NGI is one of the largest technical platforms at SciLifeLab. We provide access to technology for sequencing, genotyping and associated bioinformatics support to researchers based in Sweden.
NGI OpenLab: A New Hub for Collaborative Genomics!
We're thrilled to announce the official launch of NGI OpenLab, an innovative space designed to empower genomics research. The lab provides direct access to equipment for quality control (QC), library preparation and a walk-up sequencer for on-the-go sequencing needs.
Boost Your Genomics Research with NGI and Element Biosciences Grants
SciLifeLab’s National Genomics Infrastructure (NGI), in partnership with Element Biosciences, is offering two grant opportunities for Swedish researchers to access advanced sequencing technologies.
SciLifeLab’s National Genomics Infrastructure (NGI), in partnership with Element Biosciences, is offering two grant opportunities for Swedish researchers to access advanced sequencing technologies.
We are seeking a motivated and skilled Postdoctoral Researcher to join the Research and Development (R&D) team at the Uppsala node of the National Genomics Infrastructure (NGI), part of SciLifeLab.
MicroRNAs (miRNAs) are small, non-coding RNA that play a critical role in regulating gene expressions that are important for a multitude of biological processes. In the preparation of miRNA sequencing libraries by using QIAseq miRNA library kit, adapter dimers might occur inadvertently and compromise the sequencing performance.
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Are freshwater bacterioplankton indifferent to variable types of amino acid substrates?
M Ricão Canelhas, A Eiler, S Bertilsson
FEMS Microbiol. Ecol., 92 (2) 1574-6941 (2016)
A wide range of carbon compounds sustain bacterial activity and growth in freshwater ecosystems and the amount and quality of these substrates influence bacterial diversity and metabolic function. Biologically labile low-molecular-weight compounds, such as dissolved free amino acids, are particularly important substrates and can fuel as much as 20% of the total heterotrophic production. In this study, we show that extensive laboratory incubations with variable amino acids as substrates caused only minimal differences in bacterial growth rate, growth yield, quantitative amino acid usage, community composition and diversity. This was in marked contrast to incubations under dark or light regimes, where significant responses were observed in bacterial community composition and with higher diversity in the dark incubations. While a few individual taxa still responded to amendment with specific amino acids, our results suggest that compositional shifts in the specific supply of amino acids and possibly also other labile organic substrates have a minor impact on heterotrophic bacterioplankton communities, at least in nutrient rich lakes and compared to other prevailing environmental factors.
Homozygous loss-of-function variants in European cosmopolitan and isolate populations.
VB Kaiser, V Svinti, JG Prendergast, YY Chau, A Campbell, I Patarcic, I Barroso, PK Joshi, ND Hastie, A Miljkovic, MS Taylor, Generation Scotland, Uk10k, S Enroth, Y Memari, A Kolb-Kokocinski, AF Wright, U Gyllensten, R Durbin, I Rudan, H Campbell, O Polašek, Å Johansson, S Sauer, DJ Porteous, RM Fraser, C Drake, V Vitart, C Hayward, CA Semple, JF Wilson
Hum. Mol. Genet., 24 (19) 1460-2083 (2015)
Homozygous loss of function (HLOF) variants provide a valuable window on gene function in humans, as well as an inventory of the human genes that are not essential for survival and reproduction. All humans carry at least a few HLOF variants, but the exact number of inactivated genes that can be tolerated is currently unknown—as are the phenotypic effects of losing function for most human genes. Here, we make use of 1432 whole exome sequences from five European populations to expand the catalogue of known human HLOF mutations; after stringent filtering of variants in our dataset, we identify a total of 173 HLOF mutations, 76 (44%) of which have not been observed previously. We find that population isolates are particularly well suited to surveys of novel HLOF genes because individuals in such populations carry extensive runs of homozygosity, which we show are enriched for novel, rare HLOF variants. Further, we make use of extensive phenotypic data to show that most HLOFs, ascertained in population-based samples, appear to have little detectable effect on the phenotype. On the contrary, we document several genes directly implicated in disease that seem to tolerate HLOF variants. Overall HLOF genes are enriched for olfactory receptor function and are expressed in testes more often than expected, consistent with reduced purifying selection and incipient pseudogenisation.
Role of H1 and DNA methylation in selective regulation of transposable elements during heat stress.
S Liu, J de Jonge, MS Trejo-Arellano, J Santos-González, C Köhler, L Hennig
New Phytol., 229 (4) 1469-8137 (2021)
Heat-stressed Arabidopsis plants release heterochromatin-associated transposable element (TE) silencing, yet it is not accompanied by major reductions of epigenetic repressive modifications. In this study, we explored the functional role of histone H1 in repressing heterochromatic TEs in response to heat stress. We generated and analyzed RNA and bisulfite-sequencing data of wild-type and h1 mutant seedlings before and after heat stress. Loss of H1 caused activation of pericentromeric Gypsy elements upon heat treatment, despite these elements remaining highly methylated. By contrast, nonpericentromeric Copia elements became activated concomitantly with loss of DNA methylation. The same Copia elements became activated in heat-treated chromomethylase 2 (cmt2) mutants, indicating that H1 represses Copia elements through maintaining DNA methylation under heat. We discovered that H1 is required for TE repression in response to heat stress, but its functional role differs depending on TE location. Strikingly, H1-deficient plants treated with the DNA methyltransferase inhibitor zebularine were highly tolerant to heat stress, suggesting that both H1 and DNA methylation redundantly suppress the plant response to heat stress.
Long noncoding RNA-mediated maintenance of DNA methylation and transcriptional gene silencing.
F Mohammad, GK Pandey, T Mondal, S Enroth, L Redrup, U Gyllensten, C Kanduri
Development, 139 (15) 1477-9129 (2012)
Establishment of silencing by noncoding RNAs (ncRNAs) via targeting of chromatin remodelers is relatively well investigated; however, their role in the maintenance of silencing is poorly understood. Here, we explored the functional role of the long ncRNA Kcnq1ot1 in the maintenance of transcriptional gene silencing in the one mega-base Kcnq1 imprinted domain in a transgenic mouse model. By conditionally deleting the Kcnq1ot1 ncRNA at different stages of mouse development, we suggest that Kcnq1ot1 ncRNA is required for the maintenance of the silencing of ubiquitously imprinted genes (UIGs) at all developmental stages. In addition, Kcnq1ot1 ncRNA is also involved in guiding and maintaining the CpG methylation at somatic differentially methylated regions flanking the UIGs, which is a hitherto unknown role for a long ncRNA. On the other hand, silencing of some of the placental-specific imprinted genes (PIGs) is maintained independently of Kcnq1ot1 ncRNA. Interestingly, the non-imprinted genes (NIGs) that escape RNA-mediated silencing are enriched with enhancer-specific modifications. Taken together, this study illustrates the gene-specific maintenance mechanisms operational at the Kcnq1 locus for tissue-specific transcriptional gene silencing and activation.
Genome-wide repression of eRNA and target gene loci by the ETV6-RUNX1 fusion in acute leukemia.
S Teppo, S Laukkanen, T Liuksiala, J Nordlund, M Oittinen, K Teittinen, T Grönroos, P St-Onge, D Sinnett, AC Syvänen, M Nykter, K Viiri, M Heinäniemi, O Lohi
Approximately 20%-25% of childhood acute lymphoblastic leukemias carry the ETV6-RUNX1 (E/R) fusion gene, a fusion of two central hematopoietic transcription factors, ETV6 (TEL) and RUNX1 (AML1). Despite its prevalence, the exact genomic targets of E/R have remained elusive. We evaluated gene loci and enhancers targeted by E/R genome-wide in precursor B acute leukemia cells using global run-on sequencing (GRO-seq). We show that expression of the E/R fusion leads to widespread repression of RUNX1 motif-containing enhancers at its target gene loci. Moreover, multiple super-enhancers from the CD19+/CD20+-lineage were repressed, implicating a role in impediment of lineage commitment. In effect, the expression of several genes involved in B cell signaling and adhesion was down-regulated, and the repression depended on the wild-type DNA-binding Runt domain of RUNX1. We also identified a number of E/R-regulated annotated and de novo noncoding genes. The results provide a comprehensive genome-wide mapping between E/R-regulated key regulatory elements and genes in precursor B cell leukemia that disrupt normal B lymphopoiesis.
Next generation pan-cancer blood proteome profiling using proximity extension assay.
MB Álvez, F Edfors, K von Feilitzen, M Zwahlen, A Mardinoglu, PH Edqvist, T Sjöblom, E Lundin, N Rameika, G Enblad, H Lindman, M Höglund, G Hesselager, K Stålberg, M Enblad, OE Simonson, M Häggman, T Axelsson, M Åberg, J Nordlund, W Zhong, M Karlsson, U Gyllensten, F Ponten, L Fagerberg, M Uhlén
A comprehensive characterization of blood proteome profiles in cancer patients can contribute to a better understanding of the disease etiology, resulting in earlier diagnosis, risk stratification and better monitoring of the different cancer subtypes. Here, we describe the use of next generation protein profiling to explore the proteome signature in blood across patients representing many of the major cancer types. Plasma profiles of 1463 proteins from more than 1400 cancer patients are measured in minute amounts of blood collected at the time of diagnosis and before treatment. An open access Disease Blood Atlas resource allows the exploration of the individual protein profiles in blood collected from the individual cancer patients. We also present studies in which classification models based on machine learning have been used for the identification of a set of proteins associated with each of the analyzed cancers. The implication for cancer precision medicine of next generation plasma profiling is discussed.
Epigenome-wide DNA methylation patterns associated with fatigue in primary Sjögren's syndrome.
K Brække Norheim, J Imgenberg-Kreuz, K Jonsdottir, EA Janssen, AC Syvänen, JK Sandling, G Nordmark, R Omdal
Chronic fatigue is a common, disabling and poorly understood phenomenon. Recent studies indicate that epigenetic mechanisms may be involved in the expression of fatigue, a prominent feature of primary SS (pSS). The aim of this study was to investigate whether DNA methylation profiles of whole blood are associated with fatigue in patients with pSS.
Forty-eight pSS patients with high (n = 24) or low (n = 24) fatigue as measured by a visual analogue scale were included. Genome-wide DNA methylation was investigated using the Illumina HumanMethylation450 BeadChip array. After quality control, a total of 383 358 Cytosine-phosphate-Guanine (CpG) sites remained for further analysis. Age, sex and differential cell count estimates were included as covariates in the association model. A false discovery rate-corrected P < 0.05 was considered significant, and a cut-off of 3% average difference in methylation levels between high- and low-fatigue patients was applied.
A total of 251 differentially methylated CpG sites were associated with fatigue. The CpG site with the most pronounced hypomethylation in pSS high fatigue annotated to the SBF2-antisense RNA1 gene. The most distinct hypermethylation was observed at a CpG site annotated to the lymphotoxin alpha gene. Functional pathway analysis of genes with differently methylated CpG sites in subjects with high vs low fatigue revealed enrichment in several pathways associated with innate and adaptive immunity.
Some genes involved in regulation of the immune system and in inflammation are differently methylated in pSS patients with high vs low fatigue. These findings point to functional networks that may underlie fatigue. Epigenetic changes could constitute a fatigue-regulating mechanism in pSS.
Last Updated: 8th April 2025
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