In CshlSiepelLab/DENR: Deconvolution of Expression for Nascent RNA Sequencing Data

Quantifying nascent RNA sequencing data with transcript level resolution

DENR quantifies nascent transcript abundance based on reference annotations. Those annotations can be from anywhere as long as they can be placed in a GRanges object. Here we obtain our transcript annotations from a Txdb object.

library(DENR)
txdb_path_ds <- system.file("extdata", "test_double_strand.txdb",
                         package = "DENR")
txdb_ds <- AnnotationDbi::loadDb(file = txdb_path_ds)
gr_ds <- GenomicFeatures::transcripts(txdb_ds, c("tx_name", "gene_id"))
gr_ds$gene_id <- as.character(gr_ds$gene_id)

print(gr_ds)

Txdb objects provide a convienent way to obtain such annotations from a variety of species and assemblies through biomaRt. We also implemented some convenience functions for retrieving and locally caching Txdb objects from the ensembl biomart in a companion package nascentRNASim via function download_txdb().

Once we have a list of transcripts we can contruct a transcript_quantification object which will hold all data for further analysis. In order to do this we must specify a bin size which will define the resolution of the transcript models. Bin sizes that are too small are computationally expensive and may provide a false sense of precision while bin sizes that are too large will result in a loss of ability to differentiate signal from distinct transcripts. As a reasonable midground we select a bin size of 250bp. We also must specify the metadata column corresponding to a unique transcript id. Another column for a unique gene id may be specified but is not required.

bsize <- 250
tq <- transcript_quantifier(gr_ds, bin_size = bsize,
                            transcript_name_column = "tx_name",
                            gene_name_column = "gene_id", mask_start_bins = c(1, 1),
                            mask_end_bins = c(1, 1))

To add a specific data set to the transcript_quantifier object we use the add_data() function using the mean summary operation.

# The paths to relevant bigwig files
bwp <- system.file("extdata", "test_double_strand_plus.bw",
                         package = "DENR")
bwm <- system.file("extdata", "test_double_strand_minus.bw",
                         package = "DENR")
# Add the data
tq <- add_data(tq = tq,
               bigwig_plus = bwp,
               bigwig_minus = bwm)

All we need to do now to estimate transcript abundances is call the fit() function.

tq <- fit(tq)

To view the results we can all the transcript_abundance() or gene_abundance() function.

ta <- transcript_abundance(tq)
head(ta)

We can also create plots for specific transcripts or genomic regions

plot_model(tq, chrom = 1, start = 1, end= 11000, ymax_bw = 300, ymax_abundance = 250)

Note that if USCS chromosome names are not used (e.g., Ensembl style, 1 instead of chr1), user will need to first library(Gviz) then set options(ucscChromosomeNames=FALSE).

Optional modeling features

Using a non-uniform transcript coverage profile

Because of variable polymerase elongation rates along the transcript body, polymerase density systematically varies along the length of the transcript. To accomadate this DENR has the ability to fit a "shape profile" that attempts to capture this empirically. This empirical shape profile is then used instead of the uniform one during the abundance estimation step. To estimate a shape profile use the \code{transcript_shape_profile} as below (note the alteration of the \code{min_transcript_length} and the head and tail lengths here just for the purposes of demonstration with a synthetic data set. Generally using transcripts that short is not reccomended).

tsp <- transcript_shape_profile(transcripts = gr_ds,
                                bigwig_plus = bwp,
                                bigwig_minus = bwm,
                                bin_size = bsize, linear_head_length = 500,
                                linear_tail_length = 500,
                                min_transcript_length = 5e3)

The empirical profile can be viewed with the \code{view()} function. This example looks a fairly odd as we are running on synthetic data and allowing really short transcripts.

view(tsp)

The shape profile is then incorporated into the \code{transcript_quantifier} object and fitting proceeds as normal.

tq_shape <- apply_shape_profile(tq, tsp)
tq_shape <- fit(tq_shape)
head(transcript_abundance(tq_shape))

Using an ML model to predict inactive TSS

Nascent RNA data tends to be fairly noisy and spill over annotated transcript boundries. For this reason, pre-filtering the set transcripts to quantify abundance for can be quite useful. Specific transcripts can be specified as inactive during the fitting step using the \code{inactive_transcripts} option. You may create the list of these inactive transcripts in whatever manner you choose, e.g., based on emprical evidences from GRO-cap, PRO-cap, CAGE, RNA-seq, etc.

# Inactive transcripts selected manually
inactive_tss <- c("t1.2", "t2.1")
tq <- fit(tq = tq, inactive_transcripts = inactive_tss)

However, if you have a tensorflow backend installed you can use a pre-trained ML classifier to predict inactive TSS and feed that into the fitting step instead. For instructions on how to install tensorflow see here.

itx <- predict_inactive_transcripts(tq, bwp, bwm)
print(itx)

CshlSiepelLab/DENR documentation built on July 16, 2021, 10:42 p.m.