Julkaisut

• Characterization of a functional endothelial super-enhancer that regulates ADAMTS18 and angiogenesis Mushimiyimana, I; Niskanen. H; Beter, M; Laakkonen, JP; Kaikkonen, MU; Ylä-Herttuala, S; Laham-Karam, N. 2021. Characterization of a functional endothelial super-enhancer that regulates ADAMTS18 and angiogenesis Nucleic acids research 49 14: 8078-8096. 2021
• Genomic landscapes of non-coding RNAs regulating VEGFA and VEGFC expression in endothelial cells Mushimiyimana, Isidore; Tomas Bosch, Vanesa; Niskanen, Henri; Downes, Nicholas; Moreau, Pierre; Hartigan, Kiley; Ylä-Herttuala, Seppo; Laham-Karam, Nihay; Kaikkonen, Minna U.. 2021. Genomic landscapes of non-coding RNAs regulating VEGFA and VEGFC expression in endothelial cells Molecular and cellular biology 41 7: e00594-20. 2021
• Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease Selvarajan, Ilakya; Toropainen, Anu; Garske, Kristina M.; López Rodríguez, Maykel; Ko, Arthur; Miao, Zong; Kaminska, Dorota; Õunap, Kadri; Örd, Tiit; Ravindran, Aarthi; Liu, Oscar H.; Moreau, Pierre R.; Jawahar Deen, Ashik; Männistö, Ville; Pan, Calvin; Levonen, Anna-Liisa; Lusis, Aldons J.; Heikkinen, Sami; Romanoski, Casey E.; Pihlajamäki, Jussi; Pajukanta, Päivi; Kaikkonen, Minna U.. 2021. Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease American journal of human genetics 108 3: 411-430. 2021
• Meta-Analysis of Smooth Muscle Lineage Transcriptomes in Atherosclerosis and Their Relationships to In Vitro Models Conklin, Austin C.; Nishi, Hitoo; Schlamp, Florencia; Örd, Tiit; Õunap, Kadri; Kaikkonen, Minna U.; Fisher, Edward A.; Romanoski, Casey E.. 2021. Meta-Analysis of Smooth Muscle Lineage Transcriptomes in Atherosclerosis and Their Relationships to In Vitro Models Immunometabolism 3 3: e210022. 2021
• NRF2 is a key regulator of endothelial microRNA expression under proatherogenic stimuli Linna-Kuosmanen, Suvi; Bosch, Vanesa Tomas; Moreau, Pierre R; Bouvy-Liivrand, Maria; Niskanen, Henri; Kansanen, Emilia; Kivelä, Annukka; Hartikainen, Juha; Hippeläinen, Mikko; Kokki, Hannu; Tavi, Pasi; Levonen, Anna-Liisa; Kaikkonen, Minna U. 2021. NRF2 is a key regulator of endothelial microRNA expression under proatherogenic stimuli Cardiovascular research 117 5: 1339-1357. 2021
• Profiling of Primary and Mature miRNA Expression in Atherosclerosis Associated Cell Types Moreau, PR; Tomas Bosch, V; Bouvy-Liivrand,M; Õunap, K; Örd, T; Pulkkinen, HH; Pölönen, P; Heinäniemi, M; Ylä-Herttuala, S; Laakkonen, JP; Linna-Kuosmanen, S; Kaikkonen, MU. 2021. Profiling of Primary and Mature miRNA Expression in Atherosclerosis Associated Cell Types Arteriosclerosis, thrombosis, and vascular biology 41 7: 2149-2167. 2021
• Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci Örd, Tiit; Õunap, Kadri; Stolze, Lindsey; Aherrahrou, Rédouane; Nurminen, Valtteri; Selvarajan, Ilakya; Toropainen, Anu; Lönnberg, Tapio; Aavik, Einari; Yla-Herttuala, Seppo; Civelek, Mete; Romanoski, Casey E; Kaikkonen, Minna U. 2021. Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci Circulation research 129 2: 240-258. 2021
• Transcriptional gene regulation in endothelial cells in response to hypoxia Downes, Nicholas (toim.). 2021. Transcriptional gene regulation in endothelial cells in response to hypoxia. Itä-Suomen yliopisto. Publications of the University of Eastern Finland. Dissertations in Health Sciences 646. 2021
• Genetic Regulation of Atherosclerosis-Relevant Phenotypes in Human Vascular Smooth Muscle Cells Aherrahrou, Rédouane; Guo, Liang; Nagraj, Vijay Peter; Aguhob, Aaron Andrew; Hinkle, Jameson; Chen, Lisa; Soh, Joon Yuhl; Lue, Dillon; Alencar, Gabriel F; Boltjes, Arjan; van der Laan, Sander W; Farber, Emily; Fuller, Daniela; Anane-Wae, Rita; Akingbesote, Ngozi D; Manichaikul, Ani W; Ma, Lijiang; Kaikkonen, Minna U; Björkegren, Johan LM; Önengüt-Gümüscu, Suna; et al.. 2020. Genetic Regulation of Atherosclerosis-Relevant Phenotypes in Human Vascular Smooth Muscle Cells Circulation research 127 12: 1552-1565. 2020
• Hypoxia-Mediated Regulation of Histone Demethylases Affects Angiogenesis-Associated Functions in Endothelial Cells Hsin-Fu Liu, Oscar; Kiema, Miika; Beter, Mustafa; Ylä-Herttuala, Seppo; Laakkonen, Johanna P; Kaikkonen, Minna U. 2020. Hypoxia-Mediated Regulation of Histone Demethylases Affects Angiogenesis-Associated Functions in Endothelial Cells Arteriosclerosis thrombosis and vascular biology 40: 2665-2677. 2020
• Microanatomy of the Human Atherosclerotic Plaque by Single-Cell Transcriptomics Depuydt, Marie Ac; Prange, Koen Hm; Slenders, Lotte; Örd, Tiit; Elbersen, Danny; Boltjes, Arjan; de Jager, Saskia Ca; Asselbergs, Folkert W; de Borst, Gert J; Aavik, Einari; Lönnberg, Tapio; Lutgens, Esther; Glass, Christopher K; den Ruijter, Hester M; Kaikkonen, Minna U; Bot, Ilze; Slütter, Bram; van der Laan, Sander W; Ylä-Herttuala, Seppo; Mokry, Michal; et al. 2020. Microanatomy of the Human Atherosclerotic Plaque by Single-Cell Transcriptomics Circulation research 127 11: 1437-1455. 2020
• Systems Genetics in Human Endothelial Cells Identifies Non-coding Variants Modifying Enhancers, Expression, and Complex Disease Traits Stolze, Lindsey; Conklin, Austin; Whalen, Michael; López Rodríguez, Maykel; Õunap, Kadri; Selvarajan, Ilakya; Toropainen, Anu; Örd, Tiit; Li, Jin; Eshghi, Anna; Solomon, Alice; Fang, Yun; Kaikkonen, Minna; Romanoski, Casey. 2020. Systems Genetics in Human Endothelial Cells Identifies Non-coding Variants Modifying Enhancers, Expression, and Complex Disease Traits American journal of human genetics 106 6: P748-763. 2020
• Extensive reprogramming of the nascent transcriptome during iPSC to hepatocyte differentiation Viiri, LE; Rantapero, T; Kiamehr, M; Alexanova, A; Oittinen, M; Viiri, K; Niskanen, H; Nykter, M; Kaikkonen, MU; Aalto-Setälä, K. 2019. Extensive reprogramming of the nascent transcriptome during iPSC to hepatocyte differentiation Scientific reports 9 1: 3562. 2019
• Novel Lipid Long Intervening Noncoding RNA, Oligodendrocyte Maturation-Associated Long Intergenic Noncoding RNA, Regulates the Liver Steatosis Gene Stearoyl-Coenzyme A Desaturase As an Enhancer RNA Benhammou, Jihane N; Ko, Arthur; Alvarez, Marcus; Kaikkonen, Minna U; Rankin, Carl; Garske, Kristina M; Padua, David; Bhagat, Yash; Kaminska, Dorota; Karja, Vesa; Pihlajamäki, Jussi; Pisegna, Joseph R; Pajukanta, Päivi. 2019. Novel Lipid Long Intervening Noncoding RNA, Oligodendrocyte Maturation-Associated Long Intergenic Noncoding RNA, Regulates the Liver Steatosis Gene Stearoyl-Coenzyme A Desaturase As an Enhancer RNA Hepatology communications 3 10: 1356-1372. 2019
• Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation Cuartero, Sergi; Weiss, Felix D; Dharmalingam, Gopuraja; Guo, Ya; Ing-Simmons, Elizabeth; Masella, Silvia; Robles-Rebollo, Irene; Xiao, Xiaolin; Wang, Yi-Fang; Barozzi, Iros; Djeghloul, Dounia; Amano, Mariane T; Niskanen, Henri; Petretto, Enrico; Dowell, Robin D; Tachibana, Kikue; Kaikkonen, Minna U; Nasmyth, Kim A; Lenhard, Boris; Natoli, Gioacchino; et al.. 2018. Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation Nature immunology 19 9: 932-944. 2018
• Differential but Complementary HIF1[alfa] and HIF2[alfa] Transcriptional Regulation Downes, Nicholas L; Laham-Karam, Nihay; Kaikkonen, Minna U; Ylä-Herttuala, Seppo. 2018. Differential but Complementary HIF1[alfa] and HIF2[alfa] Transcriptional Regulation MOLECULAR THERAPY 26 7: 1735-1745. 2018
• Emerging Roles of Non-Coding RNA Transcription Kaikkonen, Minna U; Adelman, Karen. 2018. Emerging Roles of Non-Coding RNA Transcription Trends in biochemical sciences 43 9: 654-667. 2018
• Functional Variant in the GCKR Gene Affects Lactate Levels Differentially in the Fasting State and During Hyperglycemia López Rodríguez, Maykel; Fernandes Silva, Lilian; Vangipurapu, Jagadish; Modi, Shalem; Kuusisto, Johanna; Kaikkonen, Minna U; Laakso, Markku. 2018. Functional Variant in the GCKR Gene Affects Lactate Levels Differentially in the Fasting State and During Hyperglycemia Scientific Reports 8 1: 15989. 2018
• MicroRNAs mediate the senescence-associated decline of NRF2 in endothelial cells Kuosmanen, SM; Sihvola, V; Kansanen, E; Kaikkonen, MU; Levonen, AL. 2018. MicroRNAs mediate the senescence-associated decline of NRF2 in endothelial cells Redox Biology 18: 77-83. 2018
• Temporal Dynamics of Gene Expression During Endothelial Cell Differentiation From Human iPS Cells: A Comparison Study of Signalling Factors and Small Molecules Belt, H; Koponen, JK; Kekarainen, T; Puttonen, KA; Mäkinen, PI; Niskanen, H;, Oja, J; Wirth, G; Koistinaho, J; Kaikkonen, MU; Ylä-Herttuala, S. 2018. Temporal Dynamics of Gene Expression During Endothelial Cell Differentiation From Human iPS Cells: A Comparison Study of Signalling Factors and Small Molecules. Frontiers in cardiovascular medicine 5: 16. 2018
• Transcriptional Profiling of Hypoxia-Regulated Non-coding RNAs in Human Primary Endothelial Cells Moreau, Pierre R; Örd, Tiit; Downes, Nicholas L; Niskanen, Henri; Bouvy-Liivrand, Maria; Aavik, Einari; Ylä-Herttuala, Seppo; Kaikkonen, Minna U. 2018. Transcriptional Profiling of Hypoxia-Regulated Non-coding RNAs in Human Primary Endothelial Cells Frontiers in cardiovascular medicine 5 159: 12. 2018
• Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture Bouvy-Liivrand Maria, Hernández de Sande Ana, Pölönen Petri, Mehtonen Juha, Vuorenmaa Tapio, Niskanen Henri, Sinkkonen Lasse, Unelma Kaikkonen Minna, Heinäniemi Merja. 2017. Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture. NUCLEIC ACIDS RESEARCH 45 17: 9837-9849. 2017
• Endothelial cell differentiation is encompassed by changes in long range interactions between inactive chromatin regions Niskanen, Henri; Tuszynska, Irina; Zaborowski, Rafal; Heinäniemi, Merja; Ylä-Herttuala, Seppo; Wilczynski, Bartek; Kaikkonen, Minna U. 2017. Endothelial cell differentiation is encompassed by changes in long range interactions between inactive chromatin regions NUCLEIC ACIDS RESEARCH 2018; 46 4: 1724-1740. 2017
• Genome-Wide Dynamics of Nascent Noncoding RNA Transcription in Porcine Heart After Myocardial Infarction Kaikkonen Minna U, Halonen Paavo, Liu Oscar Hsin-Fu, Turunen Tiia A, Pajula Juho, Moreau Pierre, Selvarajan Ilakya, Tuomainen Tomi, Aavik Einari, Tavi Pasi, Ylä-Herttuala Seppo. 2017. Genome-Wide Dynamics of Nascent Noncoding RNA Transcription in Porcine Heart After Myocardial Infarction Circulation: Cardiovascular Genetics 10 3: e001702. 2017
• Identification and characterization of a FOXA2-regulated transcriptional enhancer at a type 2 diabetes intronic locus that controls GCKR expression in liver cells López Rodríguez M, Kaminska D, Lappalainen K, Pihlajamäki J, Kaikkonen MU, Laakso M. 2017. Identification and characterization of a FOXA2-regulated transcriptional enhancer at a type 2 diabetes intronic locus that controls GCKR expression in liver cells. Genome Medicine 9: 63. 2017
• NRF2 regulates endothelial glycolysis and proliferation with miR-93 and mediates the effects of oxidized phospholipids on endothelial activation Kuosmanen SM, Kansanen E, Kaikkonen MU, Sihvola V, Pulkkinen K, Jyrkkänen H-K, Tuoresmäki P, Hartikainen J, Hippeläinen M, Kokko H, Tavi P, Heikkinen S, Levonen A-M. 2017. NRF2 regulates endothelial glycolysis and proliferation with miR-93 and mediates the effects of oxidized phospholipids on endothelial activation. NUCLEIC ACIDS RESEARCH 2018; 46 3: 1124-1138. 2017
• SREBP1 Contributes to Resolution of Pro-inflammatory TLR4 Signaling by Reprogramming Fatty Acid Metabolism Oishi Y, Spann NJ, Link VM, Muse ED, Strid T, Edillor C, Kolar MJ, Matsuzaka T, Hayakawa S, Tao J, Kaikkonen MU, Carlin AF, Lam MT, Manabe I, Shimano H, Saghatelian A, Glass CK. 2017. SREBP1 Contributes to Resolution of Pro-inflammatory TLR4 Signaling by Reprogramming Fatty Acid Metabolism Cell metabolism 25 2: 412-427. 2017
• Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization Kaikkonen MU, Niskanen H, Romanoski CE, Kansanen E, Kivelä AM, Laitalainen J, Heinz S, Benner C, Glass CK, Ylä-Herttuala S. 2014. Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization. NUCLEIC ACIDS RESEARCH 42 20: 12570-84. 2014
• Effect of natural genetic variation on enhancer selection and function Heinz S, Romanoski CE, Benner C, Allison KA, Kaikkonen MU, Orozco LD, Glass CK. 2013. Effect of natural genetic variation on enhancer selection and function. NATURE (LONDON) 2013 Oct 13. [Epub ahead of print]: --. 2013
• NCoR Repression of LXRs Restricts Macrophage Biosynthesis of Insulin-Sensitizing Omega 3 Fatty Acids Li P, Spann NJ, Kaikkonen MU, Lu M, Oh da Y, Fox JN, Bandyopadhyay G, Talukdar S, Xu J, Lagakos WS, Patsouris D, Armando A, Quehenberger O, Dennis EA, Watkins SM, Auwerx J, Glass CK, Olefsky JM. 2013. NCoR Repression of LXRs Restricts Macrophage Biosynthesis of Insulin-Sensitizing Omega 3 Fatty Acids. CELL 2013 Sep 26;155(1): 200-14. 2013
• Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription Kaikkonen MU, Spann NJ, Heinz S, Romanoski CE, Allison KA, Stender JD, Chun HB, Tough DF, Prinjha RK, Benner C, Glass CK. 2013. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. MOLECULAR CELL Volume 51, Issue 3: 310-325. 2013
• Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription Lam MT, Cho H, Lesch HP, Gosselin D, Heinz S, Tanaka-Oishi Y, Benner C, Kaikkonen MU, Kim AS, Kosaka M, Lee CY, Watt A, Grossman TR, Rosenfeld MG, Evans RM, Glass CK. 2013. Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. NATURE (LONDON) 2013 Jun 27;498(7455): 511-5. 2013
• Control of Proinflammatory Gene Programs by Regulated Trimethylation and Demethylation of Histone H4K2 Stender JD, Pascual G, Liu W, Kaikkonen MU, Do K, Spann NJ, Boutros M, Perrimon N, Rosenfeld MG, Glass CK. 2012. Control of Proinflammatory Gene Programs by Regulated Trimethylation and Demethylation of Histone H4K2 MOLECULAR CELL 48 1: 28-38. 2012
• Non-coding RNAs as regulators of gene expression and epigenetics Kaikkonen Minna U, Lam Michael TY, Glass Christopher K. 2011. Non-coding RNAs as regulators of gene expression and epigenetics. CARDIOVASCULAR RESEARCH 90: 430-440. 2011