TABLE 2.
RNA Fragments Recovered from AD, AMC Aggregates (RNA‐seq analysis)
| Chrom. | Region | Length | 5’ gene | 5’ dist. | 3’ gene | 3’ dist. | AD reads | AMC reads | AD/AMC reads | Chi2 p< | Transcript or encoded protein |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 633888..634164 | 277 | RP5‐857 K21.3 | 36389 | RP5‐857 K21.4 | 0 | 515 | 1360 | 0.38 | 0.0001 | Transcribed processed pseudogene |
| 1 | 2281959..2282363 | 405 | SKI | 0 | MORN1 | 38889 | 1396 | 1967 | 0.71 | 0.0001 | Ski proto‐oncogene |
| 1 | 109100211..109100485 | 275 | SCARNA2 | 0 | RP5‐1065 J22.4 | 3049 | 131 | 98 | 1.34 | 0.05 | scaRNA, small Cajal‐body specific RNA2, guides mod'n of snRNAs |
| 1 | 244863775..244864066 | 292 | RP11‐11 N7.5 | 8277 | HNRNPU | 0 | 509 | 653 | 0.78 | 0.004 | Heterog. Nuclear Ribonucleoprot. U (transripts 1, 3, 4, 8) |
| 2 | 32916221..32916538 | 318 | LINC00486 | 0 | AL121656.5 | 10588 | 17 | 5 | 3.40 | 0.02 | Long Intergenic Non‐Protein Coding RNA 486 |
| 2 | 47335292..47335571 | 280 | CALM2 | 158690 | AC073283.4 | 0 | 2728 | 2093 | 1.30 | 0.0002 | Uncharacterized transcript |
| 2 | 148961908..148962183 | 276 | KIF5C | 0 | LYPD6B | 75923 | 3055 | 1856 | 1.65 | 0.0001 | Kinesin Family Member 5C (transcript KIF5C_2) |
| 2 | 181678574..181678849 | 276 | ITGA4 | 142386 | CERKL | 0 | 107 | 60 | 1.78 | 0.001 | Ceramide Kinase Like |
| 2 | 231460607..231460888 | 282 | AC017104.2 | 7453 | NCL | 0 | 41 | 27 | 1.52 | N. S. | Ceroid‐Lipofuscinosis Neuronal Protein 5 (neurodegenerative lysosome storage disease) |
| 2 | 233275721..233275994 | 274 | ATG16L1 | 0 | SCARNA5 | 0 | 400/11 | 206/5 | 1.94/2.2 | 0.0001 | Autophagy Related 16‐Like 1 / scaRNA, small Cajal‐body RNA5 |
| 2 | 240713854..240714163 | 310 | RP11‐118 M12.2 | 12168 | KIF1A | 0 | 2806 | 4988 | 0.56 | 0.0001 | Kinesin family member 1A |
| 3 | 160514943..160515216 | 274 | RNU7‐136P | 42526 | KPNA4 | 0 | 536 | 232 | 2.31 | 0.0001 | Karyopherin (Importin) Subunit Alpha 4 |
| 6 | 26204696..26204971 | 276 | HIST1H4E | 0 | HIST1H2BG | 11094 | 164 | 304 | 0.54 | 0.0001 | Histone 1 (AD‐agg‐enriched) |
| 6 | 34071883..34072162 | 280 | MIR1275 | 71831 | GRM4 | 0 | 10689 | 5521 | 1.94 | 0.0001 | Glutamate Metabotropic Receptor 4 |
| 6 | 52995648..52995925 | 278 | RN7SK | 0 | ICK | 5353 | 32569 | 12138 | 2.68 | 0.0001 | 7SK RNA |
| 6 | 99408034..99408309 | 276 | COQ3 | 13829 | PNISR | 0 | 206 | 135 | 1.53 | 0.001 | PNN Interact. Ser & Arg‐Rich Prot. (Pinin, desmosome assoc. prot.) |
| 7 | 5529123..5529444 | 322 | MIR589 | 33205 | ACTB | 0 | 1210 | 1719 | 0.70 | 0.0001 | beta actin (AD‐agg‐enriched) |
| 7 | 26200464..26200741 | 278 | CTB−119C2.1 | 25518 | HNRNPA2B1 | 0 | 168 | 99 | 1.70 | 0.0002 | HnRNP A2/B1 (AD‐agg‐enriched) |
| 8 | 9903986..9904242 | 257 | MIR597 | 162217 | LINC00599 | 0 | 1667 | 1113 | 1.50 | 0.0001 | Long Intergenic Non‐Protein Coding RNA |
| 8 | 27604977..27605252 | 276 | GULOP | 15903 | CLU | 0 | 156 | 105 | 1.49 | 0.005 | Clusterin (a.k.a. ApoJ) (AD‐agg‐enriched) |
| 9 | 35657748..35658022 | 275 | SIT1 | 6797 | RMRP_1 | 0 | 472 | 184 | 2.57 | 0.0001 | RNA Component of Mitoch. RNA Processing Endoribonuclease |
| 10 | 101799051..101799385 | 335 | NPM3 | 15637 | MGEA5 / OGA | 0 | 683 | 432 | 1.58 | 0.0001 | Hyaluronidase =OGA, removes O‐GlcNAc modifications |
| 11 | 35663281..35663611 | 331 | TRIM44 | 0 | KRT18P14 | 196637 | 1147 | 592 | 1.94 | 0.0001 | Tripartite Motif Containing 44 |
| 11 | 62841562..62841839 | 278 | RP11‐727F15.9 | 7518 | WDR74 | 0 | 304 | 149 | 2.04 | 0.0001 | WD Repeat Domain 74 |
| 11 | 65502716..65503064 | 349 | AP000769.7 | 4310 | MALAT1_1 | 0 | 30539 | 16494 | 1.85 | 0.0001 | Metastasis Assoc. Lung Adenocarcinoma Transcr. 1 (Non‐Protein) |
| 11 | 111911504..111911780 | 277 | RPL37AP8 | 22029 | CRYAB | 0 | 228 | 216 | 1.06 | N. S. | Crystalin A beta, a small HSP (AD‐agg‐enriched) |
| 11 | 123061064..123061339 | 276 | RPL31P47 | 9662 | HSPA8 | 0 | 871 | 1512 | 0.58 | 0.0001 | Heat Shock Protein Family A (Hsp70) Member 8 (= HSC70) |
| 12 | 110281619..110281909 | 291 | ATP2A2 | 0 | RN7SL769P | 78542 | 433 | 225 | 1.92 | 0.0001 | SERCA2 ATPase Sarcoplasmic/Endopl. Reticulum Ca2+ Transport2 |
| 13 | 45975357..45975649 | 293 | AL445232.1 | 60203 | ZC3H13 | 0 | 372 | 240 | 1.55 | 0.0001 | Zinc Finger CCCH‐Type Containing 13 |
| 14 | 20343094..20343370 | 277 | SNORD126 | 16567 | RPPH1 | 0 | 2313 | 634 | 3.65 | 0.0001 | Ribonuclease P RNA Component H1 |
| 14 | 23321579..23321860 | 282 | PABPN1 | 0 | SLC22A17 | 24445 | 341 | 261 | 1.31 | 0.01 | Poly(A) Binding Protein Nuclear 1 |
| 14 | 49586595..49586871 | 277 | RNA5SP384 | 33846 | RPS29 | 0 | 22800 | 4958 | 4.60 | 0.0001 | Ribosomal protein, small subunit 29 |
| 14 | 49853648..49853923 | 276 | RNU6‐539P | 13820 | Metazoa_SRP_138 | 0 | 24010 | 7554 | 3.18 | 0.0001 | RNA, cytoplasmic Signal Recognition Particle |
| 14 | 102084750..102085033 | 284 | RN7SL472P | 7277 | HSP90AA1 | 0 | 186 | 94 | 1.98 | 0.0001 | HSP 90 family (AD‐agg‐enriched) |
| 17 | 6452910..6453209 | 300 | FAM64A | 1440 | PITPNM3 | 0 | 671 | 520 | 1.29 | 0.004 | PITPNM 3, Phosphatidylinositol Transfer Protein Memb.‐ Assoc. |
| 17 | 19187969..19188246 | 278 | KYNUP1 | 18300 | SNORD3A | 0 | 342 | 99 | 3.45 | 0.0001 | small nucleolar RNA |
| 17 | 44911190..44911459 | 270 | AC015936.3 | 6643 | GFAP | 0 | 7051 | 8989 | 0.78 | 0.0002 | Glial Fibrillary Acidic Protein, GFAP (AD‐agg‐enriched) |
| 18 | 49814124..49814400 | 277 | ACAA2 | 163 | RP11‐886H22.1 | 0 | 295 | 139 | 2.12 | 0.0001 | Transcribed processed pseudogene |
| 19 | 13298568..13298866 | 299 | CTC−250I14.1 | 139779 | CACNA1A | 0 | 10268 | 5984 | 1.72 | 0.0001 | Calcium Voltage‐Gated Channel Subunit Alpha1 A |
| 19 | 36304598..36304871 | 274 | CTD−3162L10.1 | 0 | LINC00665 | 8195 | 556 | 164 | 3.39 | 0.0001 | Uncharacterized locus |
| 19 | 44907737..44908015 | 279 | APOE | 0 | CTB−129P6.7 | 1359 | 1028 | 1003 | 1.02 | N. S. | ApoE, Apolipoprotein E (AD‐agg‐enriched) |
| 19 | 48645763..48646036 | 274 | DBP | 8324 | CA11 | 0 | 407 | 573 | 0.71 | 0.0002 | Carbonic Anhydrase 11 |
| 19 | 49107777..49108115 | 339 | SNRNP70 | 0 | LIN7B | 6208 | 2096 | 1398 | 1.50 | 0.0001 | Small Nuclear Ribonucleoprotein U1 Subunit 70 |
| 20 | 23637606..23637888 | 283 | CST9 | 31729 | CST3 | 0 | 573 | 742 | 0.77 | 0.003 | Cystatin C, Cystatin 3 |
| 20 | 41533110..41533383 | 274 | RP4‐620E11.5 | 150002 | CHD6 | 0 | 1245 | 864 | 1.44 | 0.0001 | Chromodomain Helicase DNA Binding Protein 6, CHDBP6 |
| 21 | 8258828..8259116 | 289 | RNA5‐8S5 | 1894 | FP671120.6 | 0 | 1200 | 132 | 9.09 | 0.0001 | Uncharacterized transcript |
| 21 | 8435771..8435981 | 211 | FP236383.5 | 0 | FP236383.1 | 96 | 207 | 12 | 17.25 | 0.0001 | Uncharacterized transcript |
| 21 | 26021821..26022101 | 281 | LLPHP2 | 258487 | APP | 0 | 1477 | 702 | 2.10 | 0.0001 | Amyloid precursor protein, APP, A4 (AD‐agg‐enriched) |
| X | 140784311..140784609 | 299 | LINC00632 | 11631 | CDR1 | 0 | 36675 | 62951 | 0.58 | 0.0001 | Cerebellar Degeneration Related Protein 1, CDRP1 |
All peaks shown were significant at p < 0.01; peak‐coincident genes (at zero distance from peaks) are indicated by bold font. Read ratios (AD/AMC) and p values for AD‐AMC differences were not corrected for 1.6‐fold higher RNA recovery from AD relative to AMC hippocampus, since all normalized RNA‐seq libraries used 1 µg RNA. “AD‐agg enriched” indicates proteins that were also found to be significantly enriched in AD aggregates relative to controls (Ayyadevara, Balasubramaniam, Parcon, et al., 2016).