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Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection.

Pratibha Jagannatha, Yoseop Yoon, Samuel B Landry, Jack T Naritomi, Lijun Zhan, Sara Olson, Xintao Wei, Lena A Street, Liang Liu, Joshua Jeong, Cailyx Quan, Jack Reid, Lindsey V Soles, Max Segeberg, Jonathan C Schmok, Manya Jain, Elijah K F Rosales, Vicky W Chen, Maya L Gosztyla, Shuhao Xu, Avery Pong, Marko Jovanovic, Brenton R Graveley, Yongsheng Shi, Gene W Yeo

Molecular cell · 2026

PubMed ↗ DOI ↗

Abstract

Alternative polyadenylation (APA) generates transcript isoforms with distinct 3' ends, yet the repertoire of its protein regulators remains poorly defined. Using a large-scale tethered function screen, we profiled 879 human RNA-binding proteins (RBPs) and identified 63 high-confidence activators of poly(A) site (PAS) selection, most of which were not previously linked to APA. We validated these factors by knockdown PAS-seq, RNA sequencing (RNA-seq), and enhanced cross-linking and immunoprecipitation (eCLIP) analyses and developed a fine-tuned protein language model that predicts PAS selection activators and their key functional domains. We then mechanistically dissected two unexpected hits: GRB2, a signaling adaptor protein, and RNPS1, a peripheral component of the exon junction complex (EJC). Both regulate APA, at least in part, through direct interactions with distinct subunits of the cleavage and polyadenylation (CPA) machinery. Together, our study provides a comprehensive resource of APA-regulating RBPs and uncovers unexpected roles of signaling and EJC factors in APA regulation.

Linked datasets 3

GSE290248 GSE · via ncbi_elink
GEO ↗

Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [PAS-seq]

Homo sapiens

97 data files
FileTypeSize
SRR32430263_GSM8809262 RNA-Seq 789.0 MB
SRR32430264_GSM8809261 RNA-Seq 946.0 MB
SRR32430265_GSM8809260 RNA-Seq 878.0 MB
SRR32430266_GSM8809259 RNA-Seq 756.0 MB
SRR32430267_GSM8809258 RNA-Seq 753.0 MB
SRR32430268_GSM8809257 RNA-Seq 880.0 MB
SRR32430269_GSM8809256 RNA-Seq 790.0 MB
SRR32430270_GSM8809255 RNA-Seq 697.0 MB
SRR32430271_GSM8809254 RNA-Seq 839.0 MB
SRR32430272_GSM8809253 RNA-Seq 480.0 MB
SRR32430273_GSM8809252 RNA-Seq 529.0 MB
SRR32430274_GSM8809251 RNA-Seq 728.0 MB
SRR32430275_GSM8809250 RNA-Seq 611.0 MB
SRR32430276_GSM8809249 RNA-Seq 679.0 MB
SRR32430277_GSM8809248 RNA-Seq 795.0 MB
SRR32430278_GSM8809247 RNA-Seq 691.0 MB
SRR32430279_GSM8809246 RNA-Seq 685.0 MB
SRR32430280_GSM8809245 RNA-Seq 790.0 MB
SRR32430281_GSM8809244 RNA-Seq 878.0 MB
SRR32430282_GSM8809243 RNA-Seq 924.0 MB
SRR32430283_GSM8809242 RNA-Seq 950.0 MB
SRR32430284_GSM8809241 RNA-Seq 518.0 MB
SRR32430285_GSM8809240 RNA-Seq 512.0 MB
SRR32430286_GSM8809239 RNA-Seq 491.0 MB
SRR32430287_GSM8809238 RNA-Seq 513.0 MB
SRR32430288_GSM8809237 RNA-Seq 546.0 MB
SRR32430289_GSM8809236 RNA-Seq 541.0 MB
SRR32430290_GSM8809235 RNA-Seq 548.0 MB
SRR32430291_GSM8809234 RNA-Seq 676.0 MB
SRR32430292_GSM8809233 RNA-Seq 522.0 MB
SRR32430293_GSM8809232 RNA-Seq 707.0 MB
SRR32430294_GSM8809231 RNA-Seq 637.0 MB
SRR32430295_GSM8809230 RNA-Seq 704.0 MB
SRR32430296_GSM8809229 RNA-Seq 679.0 MB
SRR32430297_GSM8809228 RNA-Seq 873.0 MB
SRR32430298_GSM8809227 RNA-Seq 675.0 MB
SRR32430299_GSM8809226 RNA-Seq 1.0 GB
SRR32430300_GSM8809225 RNA-Seq 727.0 MB
SRR32430301_GSM8809224 RNA-Seq 678.0 MB
SRR32430302_GSM8809223 RNA-Seq 769.0 MB
SRR32430303_GSM8809222 RNA-Seq 692.0 MB
SRR32430304_GSM8809221 RNA-Seq 746.0 MB
SRR32430305_GSM8809220 RNA-Seq 726.0 MB
SRR32430306_GSM8809219 RNA-Seq 774.0 MB
SRR32430307_GSM8809218 RNA-Seq 729.0 MB
SRR32430308_GSM8809217 RNA-Seq 891.0 MB
SRR32430309_GSM8809216 RNA-Seq 769.0 MB
SRR32430310_GSM8809215 RNA-Seq 1015.0 MB
SRR32430311_GSM8809214 RNA-Seq 776.0 MB
SRR32430312_GSM8809213 RNA-Seq 687.0 MB
SRR32430313_GSM8809212 RNA-Seq 773.0 MB
SRR32430314_GSM8809211 RNA-Seq 1.1 GB
SRR32430315_GSM8809210 RNA-Seq 934.0 MB
SRR32430316_GSM8809209 RNA-Seq 1.0 GB
SRR32430317_GSM8809208 RNA-Seq 1.1 GB
SRR32430318_GSM8809272 RNA-Seq 1.5 GB
SRR32430319_GSM8809207 RNA-Seq 511.0 MB
SRR32430320_GSM8809271 RNA-Seq 760.0 MB
SRR32430321_GSM8809270 RNA-Seq 697.0 MB
SRR32430322_GSM8809269 RNA-Seq 711.0 MB
SRR32430323_GSM8809268 RNA-Seq 573.0 MB
SRR32430324_GSM8809267 RNA-Seq 733.0 MB
SRR32430325_GSM8809266 RNA-Seq 787.0 MB
SRR32430326_GSM8809265 RNA-Seq 775.0 MB
SRR32430327_GSM8809264 RNA-Seq 806.0 MB
SRR32430328_GSM8809263 RNA-Seq 772.0 MB
SRR32430329_GSM8809206 RNA-Seq 504.0 MB
SRR32430330_GSM8809205 RNA-Seq 622.0 MB
SRR32430331_GSM8809204 RNA-Seq 559.0 MB
SRR32430332_GSM8809203 RNA-Seq 592.0 MB
SRR32430333_GSM8809202 RNA-Seq 641.0 MB
SRR32430334_GSM8809201 RNA-Seq 719.0 MB
SRR32430335_GSM8809200 RNA-Seq 800.0 MB
SRR32430336_GSM8809199 RNA-Seq 792.0 MB
SRR32430337_GSM8809198 RNA-Seq 814.0 MB
SRR32430338_GSM8809197 RNA-Seq 913.0 MB
SRR32430339_GSM8809196 RNA-Seq 928.0 MB
SRR32430340_GSM8809195 RNA-Seq 1000.0 MB
SRR32430341_GSM8809194 RNA-Seq 1.1 GB
SRR32430342_GSM8809193 RNA-Seq 975.0 MB
SRR32430343_GSM8809192 RNA-Seq 1.2 GB
SRR32430344_GSM8809191 RNA-Seq 1.4 GB
SRR32430345_GSM8809190 RNA-Seq 558.0 MB
SRR32430346_GSM8809189 RNA-Seq 333.0 MB
SRR32430347_GSM8809188 RNA-Seq 893.0 MB
SRR32430348_GSM8809187 RNA-Seq 637.0 MB
SRR32430349_GSM8809186 RNA-Seq 592.0 MB
SRR32430350_GSM8809185 RNA-Seq 705.0 MB
SRR32430351_GSM8809184 RNA-Seq 19.0 MB
SRR32430352_GSM8809183 RNA-Seq 759.0 MB
SRR32430353_GSM8809182 RNA-Seq 719.0 MB
SRR32430354_GSM8809181 RNA-Seq 726.0 MB
SRR32430355_GSM8809180 RNA-Seq 799.0 MB
SRR32430356_GSM8809179 RNA-Seq 780.0 MB
SRR32430357_GSM8809178 RNA-Seq 863.0 MB
SRR32430358_GSM8809177 RNA-Seq 991.0 MB
SRR32430359_GSM8809176 RNA-Seq 792.0 MB
GSE290281 GSE · via ncbi_elink
GEO ↗

Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [eCLIP]

Homo sapiens

36 data files
FileTypeSize
SRR32456784_GSM8809713 OTHER 1.2 GB
SRR32456785_GSM8809712 OTHER 1.8 GB
SRR32456786_GSM8809711 OTHER 1.1 GB
SRR32456787_GSM8809710 OTHER 1.5 GB
SRR32456788_GSM8809709 OTHER 1.7 GB
SRR32456789_GSM8809708 OTHER 1.9 GB
SRR32456790_GSM8809707 OTHER 1.6 GB
SRR32456791_GSM8809706 OTHER 1.5 GB
SRR32456792_GSM8809705 OTHER 1.3 GB
SRR32456793_GSM8809704 OTHER 1.9 GB
SRR32456794_GSM8809703 OTHER 835.0 MB
SRR32456795_GSM8809702 OTHER 1.4 GB
SRR32456796_GSM8809701 OTHER 1.7 GB
SRR32456797_GSM8809700 OTHER 2.0 GB
SRR32456798_GSM8809699 OTHER 1.3 GB
SRR32456799_GSM8809698 OTHER 1.4 GB
SRR32456800_GSM8809697 OTHER 1.8 GB
SRR32456801_GSM8809696 OTHER 1.7 GB
SRR32456802_GSM8809695 OTHER 1.3 GB
SRR32456803_GSM8809694 OTHER 1.1 GB
SRR32456804_GSM8809693 OTHER 2.0 GB
SRR32456805_GSM8809692 OTHER 2.1 GB
SRR32456806_GSM8809691 OTHER 2.0 GB
SRR32456807_GSM8809690 OTHER 2.3 GB
SRR32456808_GSM8809689 OTHER 1.5 GB
SRR32456809_GSM8809688 OTHER 2.1 GB
SRR32456810_GSM8809687 OTHER 1.2 GB
SRR32456811_GSM8809686 OTHER 1.5 GB
SRR32456812_GSM8809685 OTHER 1.8 GB
SRR32456813_GSM8809684 OTHER 2.0 GB
SRR32456814_GSM8809683 OTHER 1.3 GB
SRR32456815_GSM8809682 OTHER 1.6 GB
SRR32456816_GSM8809681 OTHER 1.9 GB
SRR32456817_GSM8809680 OTHER 2.0 GB
SRR32456818_GSM8809679 OTHER 2.0 GB
SRR32456819_GSM8809678 OTHER 2.1 GB
GSE290282 GSE · via ncbi_elink
GEO ↗

Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [RNA-Seq]

Homo sapiens

92 data files
FileTypeSize
SRR32456924_GSM8809788 RNA-Seq 3.4 GB
SRR32456925_GSM8809787 RNA-Seq 1.5 GB
SRR32456926_GSM8809786 RNA-Seq 1.3 GB
SRR32456927_GSM8809785 RNA-Seq 2.1 GB
SRR32456928_GSM8809784 RNA-Seq 1.5 GB
SRR32456929_GSM8809783 RNA-Seq 1.4 GB
SRR32456930_GSM8809782 RNA-Seq 2.0 GB
SRR32456931_GSM8809781 RNA-Seq 2.5 GB
SRR32456932_GSM8809780 RNA-Seq 3.1 GB
SRR32456933_GSM8809779 RNA-Seq 1.3 GB
SRR32456934_GSM8809778 RNA-Seq 2.0 GB
SRR32456935_GSM8809777 RNA-Seq 2.4 GB
SRR32456936_GSM8809776 RNA-Seq 2.2 GB
SRR32456937_GSM8809775 RNA-Seq 2.2 GB
SRR32456938_GSM8809774 RNA-Seq 5.4 GB
SRR32456939_GSM8809773 RNA-Seq 2.0 GB
SRR32456940_GSM8809772 RNA-Seq 2.3 GB
SRR32456941_GSM8809771 RNA-Seq 2.2 GB
SRR32456942_GSM8809770 RNA-Seq 1.5 GB
SRR32456943_GSM8809769 RNA-Seq 2.4 GB
SRR32456944_GSM8809768 RNA-Seq 2.1 GB
SRR32456945_GSM8809767 RNA-Seq 2.1 GB
SRR32456946_GSM8809766 RNA-Seq 2.7 GB
SRR32456947_GSM8809765 RNA-Seq 2.3 GB
SRR32456948_GSM8809805 RNA-Seq 1.4 GB
SRR32456949_GSM8809804 RNA-Seq 2.8 GB
SRR32456950_GSM8809803 RNA-Seq 1.4 GB
SRR32456951_GSM8809802 RNA-Seq 1.9 GB
SRR32456952_GSM8809801 RNA-Seq 1.8 GB
SRR32456953_GSM8809800 RNA-Seq 909.0 MB
SRR32456954_GSM8809799 RNA-Seq 1.7 GB
SRR32456955_GSM8809798 RNA-Seq 1.2 GB
SRR32456956_GSM8809797 RNA-Seq 1.2 GB
SRR32456957_GSM8809796 RNA-Seq 1.5 GB
SRR32456958_GSM8809795 RNA-Seq 1.7 GB
SRR32456959_GSM8809794 RNA-Seq 2.2 GB
SRR32456960_GSM8809793 RNA-Seq 2.4 GB
SRR32456961_GSM8809792 RNA-Seq 2.1 GB
SRR32456962_GSM8809791 RNA-Seq 2.3 GB
SRR32456963_GSM8809790 RNA-Seq 2.2 GB
SRR32456964_GSM8809789 RNA-Seq 2.4 GB
SRR32456965_GSM8809764 RNA-Seq 2.7 GB
SRR32456966_GSM8809763 RNA-Seq 1.9 GB
SRR32456967_GSM8809762 RNA-Seq 3.2 GB
SRR32456968_GSM8809761 RNA-Seq 2.9 GB
SRR32456969_GSM8809760 RNA-Seq 1.8 GB
SRR32456970_GSM8809759 RNA-Seq 1.5 GB
SRR32456971_GSM8809758 RNA-Seq 1.8 GB
SRR32456972_GSM8809757 RNA-Seq 2.1 GB
SRR32456973_GSM8809756 RNA-Seq 2.4 GB
SRR32456974_GSM8809755 RNA-Seq 1.5 GB
SRR32456975_GSM8809754 RNA-Seq 2.8 GB
SRR32456976_GSM8809753 RNA-Seq 2.0 GB
SRR32456977_GSM8809752 RNA-Seq 1.6 GB
SRR32456978_GSM8809751 RNA-Seq 2.1 GB
SRR32456979_GSM8809750 RNA-Seq 1.9 GB
SRR32456980_GSM8809749 RNA-Seq 2.1 GB
SRR32456981_GSM8809748 RNA-Seq 2.5 GB
SRR32456982_GSM8809747 RNA-Seq 2.1 GB
SRR32456983_GSM8809746 RNA-Seq 2.2 GB
SRR32456984_GSM8809745 RNA-Seq 1.5 GB
SRR32456985_GSM8809744 RNA-Seq 4.2 GB
SRR32456986_GSM8809743 RNA-Seq 2.5 GB
SRR32456987_GSM8809742 RNA-Seq 2.1 GB
SRR32456988_GSM8809741 RNA-Seq 1.5 GB
SRR32456989_GSM8809740 RNA-Seq 1.8 GB
SRR32456990_GSM8809739 RNA-Seq 1.9 GB
SRR32456991_GSM8809738 RNA-Seq 1.7 GB
SRR32456992_GSM8809737 RNA-Seq 1.8 GB
SRR32456993_GSM8809736 RNA-Seq 2.5 GB
SRR32456994_GSM8809735 RNA-Seq 2.7 GB
SRR32456995_GSM8809734 RNA-Seq 2.6 GB
SRR32456996_GSM8809733 RNA-Seq 1.3 GB
SRR32456997_GSM8809732 RNA-Seq 1.6 GB
SRR32456998_GSM8809731 RNA-Seq 1.7 GB
SRR32456999_GSM8809730 RNA-Seq 1.7 GB
SRR32457000_GSM8809729 RNA-Seq 1.3 GB
SRR32457001_GSM8809728 RNA-Seq 1.4 GB
SRR32457002_GSM8809727 RNA-Seq 2.0 GB
SRR32457003_GSM8809726 RNA-Seq 2.0 GB
SRR32457004_GSM8809725 RNA-Seq 1.8 GB
SRR32457005_GSM8809724 RNA-Seq 1.6 GB
SRR32457006_GSM8809723 RNA-Seq 1.7 GB
SRR32457007_GSM8809722 RNA-Seq 2.2 GB
SRR32457008_GSM8809721 RNA-Seq 2.4 GB
SRR32457009_GSM8809720 RNA-Seq 2.2 GB
SRR32457010_GSM8809719 RNA-Seq 2.0 GB
SRR32457011_GSM8809718 RNA-Seq 2.2 GB
SRR32457012_GSM8809717 RNA-Seq 1.6 GB
SRR32457013_GSM8809716 RNA-Seq 1.6 GB
SRR32457014_GSM8809715 RNA-Seq 2.2 GB
SRR32457015_GSM8809714 RNA-Seq 2.9 GB

Analysis pipelines 3

Pipeline Assay Steps Dataset
GSE290248 Data Processing geo_data_processing — 1 GSE290248
GSE290281 eCLIP Data Processing geo_data_processing eCLIP 1 GSE290281
GSE290282 RNA-seq Data Processing geo_data_processing RNA-seq 3 GSE290282