclear. We examined the evolution of supergenes and mechanisms underlying distyly in Linum species that diverged c. 33 million years ago (Ma). Using haplotype-resolved genomes and population genomics, we identified and characterized the S-loci of Linum perenne (distylous) and Linum grandiflorum (style length dimorphic), and compared them to that of Linum tenue (distylous). We then tested for a conserved hormonal mechanism regulating style length polymorphism in Linum. The S-locus supergene was consistently hemizygous in short-styled individuals across all three species, although it showed variation in size, gene content, repeat elements and extent of recombination suppression. Two S-linked candidate genes, TSS1 (style length) and WDR-44 (anther height/pollen self-incompatibility), were conserved. Consistent with a brassinosteroid-dependent role of TSS1, epibrassinolide treatment revealed a conserved, morph-specific effect on style length. S-locus structural polymorphism, candidate distyly genes and mechanisms regulating style length remain conserved > 30 Ma in Linum. In combination with findings from other systems, our results suggest that the brassinosteroid pathway frequently contributes to style length polymorphism.", "doi": "10.1111/nph.70392", "pmid": "40682296", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Other": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12371154"}], "notes": [], "created": "2025-08-19T13:25:54.698Z", "modified": "2025-11-19T10:24:41.159Z"}, {"entity": "publication", "iuid": "06092f1c02924d8da8dd7a4929fd5ac3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/06092f1c02924d8da8dd7a4929fd5ac3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/06092f1c02924d8da8dd7a4929fd5ac3"}}, "title": "Origin, structure, and composition of the spider major ampullate silk fiber revealed by genomics, proteomics, and single-cell and spatial transcriptomics.", "authors": [{"family": "Sonavane", "given": "Sumalata", "initials": "S", "orcid": "0000-0002-0728-4822", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c951e7727ce4f1a9dc0abc3b62019f8.json"}}, {"family": "Hassan", "given": "Sameer", "initials": "S"}, {"family": "Chatterjee", "given": "Urmimala", "initials": "U", "orcid": "0000-0002-6681-1696", "researcher": {"href": "https://publications.scilifelab.se/researcher/418ed6f1f8a440efb4df1c0b4f2dd265.json"}}, {"family": "Soler", "given": "Lucile", "initials": "L", "orcid": "0000-0002-0121-2393", "researcher": {"href": "https://publications.scilifelab.se/researcher/f701059f90fe4c7c9b969079e74aac57.json"}}, {"family": "Holm", "given": "Lena", "initials": "L", "orcid": "0000-0002-7717-4370", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b769bc4b7e74ce48c1f26bc5d647e18.json"}}, {"family": "Mollbrink", "given": "Annelie", "initials": "A", "orcid": "0009-0007-0542-0695", "researcher": {"href": "https://publications.scilifelab.se/researcher/64c67099378344c8b7d1ff66a7bfdc48.json"}}, {"family": "Greco", "given": "Gabriele", "initials": "G", "orcid": "0000-0003-3356-7081", "researcher": {"href": "https://publications.scilifelab.se/researcher/924046db702c424f8296265c8d6599fd.json"}}, {"family": "Fereydouni", "given": "Noah", "initials": "N", "orcid": "0000-0002-1786-4337", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc54e88c9a724eecb2a2c68e9f025a97.json"}}, {"family": "Vinnere Pettersson", "given": "Olga", "initials": "O", "orcid": "0000-0002-5597-1870", "researcher": {"href": "https://publications.scilifelab.se/researcher/31689f508a984d0680d285c294669615.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Churcher", "given": "Allison", "initials": "A", "orcid": "0000-0003-1902-3002", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97e6fb500a043f08d4f882e802cd91b.json"}}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Johansson", "given": "Jan", "initials": "J"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J", "orcid": "0000-0003-1518-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/db7ebacfd8764a988ee41f2e5ab23e50.json"}}, {"family": "Rising", "given": "Anna", "initials": "A", "orcid": "0000-0002-1872-1207", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f120d653e7c47d7833be7a44c21dbaa.json"}}], "type": "journal article", "published": "2024-08-16", "journal": {"title": "Sci Adv", "issn": "2375-2548", "issn-l": "2375-2548", "volume": "10", "issue": "33", "pages": "eadn0597"}, "abstract": "Spiders produce nature's toughest fiber using renewable components at ambient temperatures and with water as solvent, making it highly interesting to replicate for the materials industry. Despite this, much remains to be understood about the bioprocessing and composition of spider silk fibers. Here, we identify 18 proteins that make up the spiders' strongest silk type, the major ampullate fiber. Single-cell RNA sequencing and spatial transcriptomics revealed that the secretory epithelium of the gland harbors six cell types. These cell types are confined to three distinct glandular zones that produce specific combinations of silk proteins. Image analysis of histological sections showed that the secretions from the three zones do not mix, and proteomics analysis revealed that these secretions form layers in the final fiber. Using a multi-omics approach, we provide substantial advancements in the understanding of the structure and function of the major ampullate silk gland as well as of the architecture and composition of the fiber it produces.", "doi": "10.1126/sciadv.adn0597", "pmid": "39141739", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Short read": "Service", "NGI Spatial omics": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11323941"}], "notes": [], "created": "2024-08-15T12:15:23.174Z", "modified": "2024-11-25T10:28:17.415Z"}, {"entity": "publication", "iuid": "0d08036c5f154cf0b2c0036250a0fa7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d08036c5f154cf0b2c0036250a0fa7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d08036c5f154cf0b2c0036250a0fa7e"}}, "title": "The regulation of methylation on the Z chromosome and the identification of multiple novel Male Hyper-Methylated regions in the chicken.", "authors": [{"family": "H\u00f6glund", "given": "Andrey", "initials": "A", "orcid": "0000-0002-1130-374X", "researcher": {"href": "https://publications.scilifelab.se/researcher/70a484451caf40f2a1a196b36bb9c423.json"}}, {"family": "Henriksen", "given": "Rie", "initials": "R"}, {"family": "Churcher", "given": "Allison M", "initials": "AM", "orcid": "0000-0003-1902-3002", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97e6fb500a043f08d4f882e802cd91b.json"}}, {"family": "Guerrero-Bosagna", "given": "Carlos M", "initials": "CM"}, {"family": "Martinez-Barrio", "given": "Alvaro", "initials": "A", "orcid": "0000-0001-5064-2093", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6ff319fe64340f2bb2350121848ecff.json"}}, {"family": "Johnsson", "given": "Martin", "initials": "M", "orcid": "0000-0003-1262-4585", "researcher": {"href": "https://publications.scilifelab.se/researcher/02b768197c08422aaad526f35c526eaf.json"}}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "20", "issue": "3", "pages": "e1010719", "issn-l": "1553-7390"}, "abstract": "DNA methylation is a key regulator of eukaryote genomes, and is of particular relevance in the regulation of gene expression on the sex chromosomes, with a key role in dosage compensation in mammalian XY systems. In the case of birds, dosage compensation is largely absent, with it being restricted to two small Male Hyper-Methylated (MHM) regions on the Z chromosome. To investigate how variation in DNA methylation is regulated on the Z chromosome we utilised a wild x domestic advanced intercross in the chicken, with both hypothalamic methylomes and transcriptomes assayed in 124 individuals. The relatively large numbers of individuals allowed us to identify additional genomic MHM regions on the Z chromosome that were significantly differentially methylated between the sexes. These regions appear to down-regulate local gene expression in males, but not remove it entirely (unlike the lncRNAs identified in the initial MHM regions). These MHM regions were further tested and the most balanced genes appear to show decreased expression in males, whilst methylation appeared to be far more correlated with gene expression in the less balanced, as compared to the most balanced genes. In addition, quantitative trait loci (QTL) that regulate variation in methylation on the Z chromosome, and those loci that regulate methylation on the autosomes that derive from the Z chromosome were mapped. Trans-effect hotspots were also identified that were based on the autosomes but affected the Z, and also one that was based on the Z chromosome but that affected both autosomal and sex chromosome DNA methylation regulation. We show that both cis and trans loci that originate from the Z chromosome never exhibit an interaction with sex, whereas trans loci originating from the autosomes but affecting the Z chromosome always display such an interaction. Our results highlight how additional MHM regions are actually present on the Z chromosome, and they appear to have smaller-scale effects on gene expression in males. Quantitative variation in methylation is also regulated both from the autosomes to the Z chromosome, and from the Z chromosome to the autosomes.", "doi": "10.1371/journal.pgen.1010719", "pmid": "38457441", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10954189"}, {"db": "pii", "key": "PGENETICS-D-23-00328"}], "notes": [], "created": "2024-11-12T10:39:26.077Z", "modified": "2024-11-25T10:31:41.001Z"}, {"entity": "publication", "iuid": "d787ebed6379499b968ca423e460aa66", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d787ebed6379499b968ca423e460aa66.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d787ebed6379499b968ca423e460aa66"}}, "title": "The methylation landscape and its role in domestication and gene regulation in the chicken.", "authors": [{"family": "H\u00f6glund", "given": "Andrey", "initials": "A"}, {"family": "Henriksen", "given": "Rie", "initials": "R"}, {"family": "Fogelholm", "given": "Jesper", "initials": "J"}, {"family": "Churcher", "given": "Allison M", "initials": "AM", "orcid": "0000-0003-1902-3002", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97e6fb500a043f08d4f882e802cd91b.json"}}, {"family": "Guerrero-Bosagna", "given": "Carlos M", "initials": "CM", "orcid": "0000-0003-1935-5875", "researcher": {"href": "https://publications.scilifelab.se/researcher/0175a0da7ca147d4a0430b085ed23669.json"}}, {"family": "Martinez-Barrio", "given": "Alvaro", "initials": "A", "orcid": "0000-0001-5064-2093", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6ff319fe64340f2bb2350121848ecff.json"}}, {"family": "Johnsson", "given": "Martin", "initials": "M"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}}], "type": "journal article", "published": "2020-12-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "volume": "4", "issue": "12", "pages": "1713-1724", "issn-l": "2397-334X"}, "abstract": "Domestication is one of the strongest examples of artificial selection and has produced some of the most extreme within-species phenotypic variation known. In the case of the chicken, it has been hypothesized that DNA methylation may play a mechanistic role in the domestication response. By inter-crossing wild-derived red junglefowl with domestic chickens, we mapped quantitative trait loci for hypothalamic methylation (methQTL), gene expression (eQTL) and behaviour. We find large, stable methylation differences, with 6,179 cis and 2,973 trans methQTL identified. Over 46% of the trans effects were genotypically controlled by five loci, mainly associated with increased methylation in the junglefowl genotype. In a third of eQTL, we find that there is a correlation between gene expression and methylation, while statistical causality analysis reveals multiple instances where methylation is driving gene expression, as well as the reverse. We also show that methylation is correlated with some aspects of behavioural variation in the inter-cross. In conclusion, our data suggest a role for methylation in the regulation of gene expression underlying the domesticated phenotype of the chicken.", "doi": "10.1038/s41559-020-01310-1", "pmid": "32958860", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-020-01310-1"}, {"db": "figshare", "key": "10.6084/m9.figshare.12803873"}, {"db": "figshare", "key": "10.6084/m9.figshare.12803876"}, {"db": "figshare", "key": "10.6084/m9.figshare.12803870"}], "notes": [], "created": "2020-09-25T11:36:26.073Z", "modified": "2024-01-16T13:48:41.219Z"}]}