The Mediator complex as a master regulator of transcription by RNA polymerase II

WF Richter, S Nayak, J Iwasa, DJ Taatjes - Nature Reviews Molecular …, 2022 - nature.com
The Mediator complex, which in humans is 1.4 MDa in size and includes 26 subunits,
controls many aspects of RNA polymerase II (Pol II) function. Apart from its size, a defining …

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 …

Transcription factors interact with RNA to regulate genes

O Oksuz, JE Henninger, R Warneford-Thomson… - Molecular cell, 2023 - cell.com
Transcription factors (TFs) orchestrate the gene expression programs that define each cell's
identity. The canonical TF accomplishes this with two domains, one that binds specific DNA …

Complementary Alu sequences mediate enhancer–promoter selectivity

L Liang, C Cao, L Ji, Z Cai, D Wang, R Ye, J Chen… - Nature, 2023 - nature.com
Enhancers determine spatiotemporal gene expression programs by engaging with long-
range promoters,,–. However, it remains unknown how enhancers find their cognate …

RNA-mediated feedback control of transcriptional condensates

JE Henninger, O Oksuz, K Shrinivas, I Sagi, G LeRoy… - Cell, 2021 - cell.com
Regulation of biological processes typically incorporates mechanisms that initiate and
terminate the process and, where understood, these mechanisms often involve feedback …

Long-range enhancer–promoter contacts in gene expression control

S Schoenfelder, P Fraser - Nature Reviews Genetics, 2019 - nature.com
Spatiotemporal gene expression programmes are orchestrated by transcriptional
enhancers, which are key regulatory DNA elements that engage in physical contacts with …

Non-coding RNAs and their integrated networks

P Zhang, W Wu, Q Chen, M Chen - Journal of integrative …, 2019 - degruyter.com
Eukaryotic genomes are pervasively transcribed. Besides protein-coding RNAs, there are
different types of non-coding RNAs that modulate complex molecular and cellular …

Long non-coding RNAs in the regulation of gene expression: physiology and disease

JCR Fernandes, SM Acuña, JI Aoki, LM Floeter-Winter… - Non-coding RNA, 2019 - mdpi.com
The identification of RNAs that are not translated into proteins was an important
breakthrough, defining the diversity of molecules involved in eukaryotic regulation of gene …

The functions and unique features of long intergenic non-coding RNA

JD Ransohoff, Y Wei, PA Khavari - Nature reviews Molecular cell …, 2018 - nature.com
Long intergenic non-coding RNA (lincRNA) genes have diverse features that distinguish
them from mRNA-encoding genes and exercise functions such as remodelling chromatin …

Functional long non-coding RNAs evolve from junk transcripts

AF Palazzo, EV Koonin - Cell, 2020 - cell.com
Transcriptome studies reveal pervasive transcription of complex genomes, such as those of
mammals. Despite popular arguments for functionality of most, if not all, of these transcripts …