Altered non-coding RNA expression profile in F1 progeny one year after parental irradiation is linked to adverse effects in zebrafish Leonardo Martín, Jorke H Kamstra, Selma Hurem, Leif C Lindeman, Dag A Brede, Håvard Aanes, Igor Babiak, Amilcar Arenal, Deborah Oughton, Brit Salbu, Jan Ludvig Lyche, Peter Aleström. Association between Control and Gamma matched piRNA clusters and Transposable Elements. Only Transposable Elements with more than 100 read counts were selected. An overlap was considered when piRNA clusters overlaps at least by 50 % to Transposable Elements. Bedtools (v2.29.1) Class Order Superfamily Transposable Element Chr Strand Start End Matching clusters Coordinate Ctrl Strand Coordinate Gamma Class I LTR Copia Copia-8-LTR_DR chr8 + 43659923 43660377 cluster 287c & 296g 43651659-43664893 +/- 43651644-43664891 Copia-6-I_DR chr8 - 45200488 45201369 cluster 290c & 298g 45197003-45205907 + 45190119-45208986 Copia-7-I_DR chr8 - 45213740 45214081 cluster 291c & 299g 45210098-45232001 -/+ 45210098-45224941 Copia6-LTR_DR chr17 + 40757100 40757415 cluster 60c & 56g 40756002-40765927 - 40756002-40766007 LTR1_DR chr6 - 22600655 22601492 cluster 261c & 274g 22584019-22604930 -/+ 22584026-22603207 LTR1_DR chr17 + 49452889 49453193 cluster 65c & 62g 49443210-49466990 -/+ 49443208-49466739 Gypsy Gypsy124-I_DR chr2 - 15196123 15200840 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 Gypsy-170-LTR_DR chr3 + 6290576 6291394 cluster 143c & 153g 6286097-6291978 - 6285828-6291930 Gypsy-32-I_DR chr4 - 28761455 28762981 cluster 148c & 159g 28762004-28772861 +/- 28764005-28772967 Gypsy154-I_DR chr4 - 29030010 29032080 cluster 152c & 163g 29025154-29033695 -/+ 29025042-29033908 Gypsy-150-LTRb_DR chr4 - 29532568 29533448 cluster 157c & 168g 29530592-29553008 +/- 29530592-29551982 Gypsy124-I_DR chr4 + 30065612 30066159 cluster 161c & 172g 30062341-30081024 -/+ 30060012-30080003 Gypsy142-I_DR chr4 + 44751764 44755919 cluster 176c & 191g 44743368-44776019 - 44742209-44774933 Gypsy147-I_DR chr4 + 49122933 49124347 cluster 189c & 203g 49120968-49134012 - 49120079-49134014 Gypsy147-I_DR chr4 + 49125376 49130915 cluster 189c & 203g 49120968-49134012 - 49120079-49134014 Gypsy150-I_DR chr4 + 59363674 59369776 cluster 197c & 213g 59360129-59378891 - 59360128-59378957 Gypsy-17-I_DR chr4 + 60924677 60931224 cluster 200c & 217g 60922021-60935014 - 60922008-60934015 Gypsy103-LTR_Dr chr4 + 72274627 72275445 cluster 221c & 236g 72271438-72279895 - 72271562-72283883 Gypsy89-I_DR chr4 + 73154720 73154796 cluster 222c & 237g 73150041-73157786 + 73150041-73158027 Gypsy65-LTR_DR chr5 + 658568 658856 cluster 229c & 243g 645052-676758 +/- 645032-676809 Gypsy65-LTR_DR chr5 + 658856 659248 cluster 229c & 243g 645052-676758 +/- 645032-676809 Gypsy164-I_DR chr5 + 47014230 47017805 cluster 231c & 245g 47014037-47023022 -/+ 47014019-47025791 Gypsy-169-I_DR chr5 + 47045061 47045229 cluster 232c & 246g 47042006-47050792 - 47042006-47050544 Gypsy-169-I_DR chr5 + 47046382 47046927 cluster 232c & 246g 47042006-47050792 - 47042006-47050544 Gypsy38-I_DR chr6 + 17287823 17293207 cluster 241c & 254g 17286028-17295986 - 17286020-17296011 Gypsy-168-I_DR chr6 + 18314756 18317278 cluster 247c & 260g 18316016-18324994 -/+ 18316020-18324992 Gypsy-28-I_DR chr6 + 20341797 20345784 cluster 250c & 264g 20335038-20350759 - 20335719-20345024 Gypsy46-I_DR chr6 - 22592271 22594583 cluster 261c & 274g 22584019-22604930 -/+ 22584026-22603207 Gypsy88-I_DR chr7 - 37941063 37941794 cluster 271c & 283g 37932012-37943901 + 37932031-37943918 Gypsy-166-I_DR chr8 + 38967470 38971772 cluster 280c & 291g 38966006-38980905 - 38966087-38980761 Gypsy148-I_DR chr8 - 43655823 43656403 cluster 287c & 296g 43651659-43664893 +/- 43651644-43664891 Gypsy148-I_DR chr8 - 43656448 43656727 cluster 287c & 296g 43651659-43664893 +/- 43651644-43664891 Gypsy157-I_DR chr9 - 15659454 15663456 cluster 299c & 309g 15660022-15668992 +/- 15657031-15668992 Gypsy122-I_DR chr9 + 15755209 15759723 cluster 300c & 310g 15753059-15763011 - 15753239-15762992 Gypsy45-I_DR chr10 - 12275894 12280654 cluster 12c &10g 12014299-12034775 - 12275057-12281024 Gypsy86-I_DR chr11 - 15191699 15192548 cluster 13c & 12g 15189937-15194076 + 15189146-15194836 Gypsy44-I_DR chr12 + 15176146 15181209 cluster 19c & 19g 15175068-15182001 - 15175044-15181991 Gypsy149-I_DR chr17 + 40760948 40761220 cluster 60c & 56g 40756002-40765927 - 40756002-40766007 Gypsy-169-I_DR chr18 + 29712190 29716284 cluster 70c & 67g 29707041-29716023 - 29707017-29716020 Gypsy58-I_DR chr18 + 32677810 32678193 cluster 81c & 80g 32676225-32683467 - 32676227-32684932 Gypsy58-I_DR chr18 + 32679051 32681491 cluster 81c & 80g 32676225-32683467 - 32676227-32684932 Gypsy-170-I_DR chr19 + 16874687 16874935 cluster 100c & 101g 16870009-16879025 - 16870012-16879026 Gypsy37-I_DR chr19 + 16956692 16958369 cluster 101c & 102g 16952015-16967014 - 16952011-16967021 Gypsy78-I_DR chr19 + 17211594 17216894 cluster 105c & 106g 17210001-17218903 -/+ 17210066-17218905 GypsyDR1 chr21 - 36646506 36647258 cluster 123c & 127g 36646488-36651902 + 36644006-36653002 Gypsy55-I_DR chr23 + 16269647 16270564 cluster 130c & 139g 16268020-16278003 - 16266341-16277989 Gypsy55-I_DR chr23 + 16272004 16273981 cluster 130c & 139g 16268020-16278003 - 16266341-16277989 Gypsy55-I_DR chr23 + 16277390 16277834 cluster 130c & 139g 16268020-16278003 - 16266341-16277989 SUSHIIDR1 chr18 - 29685655 29685772 cluster 69c & 66g 29683700-29689360 + 29681680-29689395 SUSHIIDR1 chr18 - 29685760 29687245 cluster 69c & 66g 29683700-29689360 + 29681680-29689395 SUSHIIDR1 chr18 - 29687485 29688962 cluster 69c & 66g 29683700-29689360 + 29681680-29689395 DIRS DIRS-8B_DR chr1 - 27222283 27224544 cluster 5c & 5g 27220238-27237268 +/- 27220236-27235820 DIRS-14_DR chr1 - 27224540 27224801 cluster 5c & 5g 27220238-27237268 +/- 27220236-27235820 DIRS-7_DR chr3 + 3183093 3184248 cluster 142c & 151g 3182736-3192824 -/+ 3181746-3193009 DIRS-1D-LTR_DR chr6 + 20591845 20592645 cluster 254c & 267g 20588024-20608023 - 20588014-20608024 DIRS-2_DR chr6 - 20786028 20790523 cluster 258c & 271g 20765358-20798989 -/+ 20765282-20798919 DIRS1_DR chr8 - 44993980 44995298 cluster 289c & 297g 44985635-44992025 - 44984067-45004024 DIRS-7_DR chr8 - 45204348 45205499 cluster 290c & 298g 45197003-45205907 + 45190119-45208986 DIRS-N1_DR chr17 + 40764012 40765823 cluster 60c & 56g 40756002-40765927 - 40756002-40766007 DIRS-8B_DR chr18 + 33525270 33525710 cluster 86c & 87g 33512010-33529994 +/- 33512130-33528971 ERV ERV1-N2-LTR_DR chr4 + 29601493 29601990 cluster 159c & 170g 29601046-29605599 - 29598133-29605596 ERV1-2-I_DR chr4 - 42142704 42152975 cluster 170c & 185g 42141997-42153821 + 42140426-42153840 ERV1-2-I_DR chr4 + 45434576 45435815 cluster 178c & 193g 45431099-45449941 - 45431203-45449731 ERV1-2-I_DR chr4 + 45435805 45437135 cluster 178c & 193g 45431099-45449941 - 45431203-45449731 ERV1-2-I_DR chr4 + 45437342 45442690 cluster 178c & 193g 45431099-45449941 - 45431203-45449731 ERV1-2-I_DR chr4 + 45442891 45442978 cluster 178c & 193g 45431099-45449941 - 45431203-45449731 ERV1-2-I_DR chr4 + 45443032 45443686 cluster 178c & 193g 45431099-45449941 - 45431203-45449731 ERV1-2-LTR_DR chr4 + 45443686 45444533 cluster 178c & 193g 45431099-45449941 - 45431203-45449731 ERV1-N2-I_DR chr5 - 47018154 47018531 cluster 231c & 245g 47014037-47023022 -/+ 47014019-47025791 ERV1-N2-I_DR chr5 - 47018519 47019276 cluster 231c & 245g 47014037-47023022 -/+ 47014019-47025791 ERV1-2-I_DR chr24 + 37253936 37254959 cluster 135c & 144g 37253912-37261027 - 37253938-37261996 Pao BEL33-I_DR chr1 - 26912539 26913585 cluster 1c & 2g 26910008-26915839 + 26909049-26917239 BEL2-LTR_DR chr1 + 27232772 27233264 cluster 5c & 5g 27220238-27237268 +/- 27220236-27235820 BEL17-I_DR chr2 + 13098611 13103503 cluster 110c & 112g 13098002-13104014 - 13097018-13106009 BEL3-I_DR chr4 + 45265009 45269165 cluster 177c & 192g 45264346-45272899 - 45264716-45272906 BEL25-I_DR chr4 - 61496531 61497886 cluster 207c & 221g 61494743-61504023 + 61494761-61504006 BEL25-I_DR chr4 - 61497886 61500000 cluster 207c & 221g 61494743-61504023 + 61494761-61504006 BEL25-I_DR chr4 - 61500000 61501843 cluster 207c & 221g 61494743-61504023 + 61494761-61504006 BEL5-LTR_DR chr5 + 509591 509940 cluster 226c & 241g 505497-514982 - 503412-515021 BEL5-I_DR chr8 + 39226833 39227545 cluster 282c & 292g 39217078-39231025 - 39217073-39231010 BEL27-I_DR chr14 + 15267987 15272866 cluster 34c & 34g 15267187-15273691 - 15267592-15273836 BEL21-I_DR chr17 - 40701616 40706637 cluster 57c & 54g 40698049-40706631 + 40698041-40706647 BEL35-I_DR chr18 + 32754399 32755251 cluster 82c & 81g 32750762-32758925 - 32750021-32758996 BEL35-I_DR chr18 + 32755266 32755882 cluster 82c & 81g 32750762-32758925 - 32750021-32758996 BEL10-I_DR chr19 - 17137712 17138237 cluster 104c & 105g 17134196-17144027 -/+ 17134112-17144028 BEL10-I_DR chr19 - 17138228 17138557 cluster 104c & 105g 17134196-17144027 -/+ 17134112-17144028 BEL10-I_DR chr19 - 17138551 17139796 cluster 104c & 105g 17134196-17144027 -/+ 17134112-17144028 BEL-38-I_DR chr22 + 24457301 24460978 cluster 124c & 130g 24453486-24462551 - 24453112-24465958 BEL-38-I_DR chr22 + 24461033 24462131 cluster 124c & 130g 24453486-24462551 - 24453112-24465958 BEL15-I_DR chr25 - 25802931 25807879 cluster 139c & 147g 25801015-25809024 + 25800149-25809023 Unknown BHIKHARI-4-I_DR chr8 + 38972975 38975057 cluster 280c & 291g 38966006-38980905 - 38966087-38980761 BHIKHARI-4-I_DR chr8 + 38975122 38976477 cluster 280c & 291g 38966006-38980905 - 38966087-38980761 BHIKHARI-4-I_DR chr8 + 38977537 38978323 cluster 280c & 291g 38966006-38980905 - 38966087-38980761 BHIKHARI_I-int chr16 + 15830107 15833021 cluster 48c & 48g 15827037-15836017 +/- 15827001-15836017 BHIKHARI-4-I_DR chr18 - 32094432 32096584 cluster 77c & 77g 32091000-32098983 + 32091004-32100023 LINE CR1 CR1-10_DR chr4 + 59370025 59371357 cluster 197c & 213g 59360129-59378891 - 59360128-59378957 CR1-12_DR chr8 + 37481023 37481367 cluster 276c & 288g 37477029-37491032 - 37478012-37491479 L1 L1-16_DR chr4 + 46800886 46801021 cluster 181c & 195g 46800019-46807769 - 46796018-46808793 L1-10_DR chr4 + 46801804 46802239 cluster 181c & 195g 46800019-46807769 - 46796018-46808793 L1-15_DR chr6 + 20346081 20346650 cluster 250c & 264g 20335038-20350759 - 20335719-20345024 L1-1_DR chr8 - 38807007 38807877 cluster 278c & 289g 38804111-38814876 -/+ 38804111-38814869 L2 L2-41_DRe chr5 + 510697 511321 cluster 226c & 241g 505497-514982 - 503412-515021 L2-8_DR chr6 - 20607396 20608247 cluster 254c & 267g 20588024-20608023 - 20588014-20608024 R2 R2Dr chr5 - 669017 669303 cluster 229c & 243g 645052-676758 +/- 645032-676809 R2Dr chr5 + 672331 673059 cluster 229c & 243g 645052-676758 +/- 645032-676809 R2Dr chr5 + 674110 674921 cluster 229c & 243g 645052-676758 +/- 645032-676809 RTE EXPANDER1_DR chr18 + 35029235 35031778 cluster 96c & 97g 35022094-35034747 - 35022100-35035026 Rex Rex1-23_DRe chr5 + 661583 662667 cluster 229c & 243g 645052-676758 +/- 645032-676809 Rex1-40_DRe chr8 + 45603576 45604938 cluster 294c & 302g 45596031-45617214 - 45596034-45618781 Class II TIR Tc1-Mariner Tc1-4_DR chr6 + 20794630 20794691 cluster 258c & 271g 20765358-20798989 -/+ 20765282-20798919 Tc1-4_DR chr8 + 37483919 37484607 cluster 276c & 288g 37477029-37491032 - 37478012-37491479 TZF28 chr17 - 40836421 40836608 cluster 62c & 59g 40832090-40841025 - 40830019-40840981 hAT hAT-N32_DR chr17 - 49478814 49478961 cluster 66c & 63g 49474168-49509396 - 49474286-49509859 hAT-4_DR chr18 + 35025804 35026300 cluster 96c & 97g 35022094-35034747 - 35022100-35035026 HAT1_DR chr4 + 72262741 72263561 cluster 220c & 235g 72259035-72270029 - 72259614-72270029 HAT1_DR chr4 + 72265269 72265422 cluster 220c & 235g 72259035-72270029 - 72259614-72270029 HAT1_DR chr4 + 72267726 72268391 cluster 220c & 235g 72259035-72270029 - 72259614-72270029 HAT1_DR chr8 + 37485382 37485704 cluster 276c & 288g 37477029-37491032 - 37478012-37491479 HAT1_DR chr8 + 37485995 37486340 cluster 276c & 288g 37477029-37491032 - 37478012-37491479 HAT1_DR chr8 + 37486332 37488155 cluster 276c & 288g 37477029-37491032 - 37478012-37491479 HATN13_DR chr4 + 29536253 29536808 cluster 157c & 168g 29530592-29553008 +/- 29530592-29551982 KenoDr1 chr2 + 15138763 15143939 cluster 112c & 116g 15136114-15149945 - 15136110-15149945 KenoDr1 chr2 + 15154938 15160739 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15160755 15164611 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15166428 15172206 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15172225 15175804 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15176248 15176976 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15176974 15177499 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15177546 15178494 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15178509 15178938 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15179115 15180535 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15181126 15182542 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15183856 15186481 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15188074 15189841 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15190513 15192065 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15192200 15193582 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15194367 15195020 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15195017 15195455 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15201328 15205126 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15205360 15207727 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15208265 15209041 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15209019 15209644 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15209673 15211680 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15212291 15212998 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KenoDr1 chr2 + 15214552 15215238 cluster 113c & 117g 15152000-15216011 - 15152000-15216016 KibiDr1 chr20 - 6413322 6417482 cluster 117c & 120g 6411188-6418856 -/+ 6412454-6418855 PIF Harbinger1_DR chr8 + 43653080 43653263 cluster 287c & 296g 43651659-43664893 +/- 43651644-43664891 Harbinger3_DR chr17 - 49453450 49453537 cluster 65c & 62g 49443210-49466990 -/+ 49443208-49466739 Harbinger3_DR chr17 - 49453565 49453956 cluster 65c & 62g 49443210-49466990 -/+ 49443208-49466739 IS4EU-1_DR chr8 + 43657104 43657352 cluster 287c & 296g 43651659-43664893 +/- 43651644-43664891 IS4EU-1_DR chr8 + 43657356 43657840 cluster 287c & 296g 43651659-43664893 +/- 43651644-43664891 IS4EU-1_DR chr12 + 12858281 12860852 cluster 17c & 16g 12855627-12861602 - 12855621-12861587 IS4EU-2_DR chr18 - 33871246 33871749 cluster 92c & 93g 33867003-33877844 + 33867000-33877844 Kolobok Kolobok-1_DR chr6 + 18320660 18321768 cluster 247c & 260g 18316016-18324994 -/+ 18316020-18324992 LOOPERN4_DR chr17 - 49455198 49455379 cluster 65c & 62g 49443210-49466990 -/+ 49443208-49466739 Dada Dada-tA_DR chr21 + 30147477 30148228 cluster 121c & 126g 30146527-30153953 - 30145014-30153912 Dada-tA_DR chr21 + 30149218 30151489 cluster 121c & 126g 30146527-30153953 - 30145014-30153912 CMC EnSpm-2_DR chr4 + 59663376 59664868 cluster 198c & 215g 59660011-59669977 + 59661006-59666984 EnSpm1_DR chr19 + 16871221 16872253 cluster 100c & 101g 16870009-16879025 - 16870012-16879026 Crypton Crypton LRS_DR chr4 + 34313220 34313503 cluster 166c & 176g 34309091-34317010 - 34308030-34318001 Helitron Helitron Helitron-2_DR chr4 - 54844795 54848820 cluster 192c & 208g 54841332-54851011 + 54841332-54851011 Helitron-1_DR chr4 + 61024198 61026689 cluster 204c & 220g 61021076-61030888 - 61022050-61030796 Helitron-2_DR chr16 + 9622635 9624176 cluster 46c & 46g 9618019-9635641 - 9618052-9635182 Helitron-2_DR chr16 + 9625812 9628469 cluster 46c & 46g 9618019-9635641 - 9618052-9635182 Helitron-1_DR chr18 + 32326521 32329344 cluster 78c & 78g 32319025-32329882 - 32319008-32330959 DNA/Unknown unknown DNA-TTAA-2_DR chr8 - 43652215 43652388 cluster 287c & 296g 43651659-43664893 +/- 43651644-43664891 Polinton-1_DR chr4 - 42411998 42415573 cluster 171c & 186g 42405008-42417014 - 42405002-42416999 Polinton-2_DR chr4 - 43510097 43516168 cluster 173c & 188g 43504105-43521998 - 43504126-43520443 Polinton-1_DR chr4 - 45444763 45446974 cluster 178c & 193g 45431099-45449941 - 45431203-45449731 Polinton-2_DR chr13 - 48553745 48557244 cluster 22c & 23g 48553896-48563017 +/- 48553741-48563358 Polinton-2_DR chr25 - 27228505 27244791 cluster 141c & 148g 27226301-27247590 -/+ 27226196-27247590 TDR16 chr4 - 44748295 44748420 cluster 176c & 191g 44743368-44776019 - 44742209-44774933