title: Genetic and epigenetic determinants of reactivation of Mecp2 and the inactive X chromosome in neural stem cells [MeD-seq]

first: Beatrice

last: Tan

type: Methylation profiling by high throughput sequencing

overall_design: We performed MeD-seq on female mouse Xist-/+ Mecp2+/NLucTom NSCs which were either untreated or treated with 5-AZA and Xist knockdown and then FACS-sorted into high-Tomato population (three biological replicates per condition). Untreated male cells were also used as control.

first: Hegias

last: Mira-Bontenbal

first: Ruben

last: Boers

first: Joachim

first: Wilfred

last: van IJcken

first: Joost

last: Gribnau


title: Coordinated chemokine expression defines macrophage subsets across tissues [scRNA-seq: mTumor]

status: Public on Mar 03 2023

city: Lebanon

first: Claudia

middle: V

last: Jakubzick

state: NH

address: 1 Medical Center Drive, Rm 626 W Borwell, PO#1250960

department: Microbiology and Immunology

country: USA

institute: Dartmouth College

type: Expression profiling by high throughput sequencing

summary: Lung-resident macrophages, which include alveolar macrophages and interstitial macrophages (IMs), exhibit a high degree of diversity, generally attributed to different activation states, and often complicated by the influx of monocytes into the pool of tissue-resident macrophages. To gain a deeper insight into the functional diversity of IMs, here we perform comprehensive transcriptional profiling of resident IMs and reveal ten distinct chemokine-expressing IM subsets at steady state and during inflammation. Similar IM subsets that exhibited coordinated chemokine signatures and differentially expressed genes were observed across various tissues and species, indicating conserved specialized functional roles. Other macrophage types shared specific IM chemokine profiles, while also presenting their own unique chemokine signatures. Depletion of CD206hi IMs in Pf4creR26EYFP+DTR and Pf4creR26EYFPCx3cr1DTR mice led to diminished inflammatory cell recruitment, reduced tertiary lymphoid structure formation and fewer germinal center B cells in models of allergen- and infection-driven inflammation. These observations highlight the specialized roles of IMs, defined by their coordinated chemokine production, in regulating immune cell influx and organizing tertiary lymphoid tissue architecture.

overall_design: Eight C57BL/6 mice were injected intravenously via the tail vein with 4 × 10^5 B16F10 melanoma cells cultured under standard ATCC conditions to establish a lung metastatic model. At harvest, the mice were euthanized and the lung tissues pooled together to generate biological replicates. To differentiate intravascular and extravascular leukocytes, mice were injected intravenously with APC-Cy7–conjugated anti-CD45 antibody 5 minutes before organ harvest. Lung single-cell suspensions were prepared and subjected to fluorescence-activated cell sorting on a FACSAria Fusion (BD Biosciences) to enrich for extravascular monocyte–macrophage populations (CD64^+CD11b^+ cells). Approximately 30,000 cells per sample were loaded on the Chromium Next GEM Single Cell 3′ platform (10x Genomics) and sequenced on an Illumina NextSeq 500/550 with an average depth of ~50,000 reads per cell.

first: Xin

last: Li

first: Arlind

middle: B

last: Mara

first: Shawn

middle: C

last: Musial

first: Fred

middle: W

last: Kolling

first: Sophie

middle: L

last: Gibbings

first: Nikita

last: Gerebtsov


title: The homeobox transcription factor MNX1 regulates the expression of many non-MN-specific neuronal genes in motor neurons

status: Public on Dec 31 2021

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Motor neuron (MN), together with interneuron, are the two major neuronal types in spinal cord. MNs control muscle movement and are essential for breathing, walking and fine motor skills. Malfunction of MNs is frequently associated with neuronal diseases such as spinal muscular atrophy and amyotrophic lateral sclerosis. To establish normal function, MNs need to be differentiated properly from neural progenitor cells. Thus, it is of great importance to study the mechanism for MN specification. This study focuses on Mnx1 - a conserved homeobox transcription factor gets expressed during MN specification. Mnx1 is also the most widely used MN marker. Previous studies reported that Mnx1 mutation in mouse causes early lethality - probably by affecting the controlling over respiratory system. However, the exact role of Mnx1 for MN identity remains poorly understood. Taking advantage of a recently developed in vitro model for efficient MN induction from mouse ES cells, we combined experimental and OMICs techniques to systematically investigate the molecular function of Mnx1. We identified thousands of Mnx1 binding sites - many are co-bound by core MN factor Lhx3 and Isl1 and lack active histone marks. Disruption of Mnx1 causes increased expression of 85 genes - while only 14 genes get down-regulated. Up-regulated genes are enriched with neuronal functions, usually get expressed during MN differentiation, and tend to have higher expression in motor neurons and brain compared with other tissues – indicating Mnx1 may fine tune neuronal genes to desired level. However, only a dozen of regions with increased H3K27ac marks are bound by Mnx1, and only two up-regulated genes (Pbx3 and Pou6f2) are identified as putative direct targets of Mnx1 - both are core neuronal factors with the potential to regulate other differential neuronal genes. These results suggest that Mnx1 may contribute to MN identity by fine-tuning the expression of many neuronal genes through direct regulation of a few core neuronal transcription factors. In summary, this study represents the first systematic investigation about the molecular function of the core MN factor Mnx1. It clarifies the mechanism of Mnx1 for MN identity, and also improves the understanding about the regulation mode of homeobox transcription factors.

overall_design: Using ChIP-Seq, we profiled the genome-wide binding of Mnx1 and different histone marks (H3K27ac, H3K4me1, H3K4me3, H3K27me3, H3K9me3) in induced motor neurons. Using RNA-Seq, we profiled gene expression pattern in wild-type ES cells, and wild-type and Mnx1KO induced motor neurons.

first: Ming-an

first: Sherry

last: Ralls

first: Justin

last: Demmerle

first: Carson

last: Miller

first: Gernot

last: Wolf

first: Todd

last: Macfarlan