Long non-coding RNAs: definitions, functions, challenges and recommendations

JS Mattick, PP Amaral, P Carninci… - … reviews Molecular cell …, 2023 - nature.com
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes
of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II …

Regulation of gene expression by cis-acting long non-coding RNAs

N Gil, I Ulitsky - Nature Reviews Genetics, 2020 - nature.com
Long non-coding RNAs (lncRNAs) are diverse transcription products emanating from
thousands of loci in mammalian genomes. Cis-acting lncRNAs, which constitute a …

ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data

Z Zou, T Ohta, F Miura, S Oki - Nucleic acids research, 2022 - academic.oup.com
Abstract ChIP-Atlas (https://chip-atlas. org) is a web service providing both GUI-and API-
based data-mining tools to reveal the architecture of the transcription regulatory landscape …

Long noncoding RNAs: molecular modalities to organismal functions

JL Rinn, HY Chang - Annual review of biochemistry, 2020 - annualreviews.org
We have known for decades that long noncoding RNAs (lncRNAs) can play essential
functions across most forms of life. The maintenance of chromosome length requires an …

From genotype to phenotype: genetics of mammalian long non-coding RNAs in vivo

D Andergassen, JL Rinn - Nature Reviews Genetics, 2022 - nature.com
Genome-wide sequencing has led to the discovery of thousands of long non-coding RNA
(lncRNA) loci in the human genome, but evidence of functional significance has remained …

Enhancer–promoter interactions can form independently of genomic distance and be functional across TAD boundaries

D Balasubramanian, P Borges Pinto… - Nucleic Acids …, 2024 - academic.oup.com
Abstract Topologically Associating Domains (TADs) have been suggested to facilitate and
constrain enhancer–promoter interactions. However, the role of TAD boundaries in …

[LIBRO][B] RNA, the epicenter of genetic information

J Mattick, P Amaral - 2023 - library.oapen.org
The origin story and emergence of molecular biology is muddled. The early triumphs in
bacterial genetics and the complexity of animal and plant genomes complicate an intricate …

The Tug1 lncRNA locus is essential for male fertility

JP Lewandowski, G Dumbović, AR Watson, T Hwang… - Genome biology, 2020 - Springer
Abstract Background Several long noncoding RNAs (lncRNAs) have been shown to function
as components of molecular machines that play fundamental roles in biology. While the …

The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis

JP Lewandowski, JC Lee, T Hwang, H Sunwoo… - Nature …, 2019 - nature.com
RNA has been classically known to play central roles in biology, including maintaining
telomeres, protein synthesis, and in sex chromosome compensation. While thousands of …

[HTML][HTML] Cis and trans effects differentially contribute to the evolution of promoters and enhancers

K Mattioli, W Oliveros, C Gerhardinger, D Andergassen… - Genome biology, 2020 - Springer
Background Gene expression differences between species are driven by both cis and trans
effects. Whereas cis effects are caused by genetic variants located on the same DNA …