AWG RNA Task Subgroup Progress Report February 12

AWG RNA Task Subgroup Progress Report, February 12 http: //genomewiki. cse. ucsc. edu/Encode. DCC/index. php/RNA roderic. guigo@crg. cat 11/28/2020 RNA Analysis 1

tasks • TSS – annotated – novel • Quantification of expression – platform comparison • Other analysis – Completeness of GENCODE (with RNAseq) – CAGE tags: TSS vs capping of post-processsed RNAs – classification of transcripts: coding vs non-coding – compartimentalization of transcription – Allele specific transcription 11/28/2020 RNA Analysis 2

Annotated TSS Sarah Djebali Felix Kokocinski Timo Lassmann Brownen Aken • Set of GENCODE TSS annotated with CAGE and PET ditags. – file available at http: //genome. crg. es/~sdjebali/research/Gencode_TSS. gff – behaviour as expected (somewhat) 11/28/2020 RNA Analysis 3

Novel CAGE clusters Sarah Djebali Felix Kokocinski Timo Lassmann Brownen Aken http: //genome. crg. es/~sdjebali/research/CAGEor. PET 5 p_cluster_overhavcapsite. txt • within a given condition, tags overlapping on the same strand are collapsed into tag clusters(1 bp overlap) • Many cage clusters not overlapping annotated TSS – waiting for poly. A+ CAGE 11/28/2020 RNA Analysis 4

Quantification of Expression • From tiling array data (Sarah Djebali) • From RNAseq (Ali Mortazavi) – K 562 and GM 12878 poly. A+ whole cell RNA 11/28/2020 RNA Analysis 5

PET vs Tiling Arrays at TSS K 562 poly. A+ cytosol - corr=0. 221 GM 12878 poly. A+ cytosol - corr=0. 142 Sarah Djebali Julien Lagarde K 562 poly. A+ nucleus - corr=0. 132 Prostate poly. A+ whole cell - corr=0. 239 6

Ali Moratzavi Wold / Myers RNA-seq Status • 1 x 32 bp K 562 and GM 12878 poly. A+ whole cell RNA: – GM 2 replicates: – K 562 2 replicates: ~28 M mapped reads / rep ~25 M mapped reads / rep • 2 x 75 bp K 562 and GM 12878 poly. A+ whole cell RNA: – – Hybrid mapping: bowtie, followed by blat for novel splices GM 1 rep: 36. 1 M mapped 75 mer K 562 1 rep: 33. 8 M mapped 75 mer Second rep for 2 x 75 bp samples in process • Gencode: – Converting to Gencode freeze – Exon level RPKM available for 1 x 32, 2 x 75: • Not surprisingly, noisier at the lower signals compared to locus RPKM (see next slide) • Waiting on 2 x 75 replicates to see if those are more accurate at the low end – Novel exons forthcoming 11/28/2020 RNA Analysis 7

GM 12878 K 562 Ali Moratzavi 29 K NCBI Loci 360 K Distinct Gencode Exons 11/28/2020 RNA Analysis 8

Scott Tenenbaum Ajish George Platform Comparison K 562 Poly+ long RNA. Building on the cell phenotype analysis Cytosolic Total Cellular Affy Exon Array Affy Tiling Array Solexa SR Solexa PR Helicos SR 11/28/2020 RNA Analysis 9

RNAseq assesment • RNASeq summit. UCSC early march – Rachel Harte, Mark Diekhans, Ali Mortzavi, Jeltje van Baren (+ other people) – Storage, manipulation, annotation • RGASP. Jen Harrow/Tim Hubbard. Sanger – Build on the model of EGASP – Evaluation of methods to map, build gene models and assess transcript expression – June or October – Need to discuss with NHGRI? • Platform comparison on Mod. ENCODE. Mark Gernstein • Platform comparisons issues. – Should we proactively ask vendors to providedata sets. – is ENCODE the rigth framework? 11/28/2020 RNA Analysis 10

interface with AWG • Would it make sense to generate an RNA element Matrix to be used in the Machine learning based analysis? 11/28/2020 RNA Analysis 11

Other ongoing analysis 11/28/2020 RNA Analysis 12

long noncoding RNAs Thomas Derrien Mike Lin Manolis Kellis Protein Coding genes processed transcript “nc. RNAs” filtered (1) loci 12 273 4 833 2258 transcripts 27 639 23 392 3019 exons 238888 99759 8978 11/28/2020 RNA Analysis 13

HAVANA nc. RNA analysis 6 > Histone modifications (Barski et al. , Cell, 2007) Thomas Derrien - In CD 4+ T cells H 3 K 4 Me 3 : Trimethylation of Lysine 4 in histone 3 is a mark of transcription initiation. H 3 K 4 me 3 11/28/2020 RNA Analysis 14

HAVANA nc. RNA analysis 6 > Histone modifications (Barski et al. , Cell, 2007) Thomas Derrien - In CD 4+ T cells - Selection of a subset of 237 transcripts showing expression with RNA seq data in lymphatic tissue H 3 K 4 me 3 11/28/2020 RNA Analysis 15

transcript compartimentalization • Compartment specific transcripts (Sarah Djebali) – so far using only tiling array data – issues in integrating data from different technologies – difficulties on distinguishing between transient vs estable localization 11/28/2020 RNA Analysis 16

Prediction of RNA compartment Babu Guda/Scott Tenenbaum Zhi Lu/Mark Gerstein Strategy • Use transfrags from different compartments as input and extract differential features to develop a discriminatory scoring function. • We will use both sequence-based and structure-based approaches to identify discriminatory features. • Step-I: Use an n-gram based Bayesian approach to model the density distribution of transfrags across different locations. • Step-II: Selected n-grams from step-I will be used for structure-based analysis to extract discriminatory structural motifs • Use a weight-based approach to compute a final prediction score • Use annotated transcripts for validation 11/28/2020 RNA Analysis 1 17

to be initiated soon • Allele Specific Transcription. Ali Moratzavi, Mark Gerstein • Genealogy of transcripts. Relationship between short and long RNAs. Timo Lassmann • CAGE clusters. TSS vs capped post processed RNAs. Timo Lassmann, Sarah Djebali, Felix Kokocinski, Brownen Aken 11/28/2020 RNA Analysis 18

thanks to all RNA task group 11/28/2020 RNA Analysis 19