Beyond modular enhancers: new questions in cis-regulatory evolution

JMC McDonald, RD Reed - Trends in Ecology & Evolution, 2024 - cell.com
Our understanding of how cis-regulatory elements work has advanced rapidly, outpacing
our evolutionary models. In this review, we consider the implications of new mechanistic …

Decoding the Functionality of Plant Transcription Factors: Key Factors and Mechanisms

P Dhatterwal, N Sharma… - Journal of Experimental …, 2024 - academic.oup.com
Transcription factors (TFs) intricately govern cellular processes and responses to external
stimuli by modulating gene expressions. TFs help plants to balance the trade-off between …

bHLH transcription factors cooperate with chromatin remodelers to regulate cell fate decisions during Arabidopsis stomatal development

A Liu, A Mair, JL Matos, M Vollbrecht, SL Xu… - Plos …, 2024 - journals.plos.org
The development of multicellular organisms requires coordinated changes in gene
expression that are often mediated by the interaction between transcription factors (TFs) and …

[HTML][HTML] Genetic Variations in the NRF2 Microsatellite Contribute to the Regulation of Bovine Sperm-Borne Antioxidant Capacity

K Anwar, G Thaller, M Saeed-Zidane - Cells, 2024 - mdpi.com
Nuclear factor (erythroid-derived 2)-like 2 (NRF2) is a transcription factor protein-coding
gene, considered a master regulator of the cellular stress response. The genetic variations …

[HTML][HTML] Cell fate programming by transcription factors and epigenetic machinery in stomatal development

A Liu, A Mair, JL Matos, M Vollbrecht, SL Xu… - bioRxiv, 2023 - ncbi.nlm.nih.gov
The development of multi-cellular organisms requires coordinated changes in gene
expression that are often mediated by the interaction between transcription factors (TFs) and …

Characterization of sequence determinants of enhancer function using natural genetic variation

MG Yang, E Ling, CJ Cowley, ME Greenberg… - Elife, 2022 - elifesciences.org
Sequence variation in enhancers that control cell-type-specific gene transcription
contributes significantly to phenotypic variation within human populations. However, it …

Transcription factor-binding k-mer analysis clarifies the cell type dependency of binding specificities and cis-regulatory SNPs in humans

S Tahara, T Tsuchiya, H Matsumoto, H Ozaki - BMC genomics, 2023 - Springer
Abstract Background Transcription factors (TFs) exhibit heterogeneous DNA-binding
specificities in individual cells and whole organisms under natural conditions, and de novo …

TIANA: transcription factors cooperativity inference analysis with neural attention

RZ Li, CZ Han, CK Glass - BMC bioinformatics, 2024 - Springer
Background Growing evidence suggests that distal regulatory elements are essential for
cellular function and states. The sequences within these distal elements, especially motifs …

Meta-analysis for Association of Interleukin 4 VNTR Polymorphism with Rheumatoid Arthritis Risk and Severity

PS Giri, M Dwivedi - Biochemical Genetics, 2023 - Springer
Rheumatoid Arthritis (RA) is a chronic autoimmune disease characterized by severe joint
pain. There are conflicting results for the association of Interleukin 4 (IL4) variable number …

[HTML][HTML] Microglia replacement by ER-Hoxb8 conditionally immortalized macrophages provides insight into Aicardi-Goutières Syndrome neuropathology

KM Nemec, G Uy, VS Chaluvadi, FS Purnell… - …, 2024 - pmc.ncbi.nlm.nih.gov
Microglia, the brain's resident macrophages, can be reconstituted by surrogate cells-a
process termed “microglia replacement.” To expand the microglia replacement toolkit, we …