Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes

AR Ringel, Q Szabo, AM Chiariello, K Chudzik… - Cell, 2022 - cell.com
Regulatory landscapes drive complex developmental gene expression, but it remains
unclear how their integrity is maintained when incorporating novel genes and functions …

BAP1 constrains pervasive H2AK119ub1 to control the transcriptional potential of the genome

NA Fursova, AH Turberfield, NP Blackledge… - Genes & …, 2021 - genesdev.cshlp.org
Histone-modifying systems play fundamental roles in gene regulation and the development
of multicellular organisms. Histone modifications that are enriched at gene regulatory …

EBF1 primes B-lymphoid enhancers and limits the myeloid bias in murine multipotent progenitors

A Lenaerts, I Kucinski, W Deboutte… - Journal of Experimental …, 2022 - rupress.org
Hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs) generate all cells of
the blood system. Despite their multipotency, MPPs display poorly understood lineage bias …

Dynamic antagonism between key repressive pathways maintains the placental epigenome

R Weigert, S Hetzel, N Bailly, C Haggerty, IA Ilik… - Nature Cell …, 2023 - nature.com
DNA and Histone 3 Lysine 27 methylation typically function as repressive modifications and
operate within distinct genomic compartments. In mammals, the majority of the genome is …

Computational methods for the prediction of chromatin interaction and organization using sequence and epigenomic profiles

H Tao, H Li, K Xu, H Hong, S Jiang, G Du… - Briefings in …, 2021 - academic.oup.com
The exploration of three-dimensional chromatin interaction and organization provides
insight into mechanisms underlying gene regulation, cell differentiation and disease …

Identification, characterization, and design of plant genome sequences using deep learning

Z Wang, H Yuan, J Yan, J Liu - The Plant Journal, 2024 - Wiley Online Library
Due to its excellent performance in processing large amounts of data and capturing complex
non‐linear relationships, deep learning has been widely applied in many fields of plant …

Enhancer hijacking at the ARHGAP36 locus is associated with connective tissue to bone transformation

US Melo, J Jatzlau, CA Prada-Medina, E Flex… - nature …, 2023 - nature.com
Heterotopic ossification is a disorder caused by abnormal mineralization of soft tissues in
which signaling pathways such as BMP, TGFβ and WNT are known key players in driving …

Combinatorial quantification of 5mC and 5hmC at individual CpG dyads and the transcriptome in single cells reveals modulators of DNA methylation maintenance …

A Chialastri, S Sarkar, EE Schauer, S Lamba… - Nature Structural & …, 2024 - nature.com
Inheritance of 5-methylcytosine from one cell generation to the next by DNA
methyltransferase 1 (DNMT1) plays a key role in regulating cellular identity. While recent …

CENTRE: a gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction

T Rapakoulia, S Lopez Ruiz De Vargas… - …, 2023 - academic.oup.com
Motivation Identifying target promoters of active enhancers is a crucial step for realizing
gene regulation and deciphering phenotypes and diseases. Up to now, several …

DNA methylation and hydroxymethylation have distinct genome-wide profiles related to axonal regeneration

A Madrid, LE Borth, KJ Hogan, N Hariharan… - Epigenetics, 2021 - Taylor & Francis
Alterations in environmentally sensitive epigenetic mechanisms (eg., DNA methylation)
influence axonal regeneration in the spinal cord following sharp injury. Conventional DNA …