Promoter bivalency favors an open chromatin architecture in embryonic stem cells

G Mas, E Blanco, C Ballaré, M Sansó, YG Spill, D Hu… - Nature …, 2018 - nature.com
In embryonic stem cells (ESCs), developmental gene promoters are characterized by their
bivalent chromatin state, with simultaneous modification by MLL2 and Polycomb complexes …

The role of Xist‐mediated Polycomb recruitment in the initiation of X‐chromosome inactivation

A Bousard, AC Raposo, JJ Żylicz, C Picard, VB Pires… - EMBO …, 2019 - embopress.org
Xist RNA has been established as the master regulator of X‐chromosome inactivation (XCI)
in female eutherian mammals, but its mechanism of action remains unclear. By creating …

[HTML][HTML] Using R and bioconductor in clinical genomics and transcriptomics

JL Sepulveda - The Journal of Molecular Diagnostics, 2020 - Elsevier
Bioinformatics pipelines are essential in the analysis of genomic and transcriptomic data
generated by next-generation sequencing (NGS). Recent guidelines emphasize the need …

A Novel Angiotensin II–Induced Long Noncoding RNA Giver Regulates Oxidative Stress, Inflammation, and Proliferation in Vascular Smooth Muscle Cells

S Das, E Zhang, P Senapati, V Amaram… - Circulation …, 2018 - Am Heart Assoc
Rationale: AngII (angiotensin II)-mediated vascular smooth muscle cell (VSMC) dysfunction
plays a major role in hypertension. Long noncoding RNAs have elicited much interest, but …

Toward the human cellular microRNAome

MN McCall, MS Kim, M Adil, AH Patil, Y Lu… - Genome …, 2017 - genome.cshlp.org
MicroRNAs are short RNAs that serve as regulators of gene expression and are essential
components of normal development as well as modulators of disease. MicroRNAs generally …

APPRIS 2017: principal isoforms for multiple gene sets

JM Rodriguez, J Rodriguez-Rivas… - Nucleic acids …, 2018 - academic.oup.com
Abstract The APPRIS database (http://appris-tools. org) uses protein structural and functional
features and information from cross-species conservation to annotate splice isoforms in …

Paths and timings of the peopling of Polynesia inferred from genomic networks

AG Ioannidis, J Blanco-Portillo, K Sandoval… - Nature, 2021 - nature.com
Polynesia was settled in a series of extraordinary voyages across an ocean spanning one
third of the Earth, but the sequences of islands settled remain unknown and their timings …

Whole-genome sequencing reveals that variants in the interleukin 18 receptor accessory protein 3′ UTR protect against ALS

C Eitan, A Siany, E Barkan, T Olender, KR van Eijk… - Nature …, 2022 - nature.com
The noncoding genome is substantially larger than the protein-coding genome but has been
largely unexplored by genetic association studies. Here, we performed region-based rare …

Insights into variation in meiosis from 31,228 human sperm genomes

AD Bell, CJ Mello, J Nemesh, SA Brumbaugh… - Nature, 2020 - nature.com
Meiosis, although essential for reproduction, is also variable and error-prone: rates of
chromosome crossover vary among gametes, between the sexes, and among humans of the …

[HTML][HTML] Widespread influence of 3′-end structures on mammalian mRNA processing and stability

X Wu, DP Bartel - Cell, 2017 - cell.com
The physiological relevance of structures within mammalian mRNAs has been elusive, as
these mRNAs are less folded in cells than in vitro and have predicted secondary structures …