Change search
Refine search result
1 - 5 of 5
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 1.
    Anil, Anandashankar
    et al.
    KTH, School of Biotechnology (BIO). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Spalinskas, Rapolas
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO).
    Åkerborg, Örjan
    KTH, School of Biotechnology (BIO). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Sahlén, Pelin
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO).
    HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications2018In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 34, no 4, p. 675-677Article in journal (Refereed)
    Abstract [en]

    Folding of eukaryotic genomes within nuclear space enables physical and functional contacts between regions that are otherwise kilobases away in sequence space. Targeted chromosome conformation capture methods (T2C, chi-C and HiCap) are capable of informing genomic contacts for a subset of regions targeted by probes. We here present HiCapTools, a software package that can design sequence capture probes for targeted chromosome capture applications and analyse sequencing output to detect proximities involving targeted fragments. Two probes are designed for each feature while avoiding repeat elements and non-unique regions. The data analysis suite processes alignment files to report genomic proximities for each feature at restriction fragment level and is isoform-aware for gene features. Statistical significance of contact frequencies is evaluated using an empirically derived background distribution. Targeted chromosome conformation capture applications are invaluable for locating target genes of disease-associated variants found by genome-wide association studies. Hence, we believe our software suite will prove to be useful for a wider user base within clinical and functional applications.

  • 2.
    Cavalli, Marco
    et al.
    Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, Uppsala, Sweden..
    Baltzer, Nicholas
    Uppsala Univ, Dept Cell & Mol Biol Computat Biol & Bioinformat, Uppsala, Sweden..
    Umer, Husen M.
    Uppsala Univ, Dept Cell & Mol Biol Computat Biol & Bioinformat, Uppsala, Sweden..
    Grau, Jan
    Martin Luther Univ Halle Wittenberg, Inst Comp Sci, Halle, Germany..
    Lemnian, Ioana
    Martin Luther Univ Halle Wittenberg, Inst Comp Sci, Halle, Germany..
    Pan, Gang
    Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, Uppsala, Sweden..
    Wallerman, Ola
    Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, Uppsala, Sweden..
    Spalinskas, Rapolas
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Sahlén, Pelin
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Grosse, Ivo
    Martin Luther Univ Halle Wittenberg, Inst Comp Sci, Halle, Germany.;German Ctr Integrat Biodivers Res iDiv, Leipzig, Germany..
    Komorowski, Jan
    Uppsala Univ, Dept Cell & Mol Biol Computat Biol & Bioinformat, Uppsala, Sweden.;Polish Acad Sci, Inst Comp Sci, Warsaw, Poland..
    Wadelius, Claes
    Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, Uppsala, Sweden..
    Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 2695Article in journal (Refereed)
    Abstract [en]

    Several Genome Wide Association Studies (GWAS) have reported variants associated to immune diseases. However, the identified variants are rarely the drivers of the associations and the molecular mechanisms behind the genetic contributions remain poorly understood. ChIP-seq data for TFs and histone modifications provide snapshots of protein-DNA interactions allowing the identification of heterozygous SNPs showing significant allele specific signals (AS-SNPs). AS-SNPs can change a TF binding site resulting in altered gene regulation and are primary candidates to explain associations observed in GWAS and expression studies. We identified 17,293 unique AS-SNPs across 7 lymphoblastoid cell lines. In this set of cell lines we interrogated 85% of common genetic variants in the population for potential regulatory effect and we identified 237 AS-SNPs associated to immune GWAS traits and 714 to gene expression in B cells. To elucidate possible regulatory mechanisms we integrated long-range 3D interactions data to identify putative target genes and motif predictions to identify TFs whose binding may be affected by AS-SNPs yielding a collection of 173 AS-SNPs associated to gene expression and 60 to B cell related traits. We present a systems strategy to find functional gene regulatory variants, the TFs that bind differentially between alleles and novel strategies to detect the regulated genes.

  • 3.
    Chen, Liangliang
    et al.
    Soochow Univ, Cam Su Genom Resource Ctr, Suzhou 215123, Peoples R China..
    Ye, Ying
    Soochow Univ, Cam Su Genom Resource Ctr, Suzhou 215123, Peoples R China..
    Dai, Hongxia
    Soochow Univ, Cam Su Genom Resource Ctr, Suzhou 215123, Peoples R China..
    Zhang, Heyao
    Soochow Univ, Cam Su Genom Resource Ctr, Suzhou 215123, Peoples R China..
    Zhang, Xue
    Soochow Univ, Cam Su Genom Resource Ctr, Suzhou 215123, Peoples R China..
    Wu, Qiang
    Macau Univ Sci & Technol, State Key Lab Qual Res Chinese Med, Ave Wai Long, Taipa, Macau, Peoples R China..
    Zhu, Zhexin
    St Jude Childrens Res Hosp, Dept Oncol, 262 Danny Thomas Pl, Memphis, TN 38105 USA..
    Spalinskas, Rapolas
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ren, Wenyan
    Soochow Univ, Cam Su Genom Resource Ctr, Suzhou 215123, Peoples R China..
    Zhang, Wensheng
    Soochow Univ, Cam Su Genom Resource Ctr, Suzhou 215123, Peoples R China..
    User-Friendly Genetic Conditional Knockout Strategies by CRISPR/Cas92018In: STEM CELLS INTERNATIONAL, ISSN 1687-966X, article id 9576959Article in journal (Refereed)
    Abstract [en]

    Loss-of-function studies are critically important in gene functional analysis of model organisms and cells. However, conditional gene inactivation in diploid cells is difficult to achieve, as it involves laborious vector construction, multifold electroporation, and complicated genotyping. Here, a strategy is presented for generating biallelic conditional gene and DNA regulatory region knockouts in mouse embryonic stem cells by codelivery of CRISPR-Cas9 and short-homology-arm targeting vectors sequentially or simultaneously. Collectively, a simple and rapid method was presented to knock out any DNA element conditionally. This approach will facilitate the functional studies of essential genes and regulatory regions during development.

  • 4. Tapia-Paez, I.
    et al.
    Asad, S.
    Taylan, F.
    Spalinskas, Rapolas
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Anandashankar, A.
    Nordenskjold, M.
    Wahlgren, C. F.
    Sahlén, Pelin
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Bradley, M.
    Studies of keratinocyte-specific regulatory interactions by three-dimensional mapping with a focus on atopic dermatitis2018In: British Journal of Dermatology, ISSN 0007-0963, E-ISSN 1365-2133, Vol. 179, no 1, p. E33-E33Article in journal (Refereed)
  • 5.
    Zhang, Wensheng
    et al.
    Soochow Univ, Cam Su Genom Resource Ctr, Suzhou 215123, Peoples R China.;Wellcome Sanger Inst, Hinxton CB10 1SA, England..
    Chronis, Constantinos
    Univ Calif Los Angeles, David Geffen Sch Med, Dept Biol & Chem, Los Angeles, CA 90095 USA.;Univ Calif Los Angeles, Eli & Edythe Broad Ctr Regenerat Med & Stem Cell, Los Angeles, CA USA.;Univ Calif Los Angeles, Jonsson Comprehens Canc Ctr, Bioinformat Program, Los Angeles, CA 90024 USA.;Univ Calif Los Angeles, Mol Biol Inst, Los Angeles, CA 90095 USA..
    Chen, Xi
    Wellcome Sanger Inst, Hinxton CB10 1SA, England..
    Zhang, Heyao
    Soochow Univ, Cam Su Genom Resource Ctr, Suzhou 215123, Peoples R China..
    Spalinskas, Rapolas
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Pardo, Mercedes
    Chester Beatty Labs, Inst Canc Res, London, England..
    Chen, Liangliang
    Soochow Univ, Cam Su Genom Resource Ctr, Suzhou 215123, Peoples R China..
    Wu, Guangming
    Max Planck Inst Mol Biomed, Dept Cell & Dev Biol, Rontgenstr 20, D-48149 Munster, Germany..
    Zhu, Zhexin
    Wellcome Sanger Inst, Hinxton CB10 1SA, England..
    Yu, Yong
    Wellcome Sanger Inst, Hinxton CB10 1SA, England..
    Yu, Lu
    Chester Beatty Labs, Inst Canc Res, London, England..
    Choudhary, Jyoti
    Chester Beatty Labs, Inst Canc Res, London, England..
    Nichols, Jennifer
    Univ Cambridge, Wellcome Trust Med Res Council, Stem Cell Inst, Tennis Court Rd, Cambridge CB2 1QR, England..
    Parast, Mana M.
    Univ Calif San Diego, Dept Pathol, La Jolla, CA 92093 USA.;Univ Calif San Diego, Sanford Consortium Regenerat Med, La Jolla, CA 92093 USA..
    Greber, Boris
    Max Planck Inst Mol Biomed, Dept Cell & Dev Biol, Rontgenstr 20, D-48149 Munster, Germany..
    Sahlén, Pelin
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Plath, Kathrin
    Univ Calif Los Angeles, David Geffen Sch Med, Dept Biol & Chem, Los Angeles, CA 90095 USA.;Univ Calif Los Angeles, Eli & Edythe Broad Ctr Regenerat Med & Stem Cell, Los Angeles, CA USA.;Univ Calif Los Angeles, Jonsson Comprehens Canc Ctr, Bioinformat Program, Los Angeles, CA 90024 USA.;Univ Calif Los Angeles, Mol Biol Inst, Los Angeles, CA 90095 USA..
    The BAF and PRC2 Complex Subunits Dpf2 and Eed Antagonistically Converge on Tbx3 to Control ESC Differentiation2019In: Cell Stem Cell, ISSN 1934-5909, E-ISSN 1875-9777, Vol. 24, no 1, p. 138-+Article in journal (Refereed)
    Abstract [en]

    BAF complexes are composed of different subunits with varying functional and developmental roles, although many subunits have not been examined in depth. Here we show that the Baf45 subunit Dpf2 maintains pluripotency and ESC differentiation potential. Dpf2 co-occupies enhancers with Oct4, Sox2, p300, and the BAF subunit Brg1, and deleting Dpf2 perturbs ESC self-renewal, induces repression of Tbx3, and impairs mesendodermal differentiation without dramatically altering Brg1 localization. Mesendodermal differentiation can be rescued by restoring Tbx3 expression, whose distal enhancer is positively regulated by Dpf2-dependent H3K27ac maintenance and recruitment of pluripotency TFs and Brg1. In contrast, the PRC2 subunit Eed binds an intragenic Tbx3 enhancer to oppose Dpf2-dependent Tbx3 expression and mesendodermal differentiation. The PRC2 subunit Ezh2 likewise opposes Dpf2-dependent differentiation through a distinct mechanism involving Nanog repression. Together, these findings delineate distinct mechanistic roles for specific BAF and PRC2 subunits during ESC differentiation.

1 - 5 of 5
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf