Genome-wide analysis of polyadenylation events in Schmidtea mediterranea
 
 

Annotation of 3’UTRs and alternate polyadenylation events in planaria

Graphical Abstract
Polyadenylation in planaria

In eukaryotes, 3’ untranslated regions (UTRs) play important roles in regulating post-transcriptional gene expression. The 3’UTR is defined by regulated cleavage/polyadenylation of the pre-mRNA. The advent of next-gen sequencing technology has now enabled us to identify these events on a genome-wide scale. In this study, we used poly(A)-position profiling by sequencing (3P-Seq) to capture all poly(A) sites across the genome of the freshwater planarian, Schmidtea mediterranea, an ideal model system for exploring the process of regeneration and stem cell function. We identified the 3’UTRs for ~14,000 transcripts and thus improved the existing gene annotations. We found 97 transcripts, which are polyadenylated within an internal exon, resulting in the shrinking of the ORF and loss of a predicted protein domain. Around 40% of the transcripts in planaria were alternatively polyadenylated (ApA), resulting either in an altered 3’UTR or a change in coding sequence. We identified specific ApA transcript isoforms that were subjected to miRNA mediated gene regulation using degradome sequencing. Our study also identified differentially regulated 3’UTR isoforms enriched in the neoblast population. The insights from this study highlight the importance of ApA in stem cell function and regeneration of planaria.

Transcript association

The transcripts from all the three transcriptomes - Dresden_V4 (dd_smedV4), Oxford (OX_Smed_1) and Maker (mk4) were used to associate the 3P-Peak derived from 3P-Seq. The schematic below depicts different categories of transcript association.



The following table gives the information about the transcript and the corresponding 3P-Peak that we associated to determine the 3'UTR.

Transcript Id Classification ClusterId Peak Id Peak_Height
dd_smedV4_1205_0_2Category4Cluster0Contig4116_-_22772_2282128
dd_smedV4_1205_0_2Category4Cluster0Contig4116_-_10432_10481116
dd_smedV4_194_0_1Category4Cluster2Contig2042_-_33008_3305957
dd_smedV4_194_0_1Category4Cluster2Contig2042_-_35082_3513130
dd_smedV4_5582_0_1Category4Cluster4Contig5685_-_3098_3152578
dd_smedV4_7638_0_1Category4Cluster6Contig1196_-_23420_2346825
dd_smedV4_4377_0_1Category4Cluster7Contig3280_-_4804_48495
dd_smedV4_10425_0_1Category3Cluster10Contig4185_+_39196_392404
dd_smedV4_10425_0_1Category3Cluster10Contig4185_+_39325_39369187
dd_smedV4_4569_0_1Category4Cluster11Contig1241_-_24162_242113
dd_smedV4_4569_0_1Category4Cluster11Contig1241_-_16148_16199141
dd_smedV4_4176_0_1Category4Cluster13Contig4410_+_37341_3739138
dd_smedV4_4176_0_1Category4Cluster13Contig4410_+_37404_37454124
dd_smedV4_2544_0_1Category4Cluster15Contig677_+_105256_10530420
dd_smedV4_2544_0_1Category4Cluster15Contig677_+_115448_11549712
dd_smedV4_5325_0_1Category4Cluster19Contig7189_-_11470_115201107
dd_smedV4_5325_0_3Category4Cluster20Contig7189_-_11470_115201107
dd_smedV4_3378_0_1Category4Cluster24Contig5247_-_12434_124912324
dd_smedV4_3378_0_1Category4Cluster24Contig5247_-_12549_1259883
dd_smedV4_91_0_1Category4Cluster25Contig3138_-_3264_33485176
dd_smedV4_4555_0_1Category1Cluster27Contig6712_-_883_92947
dd_smedV4_8462_0_2Category4Cluster28Contig44_-_24101_24150200
mk4.000477.08.01Category4Cluster29Contig477_+_107818_1078693063
dd_smedV4_9784_0_1Category4Cluster30Contig1035_-_26930_2697822
dd_smedV4_9784_0_1Category4Cluster30Contig1035_-_27136_2718554
dd_smedV4_9784_0_1Category4Cluster30Contig1035_-_12269_1232033
dd_smedV4_6654_0_1Category4Cluster33Contig1247_+_66401_66451132
dd_smedV4_636_0_1Category4Cluster37Contig1945_-_3659_37192122
dd_smedV4_3398_0_1Category4Cluster41Contig2215_-_23653_237121047
dd_smedV4_4575_0_1Category4Cluster42Contig1438_-_17812_178606
dd_smedV4_238_1_1Category4Cluster46Contig873_-_37793_3784128
dd_smedV4_238_1_1Category4Cluster46Contig873_-_33854_33922478
OX_Smed_1.0.13299Category4Cluster49Contig401_+_79431_7947764
OX_Smed_1.0.03600Category4Cluster50Contig4116_-_22772_2282128
OX_Smed_1.0.03600Category4Cluster50Contig4116_-_10432_10481116
mk4.001035.01.01Category3Cluster53Contig1035_-_26930_2697822
mk4.001035.01.01Category3Cluster53Contig1035_-_12269_1232033
OX_Smed_1.0.02135Category4Cluster56Contig550_+_89187_89242597
dd_smedV4_1648_0_1Category4Cluster57Contig8652_-_5842_5906650
dd_smedV4_1648_0_1Category4Cluster57Contig8652_-_5951_601422530
dd_smedV4_1760_1_1Category4Cluster58Contig466_+_57557_5760211
dd_smedV4_7869_0_1Category5Cluster59Contig292_-_80119_8016940
dd_smedV4_7869_0_1Category5Cluster59Contig292_-_80205_80254201
dd_smedV4_7869_0_1Category5Cluster59Contig292_-_80276_80321221
dd_smedV4_4962_0_1Category4Cluster60Contig3387_+_41091_4114179
mk4.002725.06.01Category1Cluster64Contig2725_-_33585_33640214
dd_smedV4_8448_0_1Category4Cluster73Contig890_+_81363_8142131
dd_smedV4_8448_0_1Category4Cluster73Contig890_+_81462_815161575
dd_smedV4_5169_0_1Category4Cluster75Contig300_-_111864_111913186
mk4.001556.02.01Category1Cluster77Contig1556_+_30969_3101710
dd_smedV4_3921_0_1Category4Cluster81Contig497_-_20599_20649114
dd_smedV4_5944_0_1Category4Cluster82Contig1005_-_85486_8553632
dd_smedV4_5944_0_1Category4Cluster82Contig1005_-_69744_697914
OX_Smed_1.0.10748Category4Cluster86Contig8407_-_441_4911082
dd_smedV4_10962_0_1Category3Cluster94Contig3915_-_17125_171725
dd_smedV4_10962_0_1Category3Cluster94Contig3915_-_14442_1449015
dd_smedV4_2963_0_1Category4Cluster97Contig1582_+_45318_45369339
dd_smedV4_2963_0_1Category4Cluster97Contig1582_+_45375_4542264
dd_smedV4_2963_0_1Category4Cluster97Contig1582_+_45630_45683902
dd_smedV4_5350_0_1Category4Cluster98Contig7246_-_6277_632664
dd_smedV4_6790_0_1Category4Cluster103Contig477_+_67294_67384627
dd_smedV4_7637_0_1Category5Cluster108Contig868_+_121422_1214699
dd_smedV4_11466_0_1Category4Cluster111Contig5137_-_18830_1887992
dd_smedV4_10250_0_1Category4Cluster115Contig668_-_82029_82076199
dd_smedV4_9427_0_2Category5Cluster117Contig13317_+_16414_164606
dd_smedV4_9009_0_1Category4Cluster119Contig1459_-_44648_4469615
dd_smedV4_8759_0_1Category2Cluster121Contig3312_-_7190_7246113
dd_smedV4_8759_0_1Category2Cluster121Contig3312_-_6701_6752118
mk4.005792.00.01Category1Cluster124Contig5792_+_24756_2481297
OX_Smed_1.0.03633Category4Cluster127Contig1754_+_33814_338637
OX_Smed_1.0.03633Category4Cluster127Contig1754_+_33904_3395448
dd_smedV4_4789_0_1Category4Cluster129Contig19546_+_10919_1097142
dd_smedV4_4789_0_1Category4Cluster129Contig19546_+_11085_111324
dd_smedV4_7193_0_1Category4Cluster130Contig2856_-_6489_653979
OX_Smed_1.0.01318Category1Cluster131Contig2725_-_33585_33640214
OX_Smed_1.0.01221Category4Cluster137Contig477_+_107818_1078693063
dd_smedV4_1571_0_1Category4Cluster139Contig2725_-_33585_33640214
dd_smedV4_3273_0_1Category4Cluster143Contig1172_-_101044_101100544
dd_smedV4_3273_0_1Category4Cluster143Contig1172_-_101143_10119119
dd_smedV4_9716_1_1Category4Cluster144Contig2805_-_26140_2618324
dd_smedV4_9716_1_1Category4Cluster144Contig2805_-_26263_263099
OX_Smed_1.0.12988Category5Cluster145Contig9111_-_13475_135144
OX_Smed_1.0.17939Category4Cluster146Contig873_-_77989_780405
OX_Smed_1.0.17939Category4Cluster146Contig873_-_72756_7281510953
dd_smedV4_6202_0_1Category5Cluster147Contig1226_+_37646_377021358
OX_Smed_1.0.02738Category4Cluster148Contig55_-_297978_29802313
mk4.000055.22.01Category1Cluster151Contig55_-_297978_29802313
dd_smedV4_10742_0_1Category1Cluster152Contig301_+_111889_111938106
dd_smedV4_2389_0_1Category4Cluster153Contig1778_+_111118_11116715
OX_Smed_1.0.23124Category4Cluster155Contig44_-_59874_599251840
OX_Smed_1.0.23124Category4Cluster155Contig44_-_59951_60000322
OX_Smed_1.0.23124Category4Cluster155Contig44_-_60078_60128108
dd_smedV4_13045_0_1Category4Cluster156Contig203_-_200804_20089973
dd_smedV4_12278_0_1Category5Cluster157Contig751_-_112048_1120961490
dd_smedV4_5628_0_1Category1Cluster158Contig5_-_28955_290184956
dd_smedV4_3927_0_1Category5Cluster159Contig4686_-_16502_1655031
dd_smedV4_1432_0_1Category4Cluster164Contig2192_+_48788_4883840
dd_smedV4_1432_0_1Category4Cluster164Contig2192_+_56949_570046047
dd_smedV4_2504_0_1Category4Cluster166Contig2311_+_28063_28116166
dd_smedV4_7343_0_2Category4Cluster167Contig3228_-_26112_26163191
OX_Smed_1.0.14230Category5Cluster168Contig3579_+_32446_32497625
dd_smedV4_11669_0_1Category4Cluster173Contig1657_+_58071_581133
dd_smedV4_13295_0_1Category5Cluster175Contig4365_-_47055_471067
dd_smedV4_3716_0_1Category3Cluster176Contig90_+_37537_375881081
dd_smedV4_3716_0_1Category3Cluster176Contig90_+_62669_62720105
OX_Smed_1.0.03403Category4Cluster177Contig2042_-_33008_3305957
OX_Smed_1.0.03403Category4Cluster177Contig2042_-_35082_3513130
OX_Smed_1.0.22835Category4Cluster179Contig662_+_90183_9023233
dd_smedV4_7201_0_1Category4Cluster180Contig2463_+_30187_302356
OX_Smed_1.0.02117Category4Cluster181Contig4747_-_13622_13685103
OX_Smed_1.0.02117Category4Cluster181Contig4747_-_13706_1374929
OX_Smed_1.0.02117Category4Cluster181Contig4747_-_13923_1396920
dd_smedV4_2272_0_1Category4Cluster184Contig457_+_36116_361711139
dd_smedV4_2272_0_1Category4Cluster184Contig457_+_36178_36228204
OX_Smed_1.0.12412Category4Cluster185Contig531_+_135010_13505816
OX_Smed_1.0.03723Category5Cluster187Contig4686_-_16502_1655031
OX_Smed_1.0.22183Category3Cluster190Contig217_+_99302_99350251
OX_Smed_1.0.22183Category3Cluster190Contig217_+_99636_9968622
dd_smedV4_5222_0_1Category3Cluster194Contig543_+_65774_6581829
dd_smedV4_5222_0_1Category3Cluster194Contig543_+_112718_11276624
dd_smedV4_4696_0_1Category3Cluster196Contig95_-_247665_24771228
dd_smedV4_4696_0_1Category3Cluster196Contig95_-_206393_20644219
dd_smedV4_4696_0_1Category3Cluster196Contig95_-_206039_206090113
dd_smedV4_4611_0_1Category4Cluster197Contig700_+_93051_9310074
dd_smedV4_4611_0_1Category4Cluster197Contig700_+_98565_98615567
mk4.000180.08.01Category1Cluster198Contig180_+_151331_151388247
dd_smedV4_6573_0_1Category1Cluster199Contig3839_+_44579_4462721
dd_smedV4_9301_0_1Category1Cluster202Contig218_-_54569_5461414
dd_smedV4_5823_0_1Category4Cluster203Contig2099_-_21903_219535
dd_smedV4_5823_0_1Category4Cluster203Contig2099_-_22112_22163201
dd_smedV4_8199_0_1Category4Cluster204Contig3765_+_5804_585458
mk4.002101.04.01Category1Cluster206Contig2101_-_35419_3546370
dd_smedV4_8417_0_1Category3Cluster207Contig9406_+_16246_16331521
dd_smedV4_8417_0_1Category3Cluster207Contig9406_+_27593_276424
dd_smedV4_8199_0_2Category4Cluster209Contig3765_+_5804_585458
mk4.002244.00.01Category3Cluster213Contig2244_+_32493_32542168
mk4.002244.00.01Category3Cluster213Contig2244_+_38258_38314332
ASA.00191.01Category5Cluster214Contig1276_-_37100_3715146
OX_Smed_1.0.02423Category4Cluster215Contig191_+_206575_2066226
OX_Smed_1.0.10266Category4Cluster217Contig4388_+_41320_4137550
dd_smedV4_3024_0_1Category4Cluster218Contig405_-_95673_957681168
dd_smedV4_3024_0_1Category4Cluster218Contig405_-_95983_9602983
dd_smedV4_3533_0_1Category4Cluster221Contig4984_-_19750_19803176
dd_smedV4_5856_0_1Category4Cluster223Contig1665_-_42290_4233416
mk4.001335.01.01Category1Cluster224Contig1335_-_8518_856787
dd_smedV4_8417_0_2Category3Cluster225Contig9406_+_16246_16331521
dd_smedV4_8417_0_2Category3Cluster225Contig9406_+_27593_276424
dd_smedV4_2072_0_2Category5Cluster226Contig3255_+_23293_23344626
dd_smedV4_2072_0_2Category5Cluster226Contig3255_+_23206_2325338
dd_smedV4_2072_0_2Category5Cluster226Contig3255_+_23122_2316775
dd_smedV4_2300_0_2Category3Cluster229Contig4625_-_18863_1891022
dd_smedV4_2300_0_2Category3Cluster229Contig4625_-_17087_1713643
dd_smedV4_14794_0_2Category4Cluster230Contig3555_-_31084_311296
dd_smedV4_2899_0_1Category4Cluster233Contig2240_+_45341_4538539
dd_smedV4_2582_0_1Category5Cluster234Contig918_-_76383_76435121
dd_smedV4_2582_0_1Category5Cluster234Contig918_-_76564_766113
dd_smedV4_2582_0_1Category5Cluster234Contig918_-_75682_7572312
dd_smedV4_1432_0_2Category4Cluster236Contig2192_+_48788_4883840
dd_smedV4_1432_0_2Category4Cluster236Contig2192_+_56949_570046047
dd_smedV4_922_0_1Category1Cluster237Contig1475_+_42248_422944
dd_smedV4_5376_0_1Category4Cluster238Contig8106_+_26617_2666544
dd_smedV4_5376_0_1Category4Cluster238Contig8106_+_26674_267223
dd_smedV4_6816_0_1Category4Cluster239Contig386_+_155610_1556685185
dd_smedV4_5074_0_1Category4Cluster241Contig5136_-_11979_12029101
dd_smedV4_2072_0_4Category5Cluster242Contig3255_+_23293_23344626
dd_smedV4_2072_0_4Category5Cluster242Contig3255_+_23206_2325338
dd_smedV4_2072_0_4Category5Cluster242Contig3255_+_23122_2316775
OX_Smed_1.0.13077Category4Cluster243Contig1644_-_42268_42318154
dd_smedV4_5187_0_1Category4Cluster248Contig1829_-_22458_22562164
dd_smedV4_4648_0_1Category4Cluster251Contig573_-_28103_2814872
dd_smedV4_3251_0_1Category4Cluster252Contig3485_-_27542_2758830
OX_Smed_1.0.03725Category3Cluster253Contig1392_-_45480_45561134
OX_Smed_1.0.03725Category3Cluster253Contig1392_-_44243_4429246
dd_smedV4_10176_0_1Category5Cluster258Contig793_-_105755_1058191185
dd_smedV4_10176_0_1Category5Cluster258Contig793_-_105639_10568732
OX_Smed_1.0.07440Category5Cluster259Contig12210_+_16447_16497293
OX_Smed_1.0.07440Category5Cluster259Contig12210_+_16572_16678194
OX_Smed_1.0.07440Category5Cluster259Contig12210_+_16498_1654713
dd_smedV4_6504_0_1Category4Cluster260Contig356_-_65318_65369795
dd_smedV4_2072_0_6Category5Cluster262Contig3255_+_23293_23344626
dd_smedV4_2072_0_6Category5Cluster262Contig3255_+_23206_2325338
dd_smedV4_2072_0_6Category5Cluster262Contig3255_+_23122_2316775
dd_smedV4_4586_0_1Category4Cluster264Contig555_+_35478_3552223
dd_smedV4_4586_0_1Category4Cluster264Contig555_+_77531_7757846
OX_Smed_1.0.17042Category4Cluster265Contig5247_-_12434_124912324
OX_Smed_1.0.17042Category4Cluster265Contig5247_-_12549_1259883
dd_smedV4_16093_0_1Category5Cluster267Contig4832_-_6732_679234
OX_Smed_1.0.10178Category4Cluster269Contig10187_-_1410_1459163
dd_smedV4_9316_0_1Category2Cluster270Contig528_-_95096_9514647
dd_smedV4_9316_0_1Category2Cluster270Contig528_-_94702_9475153
dd_smedV4_11934_0_1Category4Cluster273Contig3160_+_33568_3361825
mk4.004116.03.01Category4Cluster274Contig4116_-_22772_2282128
dd_smedV4_791_0_1Category4Cluster275Contig1750_+_35721_35771105
dd_smedV4_791_0_1Category4Cluster275Contig1750_+_35806_35856273
dd_smedV4_2373_0_1Category3Cluster280Contig265_-_141819_14186952
dd_smedV4_2373_0_1Category3Cluster280Contig265_-_119254_119304159
OX_Smed_1.0.18838Category4Cluster282Contig9102_-_1051_1102113
mk4.003285.00.01Category2Cluster283Contig3285_+_64217_64274430
mk4.003285.00.01Category2Cluster283Contig3285_+_67693_67750429

Please Note: The above table just contains around 200 entries. To download the complete list, please click here.


The computational pipeline used for the analysis has been uploaded on github.

Visit Github Page

NGS data used in this study can be downloaded from Sequence Read Archive(SRA).

SRP070102

Genome Browser

You can zoom into this jBrowse window to look for coverage of 3P-Peaks along with other information on planarian genome.

Following are the tracks that are available in the above genome browser.


  • Ox_SmedV1 - Transcript models dervied from Blythe et al. 2010.
  • dd_SmedV4 - Transcript models derived from Liu et al. 2013.
  • Asexual worms coverage RNA-Seq - Transcript models derived from Resch et al. 2012.
  • Coverge 3P-Seq - from Current study - Lakshmanan et al. 2016
  • Coverage Ion-torrent - from Current study - Lakshmanan et al.2016
  • Sexual worms coverage RNA-Seq - Transcript models derived from Resch et al. 2012.
  • X1 Coverage RNA-Seq - Data derived from "RNA Seq analysis of sorted Schmidtea mediterranea X1 and Xins cells to identify factors specific to neoblasts", ProjectID- PRJNA296017
  • Xins Coverage RNA-Seq - Data derived from "RNA Seq analysis of sorted Schmidtea mediterranea X1 and Xins cells to identify factors specific to neoblasts", ProjectID- PRJNA296017

Contact

Feel free to email us to provide some feedback on our work, give us suggestions, or request for further information.

dasaradhip@instem.res.in