bio-ribo-seq-ribosome-stalling

name	bio-ribo-seq-ribosome-stalling
description	Detect ribosome pausing and stalling at codon resolution from Ribo-seq, using local-relative occupancy metrics and A-site assignment. Use when studying elongation dynamics, codon dwell times, pause motifs, or ribosome collisions, and when judging whether a pause is real biology or a cycloheximide artifact.
tool_type	python
primary_tool	Plastid

Version Compatibility

Reference examples tested with: plastid 0.6+, numpy 1.26+, scipy 1.12+, biopython 1.83+, twobitreader 3.1+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Ribosome Stalling Detection

"Find ribosome pause sites in my data" -> Detect codon positions where ribosomes dwell longer than the local average, attribute them to A-site decoding or nascent-chain effects, and judge whether the signal is real or a drug artifact.

• Python: plastid for A-site codon density, local-relative pause scoring, and motif context

Read this first: cycloheximide destroys pause signal

A pause is only meaningful when footprint positions reflect in-vivo dwell times. Cycloheximide (CHX) pre-treatment of live cells violates this: arrest is not instantaneous, ribosomes run on after the drug, density redistributes downstream, codon-specific pausing is attenuated, and an artifactual start-codon peak appears. Hussmann 2015 showed CHX data report a WEAK NEGATIVE correlation between codon rate and tRNA abundance while flash-frozen data report a STRONG POSITIVE one -- the drug flips the conclusion. A pause analysis on CHX data largely measures the drug.

Decision rule before any dwell/pause analysis:

• Flash-frozen, no drug (or CHX only in lysis at high concentration) -> codon-resolution dwell-time analysis is valid.
• CHX pre-incubation of live cells -> restrict to qualitative/gene-level statements; do not report codon dwell times or tRNA correlations as biology.
• Harringtonine/lactimidomycin data are for initiation-site mapping, not elongation pausing (see initiation-site-mapping).

A-site vs P-site: the offset choice changes the biology

The P-site offset (~12 nt from the 5' end for canonical 28-30 nt footprints) must be calibrated per read length, not hardcoded (see ribosome-periodicity). The relevant site depends on the mechanism: tRNA-availability/decoding pauses register at the A-SITE (A-site = P-site + 3), so codon-occupancy and tRNA work assign to the A-site. Nascent-chain effects (polyproline, charge) act at the P-site/exit tunnel and upstream. State which site is used; the peak position relative to A/P/E is itself diagnostic.

Pause-metric selection

Metric	Definition	Caveat
Per-transcript z-score	(density - gene mean)/gene SD	not the field standard; SD inflated by the peaks sought; arbitrary threshold
Pause score	local density / gene-mean density at that position	needs a per-gene coverage floor; the standard local-relative metric
Codon occupancy	mean over all instances of a codon of (position density / gene mean)	normalize each gene to its own mean FIRST, then pool; assign to A-site
RUST	binarize each position vs the gene mean, average the metafootprint	outlier-robust; resists a few high peaks dominating
Disome density	footprints from two stacked ribosomes (~58-62 nt)	the cleanest in-vivo strong-pause readout (Arpat 2020)

The two normalization rules the naive z-score violates: never z-score across positions of differently-expressed genes (high-expression genes dominate) -- normalize each gene to its own mean first; and require a real per-gene coverage floor (a few hundred in-frame footprints), far above a sum > 100 cutoff, or per-position metrics are noise.

Calculate A-site codon density (plastid)

Goal: Get a per-codon occupancy vector for each CDS at the A-site.

Approach: Map footprints to the A-site offset, fetch the CDS count vector, and reduce each codon to its summed in-frame count.

from plastid import BAMGenomeArray, GTF2_TranscriptAssembler, FivePrimeMapFactory
import numpy as np

def asite_codon_occupancy(bam_path, gtf_path, asite_offset=15):
    '''Per-codon A-site occupancy per CDS. A-site offset = P-site (~12) + 3.

    A single fixed offset is a simplification valid only when one read length
    dominates. For production, calibrate per length (ribosome-periodicity) and
    map with VariableFivePrimeMapFactory.from_file using A-site = P-site + 3.
    '''
    alignments = BAMGenomeArray(bam_path, mapping=FivePrimeMapFactory(offset=asite_offset))
    out = {}
    for tx in GTF2_TranscriptAssembler(gtf_path):
        if tx.cds_start is None:
            continue
        cds = tx.get_cds()
        counts = cds.get_counts(alignments)          # numpy vector over the CDS
        n_codons = len(counts) // 3
        # Sum the 3 positions of each codon into a SCALAR (one value per codon)
        per_codon = np.array([counts[i*3:i*3+3].sum() for i in range(n_codons)])
        out[tx.get_name()] = per_codon
    return out

cds.get_counts(alignments) is the count method on the SegmentChain; BAMGenomeArray has no count_in_region/get_density. Reducing each codon to a scalar (sum of its three positions) is essential -- storing the whole vector at each codon makes every downstream metric garbage.

Score pauses with a local-relative metric

Goal: Flag codons where occupancy exceeds the gene's own average.

Approach: Divide each position by the gene mean (a pause score), require adequate coverage, and threshold.

def pause_scores(per_codon_occupancy, min_total=500, score_threshold=5.0):
    '''Pause score = codon occupancy / gene-mean occupancy (local-relative).

    min_total: per-gene footprint floor; below this, scores are noise.
    score_threshold: fold-over-gene-mean to call a pause (tune per dataset).
    '''
    pauses = []
    for tx, occ in per_codon_occupancy.items():
        if occ.sum() < min_total:
            continue
        mean = occ.mean()
        if mean == 0:
            continue
        scores = occ / mean
        for pos in np.where(scores > score_threshold)[0]:
            pauses.append({'transcript': tx, 'codon': int(pos),
                           'pause_score': float(scores[pos])})
    return pauses

Codon occupancy across genes

Goal: Estimate per-codon-type dwell, averaged across the transcriptome.

Approach: Normalize each gene to its own mean BEFORE pooling, then average per codon identity (the A-site codon).

Pool mean-of-ratios, not ratio-of-means: a raw average across genes is dominated by highly expressed genes. The per-codon occupancy is then a relative dwell estimate -- and only on no-drug data. The tRNA-availability correlation (codon occupancy vs tRNA adaptation index) is modest, sign- and protocol-dependent, and reflects charged-tRNA levels rather than gene copy number; report the effect size, not a presumed strong negative correlation.

Known pause mechanisms

Motif / feature	Mechanism
Polyproline (PPP, PPG)	Rigid proline geometry stalls peptidyl transfer; rescued by eIF5A (eukaryotes) / EF-P (bacteria)
Poly-basic (Lys/Arg runs)	Basic nascent chain drags on the negatively-charged exit tunnel; poly-Lys also involves sliding on A-rich codons
Rare/low-tRNA codons	Slow A-site decoding; real but modest, and inflated in CHX data
Internal Shine-Dalgarno (bacteria)	Anti-SD base-pairing with 16S rRNA; real but contested (protocol-dependent)

Ribosome collisions and disome-seq (the modern readout)

When a ribosome stalls, the trailing ribosome collides into it, forming a disome whose ~58-62 nt footprint maps collision sites transcriptome-wide -- a cleaner in-vivo strong-pause readout than monosome relative density (Arpat 2020; ~10% of ribosomes can be in disomes). The collided-disome interface is the trigger for ribosome quality control: ZNF598 (mammals) / Hel2 (yeast) ubiquitinate small-subunit proteins, recruiting the splitting machinery and no-go decay. A monosome pause that coincides with a disome peak, replicates, and survives in no-drug data is strong evidence of a real, acted-upon stall.

Extract pause-site sequence context

Goal: Find amino-acid motifs enriched at pause sites.

Approach: Build the per-transcript CDS sequences from a genome (plastid's get_sequence needs a genome, not a SegmentChain), then translate a window centered on the A-site codon of each pause.

from Bio.Seq import Seq
import twobitreader

def cds_sequences_from_genome(gtf_path, twobit_path):
    '''Map transcript name -> spliced CDS nucleotide sequence.'''
    from plastid import GTF2_TranscriptAssembler
    genome = twobitreader.TwoBitFile(twobit_path)   # dict-like {chrom: seq}
    seqs = {}
    for tx in GTF2_TranscriptAssembler(gtf_path):
        if tx.cds_start is None:
            continue
        seqs[tx.get_name()] = tx.get_cds().get_sequence(genome)
    return seqs

def pause_motifs(pauses, cds_sequences, window_codons=5):
    '''Amino-acid context around each pause (centered on the A-site codon).'''
    motifs = []
    for p in pauses:
        seq = cds_sequences.get(p['transcript'])
        if not seq:
            continue
        c = p['codon']
        s, e = max(0, (c - window_codons) * 3), min(len(seq), (c + window_codons + 1) * 3)
        if (e - s) % 3 == 0:
            motifs.append(str(Seq(seq[s:e]).translate()))
    return motifs

Common Errors

Symptom	Cause	Fix
Strong start-codon "pause", odd tRNA correlation	CHX pre-treatment artifacts	Use flash-frozen no-drug data; restrict CHX data to gene-level claims
AttributeError on count_in_region/get_density	Not BAMGenomeArray methods	Use cds.get_counts(alignments)
Every codon occupancy identical	Whole count vector stored per codon	Store a scalar: sum the 3 positions of each codon
TypeError from get_sequence	Passed a SegmentChain, not a genome	Load a genome FASTA/2bit; call cds.get_sequence(genome)
Pauses dominated by one highly expressed gene	Global z-score / ratio-of-means	Normalize each gene to its own mean first; mean-of-ratios
Noisy, irreproducible pauses	Coverage floor too low (sum > 100)	Require a few hundred in-frame footprints per gene
tRNA correlation overstated	Assumed strong negative on CHX data	Report effect size; depends on charging and harvest

Related Skills

• ribosome-periodicity - Calibrate the A-site offset before scoring occupancy
• orf-detection - Locate the ORFs that pause sites fall within
• initiation-site-mapping - Distinguish initiation drugs from elongation pausing
• translation-efficiency - Gene-level translation context

References

• Hussmann JA, Patchett S, Johnson A, Sawyer S, Press WH. 2015. Understanding biases in ribosome profiling experiments reveals signatures of translation dynamics in yeast. PLoS Genet 11(12):e1005732. doi:10.1371/journal.pgen.1005732
• Gerashchenko MV, Gladyshev VN. 2014. Translation inhibitors cause abnormalities in ribosome profiling experiments. Nucleic Acids Res 42(17):e134. doi:10.1093/nar/gku671
• O'Connor PBF, Andreev DE, Baranov PV. 2016. Comparative survey of the relative impact of mRNA features on local ribosome profiling read density. Nat Commun 7:12915. doi:10.1038/ncomms12915
• Arpat AB, Liechti A, De Matos M, Dreos R, Janich P, Gatfield D. 2020. Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing. Genome Res 30(7):985-999. doi:10.1101/gr.257741.119
• Charneski CA, Hurst LD. 2013. Positively charged residues are the major determinants of ribosomal velocity. PLoS Biol 11(3):e1001508. doi:10.1371/journal.pbio.1001508
• Schuller AP, Wu CC, Dever TE, Buskirk AR, Green R. 2017. eIF5A functions globally in translation elongation and termination. Mol Cell 66(2):194-205. doi:10.1016/j.molcel.2017.03.003
• Li GW, Oh E, Weissman JS. 2012. The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature 484(7395):538-541. doi:10.1038/nature10965