Towards a map of cis-regulatory sequences in the human genome

M Niu, E Tabari, P Ni, Z Su - Nucleic acids research, 2018 - academic.oup.com
… a good understanding of coding sequences in the human reference genome. In contrast,
although cis-regulatory sequences are as important as coding sequences in specifying various …

A map of cis-regulatory modules and constituent transcription factor binding sites in 80% of the mouse genome

P Ni, D Wilson, Z Su - BMC genomics, 2022 - Springer
… However, the power of such comparative genomics approach is hampered in … cis-regulatory
sequences due to the lack of a good understanding of mouse orthologous sequences and …

Transposable elements as a potent source of diverse cis-regulatory sequences in mammalian genomes

V Sundaram, J Wysocka - Philosophical Transactions of …, 2020 - royalsocietypublishing.org
… substrate for evolving diverse cis-regulatory elements for the host, most genomic TEs are …
60% in the human and mouse genomes) is located in introns [95]. For genes that are active, …

A map of cis-regulatory elements and 3D genome structures in zebrafish

H Yang, Y Luan, T Liu, HJ Lee, L Fang, Y Wang… - Nature, 2020 - nature.com
… We converted the cis-regulatory elements from zebrafish genomic locations(danRer10) to
human and mouse genomic locations (hg38 and mm10, respectively), using the liftOver tools …

[HTML][HTML] The cis-regulatory atlas of the mouse immune system

H Yoshida, CA Lareau, RN Ramirez, SA Rose, B Maier… - Cell, 2019 - cell.com
… ) expression to the genome-wide accessibility … cis-regulatory elements where binding of
given TFs is likely functionally relevant, validated by chromatin immunoprecipitation sequencing (…

A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome

Y Zhao, Y Hou, Y Xu, Y Luan, H Zhou, X Qi… - Nature …, 2021 - nature.com
… more than 220,000 cis-regulatory elements in the pig genome. Surprisingly, … cis-regulatory
elements between human and pig genomes than those between human and mouse genomes

Hold out the genome: a roadmap to solving the cis-regulatory code

CG de Boer, J Taipale - Nature, 2024 - nature.com
… In this Perspective article, we focus on how cis-regulatory DNA sequences control gene
transcription rates via interactions between transcription factors and chromatin. Although the …

Cis-regulatory sequences in plants: their importance, discovery, and future challenges

RJ Schmitz, E Grotewold, M Stam - The plant cell, 2022 - academic.oup.com
… , but also distinct, molecular signatures at cis-regulatory sequences compared to animals.
Although in plant species with smaller genomes, such as Arabidopsis thaliana (Arabidopsis), …

Characterizing cis-regulatory elements using single-cell epigenomics

S Preissl, KJ Gaulton, B Ren - Nature Reviews Genetics, 2023 - nature.com
… Cell type-specific gene expression patterns and dynamics during development or in
disease are controlled by cis-regulatory elements (CREs), such as promoters and enhancers. …

Massively parallel cis-regulatory analysis in the mammalian central nervous system

SQ Shen, CA Myers, AEO Hughes, LC Byrne… - Genome …, 2016 - genome.cshlp.org
… retina by ex vivo plasmid electroporation and into the mouse cerebral cortex by in vivo
AAV injection. We demonstrate tissue-specific cis-regulatory activity of DHSs and provide …