ArticleDevelopmental cell2016
Alternative Computational Analysis Shows No Evidence for Nucleosome Enrichment at Repetitive Sequences in Mammalian Spermatozoa.
Article in Developmental cell, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed, 45 citations in OpenAlex.
- Protamine lacunae preserve the paternal chromatin landscape in sperm.bioRxiv : the preprint server for biology · 2025Article
- Functional Study of Four Histone Genes Involved in the Spermatogenesis ofAnimals : an open access journal from MDPI · 2025Article
- Nucleosomes in mammalian sperm: conveying paternal epigenetic inheritance or subject to reprogramming between generations?Current opinion in genetics & development · 2023Review
- T3E: a tool for characterising the epigenetic profile of transposable elements using ChIP-seq data.Mobile DNA · 2022Article
- Chromatin alterations during the epididymal maturation of mouse sperm refine the paternally inherited epigenome.Epigenetics & chromatin · 2022Article
- Paternal epigenetic influences on placental health and their impacts on offspring development and disease.Frontiers in genetics · 2022Review
- Epigenetic landscape of testis specific histone H2B variant and its influence on sperm function.Clinical epigenetics · 2021Article
- Sperm histone H3 lysine 4 trimethylation is altered in a genetic mouse model of transgenerational epigenetic inheritance.Nucleic acids research · 2020Article
- Article
- Gcn5-Mediated Histone Acetylation Governs Nucleosome Dynamics in Spermiogenesis.Developmental cell · 2019Article
- In the human sperm nucleus, nucleosomes form spatially restricted domains consistent with programmed nucleosome positioning.Biology open · 2019Article
- Tools and best practices for retrotransposon analysis using high-throughput sequencing data.Mobile DNA · 2019Article
- Review
- Mapping of histone-binding sites in histone replacement-completed spermatozoa.Nature communications · 2018Article
- Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance.BMC biology · 2018Article
- A multi-scale analysis of bull sperm methylome revealed both species peculiarities and conserved tissue-specific features.BMC genomics · 2018Article
- Review
- A Decade of Exploring the Mammalian Sperm Epigenome: Paternal Epigenetic and Transgenerational Inheritance.Frontiers in cell and developmental biology · 2018Review
- Zygotic Genome Activation in Vertebrates.Developmental cell · 2017Review
- Epigenetic modifications and reprogramming in paternal pronucleus: sperm, preimplantation embryo, and beyond.Cellular and molecular life sciences : CMLS · 2017Review
Corrections and comments
- Comment on
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Samans et al. (2014) reported the enrichment of nucleosomes in human and bovine spermatozoa at centromere repeats and retrotransposon sequences such as LINE-1 and SINE. We demonstrate here that nucleosomal enrichments at repetitive sequences as reported result from bioinformatic analyses that make redundant use of sequencing reads that map to multiple locations in the genome. To illustrate that this computational approach is flawed, we observed comparable artificial enrichments at repetitive sequences when aligning control genomic DNA or simulated reads of uniform genome coverage. These results imply that the main conclusions of the article by Samans et al. (2014) are confounded by an inappropriate computational methodology used to analyze the primary data.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.