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#35961784   2022/08/12 To Up

TMPRSS3 expression is limited in spiral ganglion neurons: implication for successful cochlear implantation.

It is well established that biallelic mutations in transmembrane protease, serine 3 () cause hearing loss. Currently, there is controversy regarding the audiological outcomes after cochlear implantation (CI) for -associated hearing loss. This controversy creates confusion among healthcare providers regarding the best treatment options for individuals with -related hearing loss.
Yuan-Siao Chen, Ernesto Cabrera, Brady J Tucker, Timothy J Shin, Jasmine V Moawad, Douglas J Totten, Kevin T Booth, Rick F Nelson

2397 related Products with: TMPRSS3 expression is limited in spiral ganglion neurons: implication for successful cochlear implantation.

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#35961778   2022/08/12 To Up

Comparative functional genomics identifies unique molecular features of EPSCs.

Extended pluripotent or expanded potential stem cells (EPSCs) possess superior developmental potential to embryonic stem cells (ESCs). However, the molecular underpinning of EPSC maintenance in vitro is not well defined. We comparatively studied transcriptome, chromatin accessibility, active histone modification marks, and relative proteomes of ESCs and the two well-established EPSC lines to probe the molecular foundation underlying EPSC developmental potential. Despite some overlapping transcriptomic and chromatin accessibility features, we defined sets of molecular signatures that distinguish EPSCs from ESCs in transcriptional and translational regulation as well as metabolic control. Interestingly, EPSCs show similar reliance on pluripotency factors Oct4, Sox2, and Nanog for self-renewal as ESCs. Our study provides a rich resource for dissecting the regulatory network that governs the developmental potency of EPSCs and exploring alternative strategies to capture totipotent stem cells in culture.
Vikas Malik, Ruge Zang, Alejandro Fuentes-Iglesias, Xin Huang, Dan Li, Miguel Fidalgo, Hongwei Zhou, Jianlong Wang

1768 related Products with: Comparative functional genomics identifies unique molecular features of EPSCs.

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#35961775   2022/08/12 To Up

Recent, full-length gene retrocopies are common in canids.

Gene retrocopies arise from the reverse transcription and insertion into the genome of processed mRNA transcripts. Although many retrocopies have acquired mutations that render them functionally inactive, most mammals retain active LINE-1 sequences capable of producing new retrocopies. New retrocopies, referred to as retro copy number variants (retroCNVs), may not be identified by standard variant calling techniques in high-throughput sequencing data. Although multiple functional retroCNVs have been associated with skeletal dysplasias in dogs, the full landscape of canid retroCNVs has not been characterized. Here, retroCNV discovery was performed on a whole-genome sequencing data set of 293 canids from 76 breeds. We identified retroCNV parent genes via the presence of mRNA-specific 30-mers, and then identified retroCNV insertion sites through discordant read analysis. In total, we resolved insertion sites for 1911 retroCNVs from 1179 parent genes, 1236 of which appeared identical to their parent genes. Dogs had on average 54.1 total retroCNVs and 1.4 private retroCNVs. We found evidence of expression in testes for 12% (14/113) of the retroCNVs identified in six Golden Retrievers, including four chimeric transcripts, and 97 retroCNVs also had significantly elevated across dog breeds, possibly indicating selection. We applied our approach to a subset of human genomes and detected an average of 4.2 retroCNVs per sample, highlighting a 13-fold relative increase of retroCNV frequency in dogs. Particularly in canids, retroCNVs are a largely unexplored source of genetic variation that can contribute to genome plasticity and that should be considered when investigating traits and diseases.
Kevin Batcher, Scarlett Varney, Daniel York, Matthew Blacksmith, Jeffrey M Kidd, Robert Rebhun, Peter Dickinson, Danika Bannasch

1666 related Products with: Recent, full-length gene retrocopies are common in canids.

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#35961773   2022/08/12 To Up

Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs.

In eukaryotes, capped RNAs include long transcripts such as messenger RNAs and long noncoding RNAs, as well as shorter transcripts such as spliceosomal RNAs, small nucleolar RNAs, and enhancer RNAs. Long capped transcripts can be profiled using Cap Analysis Gene Expression (CAGE) sequencing and other methods. Here, we describe a sequencing library preparation protocol for short capped RNAs, apply it to a differentiation time course of the human cell line THP-1, and systematically compare the landscape of short capped RNAs to that of long capped RNAs. Transcription initiation peaks associated with genes in the sense direction had a strong preference to produce either long or short capped RNAs, with 1 out of 6 peaks detected in the short capped RNA libraries only. Gene-associated short capped RNAs had highly specific 3' ends, typically overlapping splice sites. Enhancers also preferentially generated either short or long capped RNAs, with 10% of enhancers observed in the short capped RNA libraries only. Both enhancers producing short or long capped RNAs showed enrichment for GWAS-associated disease SNPs. We conclude that deep sequencing of short capped RNAs reveals new families of noncoding RNAs and elucidates the diversity of transcripts generated at known and novel promoters and enhancers.
Michiel Jan Laurens De Hoon, Alessandro Bonetti, Charles Plessy, Yoshinari Ando, Chung-Chau Hon, Yuri Ishizu, Masayoshi Itoh, Sachi Katoh, Dongyan Lin, Sho Maekawa, Mitsuyoshi Murata, Hiromi Nishiyori, Jay W Shin, Jens Stolte, Ana Maria Suzuki, Michihira Tagami, Hazuki Takahashi, Supat Thongjuea, Alistair Rr Forrest, Yoshihide Hayashizaki, Juha Kere, Piero Carninci

1071 related Products with: Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs.

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#35961769   2022/08/12 To Up

Human defensin 5-based compounds: a new approach to fight obesity?


Marc Claret, Ruben Nogueiras

2611 related Products with: Human defensin 5-based compounds: a new approach to fight obesity?