Fourth report on chicken genes and chromosomes 2022

J Smith, JM Alfieri, N Anthony, P Arensburger… - … and genome research, 2023 - karger.com
The chicken continues to hold its position as a leading model organism within many areas of
research, as well as being a major source of protein for human consumption. The First …

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases

M Lizio, I Abugessaisa, S Noguchi, A Kondo… - Nucleic acids …, 2019 - academic.oup.com
The FANTOM web resource (http://fantom. gsc. riken. jp/) was developed to provide easy
access to the data produced by the FANTOM project. It contains the most complete and …

Comparative transcriptomics of primary cells in vertebrates

T Alam, S Agrawal, J Severin, RS Young… - Genome …, 2020 - genome.cshlp.org
Gene expression profiles in homologous tissues have been observed to be different
between species, which may be due to differences between species in the gene expression …

Dosage compensation of Z sex chromosome genes in avian fibroblast cells

R Deviatiiarov, H Nagai, G Ismagulov, A Stupina… - Genome Biology, 2023 - Springer
In birds, sex is genetically determined; however, the molecular mechanism is not well-
understood. The avian Z sex chromosome (chrZ) lacks whole chromosome inactivation, in …

Alternative transcription start sites contribute to acute-stress-induced transcriptome response in human skeletal muscle

PA Makhnovskii, OA Gusev, RO Bokov, GR Gazizova… - Human Genomics, 2022 - Springer
Background More than half of human protein-coding genes have an alternative transcription
start site (TSS). We aimed to investigate the contribution of alternative TSSs to the acute …

Mapping and Functional Dissection of the Rumpless Trait in Piao Chicken Identifies a Causal Loss of Function Mutation in the Novel Gene Rum

Y Guo, J Tian, C Song, W Han, C Zhu… - Molecular biology …, 2023 - academic.oup.com
Rumpless chickens exhibit an abnormality in their tail development. The genetics and
biology of this trait has been studied for decades to illustrate a broad variation in both the …

Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq

RA Policastro, RT Raborn, VP Brendel… - Genome …, 2020 - genome.cshlp.org
Accurate mapping of transcription start sites (TSSs) is key for understanding transcriptional
regulation. However, current protocols for genome-wide TSS profiling are laborious and/or …

Cysteine enrichment mediates co-option of uricase in reptilian skin and transition to uricotelism

G Mori, A Liuzzi, L Ronda, M Di Palma… - Molecular Biology …, 2023 - academic.oup.com
Uric acid is the main means of nitrogen excretion in uricotelic vertebrates (birds and reptiles)
and the end product of purine catabolism in humans and a few other mammals. While …

Global Analysis of Transcription Start Sites in the New Ovine Reference Genome (Oar rambouillet v1.0)

M Salavati, A Caulton, R Clark, I Gazova… - Frontiers in …, 2020 - frontiersin.org
The overall aim of the Ovine FAANG project is to provide a comprehensive annotation of the
new highly contiguous sheep reference genome sequence (Oar rambouillet v1. 0). Mapping …

Cis-regulatory interfaces reveal the molecular mechanisms underlying the notochord gene regulatory network of Ciona

LJ Negrón-Piñeiro, Y Wu, S Popsuj… - Nature …, 2024 - nature.com
Tissue-specific gene expression is fundamental in development and evolution, and is
mediated by transcription factors and by the cis-regulatory regions (enhancers) that they …