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Supplementary Material Localizing Regions in the Genome

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Supplementary Material Localizing regions in the genome contributing to ADHD, aggressive and antisocial behavior Running title: Genetic overlap between ADHD, aggression and antisocial behavior Mariana Lizbeth Rodríguez López1, Barbara Franke1,2*, Marieke Klein1,3 1 Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Department of Human Genetics, Nijmegen, The Netherlands 2 Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Department of Psychiatry, Nijmegen, The Netherlands 3 University Medical Center Utrecht, UMC Utrecht Brain Center, Department of Psychiatry, Utrecht, the Netherlands Supplementary Tables: 5 Supplementary Figures: 2 Supplementary Table 1 | Category traits from LDHub GWAS-ss database. Category Number of traits Aging 3 Anthropometric 22 Autoimmune 11 Bone 5 Brain Volume 7 Cancer 5 Cardiometabolic 2 Cognitive 1 Education 5 Glycemic 8 Haemotological 3 Hormone 2 Kidney 6 Lipids 4 Lung Function 8 Metabolites 107 Metal 2 Neurological 3 Other 1 Personality 4 Psychiatric 11 Reproductive 4 Sleeping 5 Smoking 4 Behaviour Uric Acid 1 Total 234 A list of all categories from all the traits LDHub platform. We performed genetic correlation analyses for all traits with both AGG and ASB, giving a total of 234 rg scores for each one of our two traits. Supplementary Table 2 | Summary of data from GTEx project (https://gtexportal.org/home/). GTEx - Gene expression in 12 brain-related tissues Anterior Caudate Frontal cingulate (basal Cerebellar Cortex Nucleus Substantia Tissues Amygdala cortex ganglial) Hemisphere Cerebellum Cortex (BA9) Hippocampus Hypothalamus accumbens Putamen nigra Group 1 PBXIP1 83.295 92.11 136.3 42.495 50.13 86.42 72.98 51.38 83.98 135.9 95.535 103.7 PYGO2 19.865 23.33 22.93 58.905** 57.1** 30.665 30.97 19.49 28.93 26.55 18.26 20.235 KCNT2 1.2525 1.856 0.8475 0.3605 0.85 2.4595 3.221* 1.539 2.246 1.142 0.7494 1.1555 CFHR1 0.03493 0.0595 0.016485 0 0 0.029725 0.03561 0.05782 0.1552 0.01877 0.01452 0.09924 F13B 0 0 0 0 0 0 0 0 0 0 0 0 ZBTB41 4.0555 4.681 4.0645 21.005** 19.24** 5.2035 7.079 4.327 5.938 4.999 3.072 4.5755 ZC3H8 3.987 5.256 4.829 16.335** 12.05** 5.8525 7.851* 4.174 5.688 6.062 3.81 4.5175 ZC3H6 2.258 2.435 2.835 9.2065** 8.476* 3.323 3.629 2.639 2.979 3.42 2.303 2.648 TTL 6.8825 6.923 7.939 6.637 6.429 8.809** 9.624** 8.117* 6.115 8.315* 8.3165* 7.1635 TBC1D14 11.735 13.8 12.445 12.505 14.12 14.94 15.41 10.51 12.38 15.09 8.727 11.15 C5orf51 8.315 9.273 9.3295 23.25** 17.05 8.183 12.66 9.085 11.75 10.41 7.2935 10.67 FBXO4 2.5295 2.412 2.405 5.5165 4.776 2.481 2.712 2.412 3.399 2.987 2.1895 2.682 GHR 0.6335 0.8804 0.6436 0.3533 0.4992 0.77815 0.9152 0.6902 1.715 0.8455 0.507 1.1485 CCDC152 3.024 1.502 2.888 0.77565 0.9818 1.872 1.943 2.848 4.652 2.928 2.261 3.594 SEPP1 25.305 13.02 34.605 11.75 21.34 17.61 17.42 38.15 27.07 23.3 31.23 69.42 ZNF131 4.107 4.919 4.843 20.61** 16.16** 5.59 7.157 4.49 5.125 5.408 3.692 4.4385 HMGCS1 26.14 38.67 17.27 37.37 30.48 43.64 62.84* 25 44.03 22.86 13.29 21.655 NKAIN2 16.775* 15.88* 9.8155 13.125* 8.768 10.87* 17.97** 23.25** 13.4* 9.397 9.199 23.99** GATA4 0.01081 0.009618 0.01293 0.014995 0.02724 0.014875 0.01265 0.01436 0.01566 0.01179 0.010335 0.01081 TMEM71 0.38965 0.3923 0.443 0.2385 0.234 0.3438 0.3669 0.4123 0.584 0.3732 0.43025 0.47885 TG 1.02 0.5413 0.4633 0.5515 0.717 0.541 0.4967 0.7798 0.4466 0.4407 0.3571 0.4067 SLA 2.6845 2.208 2.0815 1.2075 1.307 1.253 1.376 2.968 2.232 2.725 1.494 3.165 CHUK 4.0345 3.989 4.9745 10.76* 10.03 3.918 4.755 4.255 6.679 4.882 4.2505 5.2315 CWF19L1 4.8505 6.225 5.869 21.69** 18.36* 8.19 9.456 5.533 7.615 7.45 5.029 6.0695 BLOC1S2 35.795 42.05* 28.775 49.665** 39.27 40.46 58.26** 33.11 48.46** 35.55 26.53 45.475* ATRNL1 5.4335* 10.27** 4.1875 0.85805 2.225 18.255** 25.43** 4.859 3.722 5.022 3.125 1.903 KCNK18 0 0.0276* 0.16495** 0 0 0.034725* 0.05654** 0 0.07626** 0.1824** 0.03221* 0 TMEM132B 7.937* 12.46** 8.6615* 1.7025 1.323 14.795** 17.8** 7.022* 4.371* 11.73** 6.917* 3.3505 MLLT6 33.17 41.72 27.875 96.45* 103.6* 52.765 46.42 28.87 26.22 31.24 24.98 25.86 PCGF2 12.515 16.2 12.455 54.53 54.1 21.69 20.86 11.7 18.3 15.2 11.02 10.7 ANKRD54 13.155 15.42 12.6 32.335** 32.58** 17.85 18.08 12.63 18.47 13.93 11.08 12.03 TMEM184B 33.285 47.09 30.875 58.175* 76.82** 66.08** 57.05 36.68 40.53 34.47 29.73 36.585 GTPBP1 12.1 13.6 12.655 39.09* 41.08** 18.73 17.15 13.16 14.21 15.6 10.955 12.095 SUN2 36.555 22.13 47.785 48.02 55.66 40.12 35.58 49.63 32.79 30.4 46.46 46.79 Group 2 DAB1 3.487* 4.671* 1.1335 24.035** 18.68 ** 3.73* 4.35* 4.86** 3.439* 1.432 0.8718 2.5095 F13B 0 0 0 0 0 0 0 0 0 0 0 0 RBM43 1.7745 1.542 2.121 0.7295 0.833 1.354 1.712 1.418 2.189 2.418 1.4555 1.7525 NMI 3.3705 2.543 3.1935 1.1825 1.421 2.403 2.298 2.922 3.216 2.854 2.817 3.987 SHOX2 0.01234 0.01641 0.010064 0.02929 0.02808 0.023865 0.0188 0.009096 0.136 0.02091 0.010615 0.074495 RSRC1 4.481 5.631 5.3415 17.26** 11.09** 5.625 9.453* 4.501 6.478 6.062 3.7855 5.326 HMGCS1 26.14 38.67 17.27 37.37 30.48 43.64 62.84* 25 44.03 22.86 13.29 21.655 CCL28 0.6247 0.6295 0.3163 0.100535 0.144 0.86005 1.027 0.4091 0.625 0.2951 0.174 0.4703 MSRA 6.2405 8.598 6.1115** 29.7** 28.09 10.08 11.05* 7.369 5.962 6.695 4.88 6.181 PRSS55 0.1154 0.1309 0.11825 0.57605 0.5789 0.14815 0.141 0.1179 0.05924 0.1043 0.11545 0.08649 FAM167A 14.395* 19.29** 14.09* 7.613 12.58 19.525** 16.77* 9.731 11.33 12.71 11.785 10.905 BLK 0.01749 0.01973 0.016935 0.08194 0.1098 0.026865 0.02019 0.03163 0.04851 0.01234 0.0171 0.035155 GATA4 0.01081 0.009618 0.01293 0.014995 0.02724 0.014875 0.01265 0.01436 0.01566 0.01179 0.010335 0.01081 NEIL2 20.405 21.24 18.465 28.14** 26.35* 24.005 27.17* 17.57 28.91** 24.13* 15.95 22.915 FDFT1 30.84 34.31 24.1 39.735 37.45 41.945 49.73 31.45 43.87 27.17 20.88 35.09 CTSB 65.295 89.44 88.39 104.6 93.59 119.65 142.7 68.3 104.2 91.24 70.485 98.18 DEFB136 0 0 0 0 0 0 0 0 0 0 0 0 DEFB134 0.075625 0.06506 0.11595 0.5516 0.5019 0.097625 0.08884 0.02926 0.08835 0.09981 0.058605 0 USP17L7 0 0.02502 0.04138 0.07753 0.1282 0.027565 0.02539 0.01203 0 0.03694 0.02931 0 KIAA1456 1.475 3.078 2.946 105.9** 92.84** 3.525* 4.485** 2.366 2.776 3.115* 1.705 1.6125 NOX4 0.1155 0.06863 0.15025 0.036925 0.04916 0.11765 0.1186 0.1321 0.159 0.09159 0.1528 0.2001 LRP1 0 0 0 0 0 0 0 0 0.02956 0 0 0.016335 NXPH4 1.5055 1.937 0.7042 28.445** 31.54** 1.563 1.725 0.9111 2.86* 0.4112 0.7665 1.0036 STAC3 1.6805 1.695 1.842 4.2185 4.353 1.7835 1.701 1.769 1.781 1.713 1.7585 1.8685 R3HDM2 21.13 27.33 21.83 83.45** 80.54** 42.855 43.62* 20.9 23.26 25.5 18.29 20.485 INHBC 0.06522 0.07656 0.059665 0.6836 0.7682 0.097185 0.09135 0.04705 0.0478 0.08805 0.065755 0.0623 INHBE 0.115 0.2444 0.1075 1.2605 1.29 0.2567 0.2883 0.07665 0.2749 0.2486 0.06807 0.2074 ARHGEF40 13.52 12.13 13.145 31.395 35.83 13.22 9.816 11.27 15.91 13.19 11.51 14.32 ATP5G1 80.29 98.44 94.955 100.7 88.54 99.605 132.3** 80.51 87.83 108.9* 81.8 81.525 UBE2Z 24.55 30.01 22.435 53.51 47.08 39.355 45.63 27.55 33.21 29.55 19.425 25.575 SNF8 14.515 17.22 16.65 27.275 24.38 19.185 21.23 14.52 17.62 18.5 15.22 17.215 GIP 0 0 0 0 0 0 0 0 0 0 0 0 C19orf66 25.295 31.29 29.63 54.805 57.75 45.24 41.33 25.97 37.12 31.77 25.76 21.31 BCL3 3.375 3.374 2.8825 1.7795 2.944 5.2995 4.1 2.908 5.248 2.613 2.266 5.2565 KLC3 0.07445 0.2325 0.40385 0.045445 0.05787 0.2108 0.2143 0.07716 0.1107 0.5094 0.2935 0.07667 ERCC2 8.8075 10.89 8.445 14.18* 16.12* 14.135* 12.93 7.96 9.207 10.52 7.2585 7.3945 IGLON5 12.49* 20.93* 6.529 127.8** 131.6** 27.85** 28.63** 15.6* 32.96** 9.206 6.0315 19.79* VSIG10L 1.728 2.634 1.8855 7.122 6.86 2.5915 3.004 2.167 3.497 2.411 1.4695 3.37 ETFB 24.075 26.57 28.12 21.525 20.28 25.56 28.38 24.41 24.93 33.8* 27.555 32.19 Group 3 SRSF10 1.36 1.55 1.812 5.4905 4.688 1.585 1.983 1.522 1.928 1.863 1.2575 1.666 RCAN3 1.331 1.176 2.1395 59.835** 39.96** 1.072 1.386 1.719 7.823 2.149 2.1295 4.5765 Results show the median Transcripts Per Million (TPM) for each gene from the candidate loci across 12 brain-related tissues.
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    LARGE SCALE ORGANIZATION OF CHROMATIN MARIO Nicodemi Dip.to di Fisica, Uni.NA “Federico II”, INFN In the cell nucleus chromosomes have a complex architecture serving vital functional purposes. Problem: how is their 3D structure orchestrated? Our contribution: a model of the molecular mechanisms of their self- organization by use of classical polymer physics. (Mirò, Chiffres & Constellations 1941) Research collaborators MRC, Imperial College, London Ana Pombo,, Mita Chotalia, Ines de Santiago, Liron-Mark Lavitas, Sheila Xie, Kedar Natarajan, Carmelo Ferrai, Robert Beagrie, ... Biology, McGill, CA Josée Dostie, James Fraser Physics, Univ. di Napoli, Italy Mariano Barbieri, Ilaria Cataudella, Antonio Scialdone, Melania Barile, Paolo Casale, Valentino Bianco, Emanuela de Falco, Deborah Pallotti, Gaetano Pellegrino, Andrea Piccolo, ... Chromatin organization (I) (A) Linear expression units in compact genomes v.s. spatially assembled units in complex genomes. (B) Colocalization of coregulated genes. (C) ChromatinGene localization organizationat transcription factories (TFs). Example: the Xicʼs of the X Chromosome territories and map chrom.s colocalize at XCI (Heard et al.; Lee et al. ʻ07) Chromatin organizationNuclear scale (I) (A) Linear expression units in compact genomes v.s. spatially assembled units in complex genomes. (B) Colocalization of coregulated genes. (C) Gene localization at transcription factories (TFs). Colocalization of coregulated genes at transcription factories Example: the Xicʼs of the X Transcription chrom.s colocalize at XCI Factory (Heard et al.; Lee et al. ʻ07) (Pictures: Dekker et al. Science ʻ08) Distal regulatory elements Gene Gene Expression Units Assembly of expression units Gene scale (Pictures: Bolzer et al. PLoS Bio. ʼ05; Dekker et al. Science ʼ08) (Pictures: Dekker et al.
  • Chromosomal Localization of the Mammalian Peptide-Methionine Sulfoxide Reductase Gene and Its Differential Expression in Various Tissues JACKOB MOSKOVITZ*, NANCY A

    Chromosomal Localization of the Mammalian Peptide-Methionine Sulfoxide Reductase Gene and Its Differential Expression in Various Tissues JACKOB MOSKOVITZ*, NANCY A

    Proc. Natl. Acad. Sci. USA Vol. 93, pp. 3205-3208, April 1996 Biochemistry Chromosomal localization of the mammalian peptide-methionine sulfoxide reductase gene and its differential expression in various tissues JACKOB MOSKOVITZ*, NANCY A. JENKINSt, DEBRA J. GILBERTt, NEAL G. COPELANDt, FRANTISEK JURSKY*, HERBERT WEISSBACH*, AND NATHAN BROT* *Roche Institute of Molecular Biology, Roche Research Center, Nutley, NJ 07110-1199; and tAdvanced BioScience Laboratory-Basic Research Program, Frederick Cancer Research and Development Center, P.O. Box B, Frederick, MD 21702-1201 Contributed by Herbert Weissbach, December 26, 1996 ABSTRACT Peptide methionine sulfoxide reductase agarose gel electrophoresis, Southern blot transfer, and hy- (MsrA; EC 1.8.4.6) is a ubiquitous protein that can reduce bridization were performed as described (11). All blots were methionine sulfoxide residues in proteins as well as in a large prepared using Hybond-N+ nylon membrane (Amersham). number of methyl sulfoxide compounds. The expression of The probe, a 228-bp PCR-generated mouse cDNA fragment MsrA in various rat tissues was determined by using immu- (6), was labeled with [a-32P]dCTP by random priming (Strat- nocytochemical staining. Although the protein was found in agene), and the blots were washed at 65°C in a buffer con- all tissues examined, it was specifically localized to renal taining 0.8x SSCP and 0.1% SDS (lx SSCP = 120 mM medulla and retinal pigmented epithelial cells, and it was NaCl/15 mM sodium citrate/20 mM sodium phosphate, pH prominent in neurons and throughout the nervous system. In 6.8). A 5.8-kb fragment was detected in Sph I-digested addition, blood and alveolar macrophages showed high ex- C57BL/6J (B) genomic DNA and an 8.2-kb fragment, in Sph pression of the enzyme.
  • Supplementary Table 1: Adhesion Genes Data Set

    Supplementary Table 1: Adhesion Genes Data Set

    Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like,