Results 41 to 50 of about 2,288,208 (167)

RobusTAD: reference panel based annotation of nested topologically associating domains

Genome Biology
Topologically associating domains (TADs) are fundamental units of 3D genomes and play essential roles in gene regulation. Hi-C data suggests a hierarchical organization of TADs.
Yanlin Zhang, Rola Dali, Mathieu Blanchette   +2 more
doaj   +1 more source

Evolutionary stability of topologically associating domains is associated with conserved gene regulation

BMC Biology, 2018
Background The human genome is highly organized in the three-dimensional nucleus. Chromosomes fold locally into topologically associating domains (TADs) defined by increased intra-domain chromatin contacts.
Jan Krefting, Miguel A. Andrade-Navarro, Jonas Ibn-Salem   +2 more
doaj   +1 more source

Gapless Complete Genome and Multi‐Omics Illuminate Immune Adaptation and Host‐Virus Interactions in a Coronavirus Reservoir

Advanced Science, EarlyView.
We present a complete T2T genome assembly for a key bat reservoir. Integrating population genomics, comparative genomics, transcriptomics, single‐cell omics, and functional assays, we resolve previously inaccessible genomic regions and identify evolutionary signatures associated with immune adaptation.
Yuting Wang, Sheng Zhang, Linxia Ouyang, Xin Du, Xin Huang, Zhilin Wang, Huixian Xie, Jiale Tang, Liyi Lou, Wenqing Ling, Weihao Wang, Jiang Zhou, Zhen Liu, Yibo Hu, Fuwen Wei, Guangping Huang   +15 more
wiley   +1 more source

Image2_Glucocorticoid stimulation induces regionalized gene responses within topologically associating domains.tif

, 2023
Transcription-factor binding to cis-regulatory regions regulates the gene expression program of a cell, but occupancy is often a poor predictor of the gene response.
Arnaud Droit (36418), Audrey Baguette (15147638), Christophe Tav (16682574), Michèle Fournier (16682577), Fatemeh Khadangi (16682580), Maxime C. Côté (16682583), Félix-Antoine Bérubé-Simard (249095), Éric Fournier (2717455), Maruhen A. D. Silveira (16682586), Guillaume Bourque (123960), Steve Bilodeau (3045234)   +10 more
core   +1 more source

STRIDE: A Sequencing Depth Robust Metric for Sparse Chromosome Conformation Capture Data Comparison

Advanced Science, EarlyView.
A mean first passage time (MFPT)‐based representation transforms sparse Hi‐C contact maps into robust topological representations, preserving biologically meaningful chromatin features and facilitating robust analysis of TADs, chromatin loops, differential chromatin contacts, and sparse single‐cell Hi‐C data.
Bingxiang Xu, Xiaomeng Gao, Weichu Tao, Zhihua Zhang, Feifei Li   +4 more
wiley   +1 more source

Position effects of 22q13 rearrangements on candidate genes in Phelan-McDermid syndrome.

PLoS ONE, 2021
Phelan-McDermid syndrome (PMS) is a multi-system disorder characterized by significant variability in clinical presentation. The genetic etiology is also variable with differing sizes of deletions in the chromosome 22q13 region and types of genetic ...
Sujata Srikanth, Lavanya Jain, Cinthya Zepeda-Mendoza, Lauren Cascio, Kelly Jones, Rini Pauly, Barb DuPont, Curtis Rogers, Sara Sarasua, Katy Phelan, Cynthia Morton, Luigi Boccuto   +11 more
doaj   +1 more source

A single base‐pair variation in a limb‐specific Lhx9 cis‐regulatory region modulates HAND2‐associated posterior repression

Developmental Dynamics, EarlyView.
Abstract LIM Homeobox 9 (Lhx9) is a transcription factor involved in vertebrate limb development. Despite conserved anterior expression, its distal expression is species‐specific. In chickens, distal expression is restricted to the anterior mesoderm; in mice, it extends into posterior mesoderm.
Jeanyoung Kim, Grace Santrach, William M. Sparks, Molly Ahola, Jessica C. Britton, Novalee Erickson, Shimako Kawauchi, Eunyoung Kim, Charmaine U. Pira, Kerby C. Oberg   +9 more
wiley   +1 more source

Enhancer Chromatin and 3D Genome Architecture Changes from Naive to Primed Human Embryonic Stem Cell States

Stem Cell Reports, 2019
Summary: During mammalian embryogenesis, changes in morphology and gene expression are concurrent with epigenomic reprogramming. Using human embryonic stem cells representing the preimplantation blastocyst (naive) and postimplantation epiblast (primed ...
Stephanie L. Battle, Naresh Doni Jayavelu, Robert N. Azad, Jennifer Hesson, Faria N. Ahmed, Eliah G. Overbey, Joseph A. Zoller, Julie Mathieu, Hannele Ruohola-Baker, Carol B. Ware, R. David Hawkins   +10 more
doaj   +1 more source

The epigenetic landscape of plant defense: Unlocking nature's toolkit for new plant protection

New Plant Protection, EarlyView.
This review examines how epigenetic mechanisms regulate plant immune gene activation, repression, and priming, then links these natural regulatory layers to emerging epigenetic editing, discussing their potential for precise, heritable crop protection and the challenges.
Xuexia Liu, Zhenhui Zhong
wiley   +1 more source

Forces driving the three‐dimensional folding of eukaryotic genomes

Molecular Systems Biology, 2018
The last decade has radically renewed our understanding of higher order chromatin folding in the eukaryotic nucleus. As a result, most current models are in support of a mostly hierarchical and relatively stable folding of chromosomes dividing ...
Alvaro Rada‐Iglesias, Frank G Grosveld, Argyris Papantonis   +2 more
doaj   +1 more source