Hematopoiesis is the process of blood cell formation starting from hematopoietic stem/progenitor cells (HSPCs). The understanding of regulatory networks involved in hematopoiesis and their impact on gene expression is crucial to decipher the molecular mechanisms that control hematopoietic development in physiological and pathological conditions, and to develop novel therapeutic strategies. An increasing number of epigenetic studies aim at defining, on a genome-wide scale, the cis-regulatory sequences (e.g., promoters and enhancers) used by human HSPCs and their lineage-restricted progeny at different stages of development. In parallel, human genetic studies allowed the discovery of genetic variants mapping to cis-regulatory elements and associated with hematological phenotypes and diseases. Here, we summarize recent epigenetic and genetic studies in hematopoietic cells that give insights into human hematopoiesis and provide a knowledge basis for the development of novel therapeutic approaches. As an example, we discuss the therapeutic approaches targeting cis-regulatory regions to reactivate fetal hemoglobin for the treatment of β-hemoglobinopathies. Epigenetic studies allowed the definition of cis-regulatory sequences used by human hematopoietic cells. Promoters and enhancers are targeted by transcription factors and are characterized by specific histone modifications. Genetic variants mapping to cis-regulatory elements are often associated with hematological phenotypes and diseases. In some cases, these variants can alter the binding of transcription factors, thus changing the expression of the target genes. Targeting cis-regulatory sequences represents a promising therapeutic approach for many hematological diseases. Stem Cells Translational Medicine 2017;6:2106-2114.
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http://dx.doi.org/10.1002/sctm.17-0192 | DOI Listing |
Alzheimers Dement
December 2024
Lawrence Chen Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
Background: Abnormal tau protein accumulation selectively affects distinct brain regions and specific neuron and glia populations in tau-related dementias like Alzheimer's disease (AD), frontotemporal dementia (FTD, Pick's disease type), and Progressive supranuclear palsy (PSP). The regulatory mechanisms governing cell-type vulnerability remain unclear.
Method: In a cross-disorder single-nucleus analysis, we examined 663,896 nuclei, assessing chromatin accessibility in three brain regions (motor cortex, visual cortex and insular cortex) across PSP, AD, and FTD in 40 individuals.
Alzheimers Dement
December 2024
Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA.
Background: Many independent studies have found rare variants associated with AD. Current gene-based tests for rare-variants generally consider the impact of low-frequency coding variants as an independent effect from the common regulatory variants that surround them. In this work, we propose to increase the statistical power of kernel-based rare-variant association tests by accounting for the surrounding cis-regulatory variants' effects on gene expression.
View Article and Find Full Text PDFAlzheimers Dement
December 2024
Northwestern University, Chicago, IL, USA.
Background: Much attention has been paid to the role of the perenchymal brain immune response in Alzheimer's disease (AD). Yet, the peripheral immune system in AD has not been thoroughly studied with modern sequencing methods.
Method: Here, we used a combination of single-cell sequencing strategies, including assay for transposase-accessible chromatin and RNA sequencing, to investigate the epigenetic and transcriptional alterations to the AD peripheral immune system.
Sci Rep
January 2025
School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK.
The Arabidopsis Knotted1-like homeobox (KNOX) gene SHOOT MERISTEMLESS (STM) encodes a homeodomain transcription factor that operates as a central component of the gene regulatory network (GRN) controlling shoot apical meristem formation and maintenance. It regulates the expression of target genes that include transcriptional regulators associated with meristem function, particularly those involved in pluripotency and cellular differentiation, as well as genes involved in hormone metabolism and signaling. Previous studies have identified KNOX-regulated genes and their associated cis-regulatory elements in several plant species.
View Article and Find Full Text PDFNat Commun
January 2025
Laboratory of Systems Biology and Genetics, Institute of Bio-engineering and Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
Gene regulation is inherently multiscale, but scale-adaptive machine learning methods that fully exploit this property in single-nucleus accessibility data are still lacking. Here, we develop ChromatinHD, a pair of scale-adaptive models that uses the raw accessibility data, without peak-calling or windows, to link regions to gene expression and determine differentially accessible chromatin. We show how ChromatinHD consistently outperforms existing peak and window-based approaches and find that this is due to a large number of uniquely captured, functional accessibility changes within and outside of putative cis-regulatory regions.
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