scholarly journals Cistrome Data Browser and Toolkit: analyzing human and mouse genomic data using compendia of ChIP-seq and chromatin accessibility data

2020 ◽  
Vol 8 (3) ◽  
pp. 267-276
Author(s):  
Rongbin Zheng ◽  
Xin Dong ◽  
Changxin Wan ◽  
Xiaoying Shi ◽  
Xiaoyan Zhang ◽  
...  
Keyword(s):  
Genomic Data ◽  
Chromatin Accessibility ◽  
Human And Mouse ◽  
Mouse Genomic

scholarly journals Bcl11b prevents fatal autoimmunity by promoting Treg cell program and constraining innate lineages in Treg cells

2019 ◽  
Vol 5 (8) ◽  
pp. eaaw0480 ◽  
Author(s):  
Theodore T. Drashansky ◽  
Eric Helm ◽  
Zhiguang Huo ◽  
Nina Curkovic ◽  
Preet Kumar ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Steady State ◽  
Treg Cell ◽  
Nk Cell ◽  
Treg Cells ◽  
Chromatin Accessibility ◽  
Peripheral Tolerance ◽  
Identity Control ◽  
And Function ◽  
Human And Mouse

Regulatory T (Treg) cells are essential for peripheral tolerance and rely on the transcription factor (TF) Foxp3 for their generation and function. Several other TFs are critical for the Treg cell program. We found that mice deficient in Bcl11b TF solely in Treg cells developed fatal autoimmunity, and Bcl11b-deficient Treg cells had severely altered function. Bcl11b KO Treg cells showed decreased functional marker levels in homeostatic conditions, inflammation, and tumors. Bcl11b controlled expression of essential Treg program genes at steady state and in inflammation. Bcl11b bound to genomic regulatory regions of Treg program genes in both human and mouse Treg cells, overlapping with Foxp3 binding; these genes showed altered chromatin accessibility in the absence of Bcl11b. Additionally, Bcl11b restrained myeloid and NK cell programs in Treg cells. Our study provides new mechanistic insights on the Treg cell program and identity control, with major implications for therapies in autoimmunity and cancer.

Novel conserved elements upstream of theH19gene are transcribed and act as mesodermal enhancers

Development ◽  
2002 ◽  
Vol 129 (5) ◽  
pp. 1205-1213
Author(s):  
Robert A. Drewell ◽  
Katharine L. Arney ◽  
Takahiro Arima ◽  
Sheila C. Barton ◽  
James D. Brenton ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Reporter Gene ◽  
Differentially Methylated Region ◽  
Genomic Sequencing ◽  
Strong Homology ◽  
Imprinting Control Region ◽  
Enhancer Function ◽  
Human And Mouse ◽  
Mouse Genomic

The reciprocally imprinted H19 and Igf2 genes form a co-ordinately regulated 130 kb unit in the mouse controlled by widely dispersed enhancers, epigenetically modified silencers and an imprinting control region (ICR). Comparative human and mouse genomic sequencing between H19 and Igf2 revealed two novel regions of strong homology upstream of the ICR termed H19 upstream conserved regions (HUCs). Mouse HUC1 and HUC2 act as potent enhancers capable of driving expression of an H19 reporter gene in a range of mesodermal tissues. Intriguingly, the HUC sequences are also transcribed bi-allelically in mouse and human, but their expression pattern in neural and endodermal tissues in day 13.5 embryos is distinct from their enhancer function. The location of the HUC mesodermal enhancers upstream of the ICR and H19, and their capacity for interaction with both H19 and Igf2 requires critical re-evaluation of the cis-regulation of imprinted gene expression of H19 and Igf2 in a range of mesodermal tissues. We propose that these novel sequences interact with the ICR at H19 and the epigenetically regulated silencer at differentially methylated region 1 (DMR1) of Igf2.

scholarly journals Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

2016 ◽  
Vol 45 (D1) ◽  
pp. D658-D662 ◽  
Author(s):  
Shenglin Mei ◽  
Qian Qin ◽  
Qiu Wu ◽  
Hanfei Sun ◽  
Rongbin Zheng ◽  
...  
Keyword(s):  
Chromatin Accessibility ◽  
Data Portal ◽  
Human And Mouse

scholarly journals Mammalian Septins Nomenclature

2002 ◽  
Vol 13 (12) ◽  
pp. 4111-4113 ◽  
Author(s):  
Ian G. Macara ◽  
Richard Baldarelli ◽  
Christine M. Field ◽  
Michael Glotzer ◽  
Yasuhide Hayashi ◽  
...  
Keyword(s):  
Human Genome ◽  
Gene Product ◽  
Genome Organization ◽  
Splice Variants ◽  
Gene Products ◽  
Gene Nomenclature ◽  
Nomenclature System ◽  
Nomenclature Committee ◽  
Human And Mouse ◽  
Mouse Genomic

There are 10 known mammalian septin genes, some of which produce multiple splice variants. The current nomenclature for the genes and gene products is very confusing, with several different names having been given to the same gene product and distinct names given to splice variants of the same gene. Moreover, some names are based on those of yeast or Drosophilaseptins that are not the closest homologues. Therefore, we suggest that the mammalian septin field adopt a common nomenclature system, based on that adopted by the Mouse Genomic Nomenclature Committee and accepted by the Human Genome Organization Gene Nomenclature Committee. The human and mouse septin genes will be namedSEPT1–SEPT10 and Sept1–Sept10, respectively. Splice variants will be designated by an underscore followed by a lowercase “v” and a number, e.g., SEPT4_v1.

scholarly journals A cytomegalovirus DNA sequence containing tracts of tandemly repeated CA dinucleotides hybridizes to highly repetitive dispersed elements in mammalian cell genomes.

1983 ◽  
Vol 3 (8) ◽  
pp. 1389-1402 ◽  
Author(s):  
K T Jeang ◽  
G S Hayward
Keyword(s):  
Plasmid Dna ◽  
Genomic Library ◽  
Mammalian Species ◽  
5S Rdna ◽  
Rdna Genes ◽  
Left Handed ◽  
Mammalian Genomes ◽  
Genomic Dnas ◽  
Human And Mouse ◽  
Mouse Genomic

A single 880-base-pair region within the genome of simian cytomegalovirus strain Colburn contains sequences that hybridize intensely with both human and mouse total genome DNA probes. This sequence was also found in a second simian cytomegalovirus isolate and was retained in both plaque-purified virus subclones and in plasmid DNA clones containing the SalI P fragment. Cleaved genomic DNAs from several mammalian species all exhibited strong dispersed hybridization with the SalI-P probes, and over 70% of the lambda clones in a mouse genomic library plus several selected clones containing globin, 45S rDNA, or 5S rDNA genes all formed hybrids with SalI-P. The appropriate region of cytomegalovirus SalI-P contains relatively A + T-rich unique sequences interrupted by three stretches of the simple alternating dinucleotides, (CA)15, (CA)22, and (CA)21, which we show to be responsible for most of the cell-virus homology. We conclude that discrete, tandemly repeated (CA) dinucleotide tracts capable of forming left-handed Z-DNA helices punctuate mammalian genomes at greater than 10(5) copies per cell and that three adjacent copies of what appear to be a family of interspersed repetitive elements containing these (CA)n stretches are carried in the genomes of simian cytomegaloviruses.

A cytomegalovirus DNA sequence containing tracts of tandemly repeated CA dinucleotides hybridizes to highly repetitive dispersed elements in mammalian cell genomes

1983 ◽  
Vol 3 (8) ◽  
pp. 1389-1402
Author(s):  
K T Jeang ◽  
G S Hayward
Keyword(s):  
Plasmid Dna ◽  
Genomic Library ◽  
Mammalian Species ◽  
5S Rdna ◽  
Rdna Genes ◽  
Left Handed ◽  
Mammalian Genomes ◽  
Genomic Dnas ◽  
Human And Mouse ◽  
Mouse Genomic

A single 880-base-pair region within the genome of simian cytomegalovirus strain Colburn contains sequences that hybridize intensely with both human and mouse total genome DNA probes. This sequence was also found in a second simian cytomegalovirus isolate and was retained in both plaque-purified virus subclones and in plasmid DNA clones containing the SalI P fragment. Cleaved genomic DNAs from several mammalian species all exhibited strong dispersed hybridization with the SalI-P probes, and over 70% of the lambda clones in a mouse genomic library plus several selected clones containing globin, 45S rDNA, or 5S rDNA genes all formed hybrids with SalI-P. The appropriate region of cytomegalovirus SalI-P contains relatively A + T-rich unique sequences interrupted by three stretches of the simple alternating dinucleotides, (CA)15, (CA)22, and (CA)21, which we show to be responsible for most of the cell-virus homology. We conclude that discrete, tandemly repeated (CA) dinucleotide tracts capable of forming left-handed Z-DNA helices punctuate mammalian genomes at greater than 10(5) copies per cell and that three adjacent copies of what appear to be a family of interspersed repetitive elements containing these (CA)n stretches are carried in the genomes of simian cytomegaloviruses.

scholarly journals PRDM9 directs recombination hotspots to prevent competition with meiotic transcription

2021 ◽  
Author(s):  
Enrique Jimenez Schwarzkopf ◽  
Omar E Cornejo
Keyword(s):  
Dna Sequence ◽  
Genomic Data ◽  
Whole Genome ◽  
Sequence Motifs ◽  
Potential Competition ◽  
Recombination Hotspots ◽  
Dna Sequence Motifs ◽  
Mouse Genomic ◽  
Functional Orthologs

PRDM9 drives recombination hotspots in some mammals, including mice and apes. Non-functional orthologs of PRDM9 are present in a wide variety of vertebrates, but why it is functionally maintained in some lineages is not clear. One possible explanation is that PRDM9 plays a role in ensuring that meiosis is successful. During meiosis, available DNA may be a limiting resource given the tight packaging of chromosomes and could lead to competition between two key processes: meiotic transcription and recombination. Here we explore this potential competition and the role that PRDM9 might play in their interaction. Leveraging existing mouse genomic data, we use resampling schemes that simulate shuffled features along the genome and models that account for the rarity of features in the genome, to test if PRDM9 influences interactions between recombination hotspots and meiotic transcription in a whole genome framework. We also explored possible DNA sequence motifs associated to clusters of hotspots not tied to transcription or PRDM9. We find evidence of competition between meiotic transcription and recombination, with PRDM9 appearing to relocate recombination to avoid said conflict. We also find that retrotransposons may be playing a role in directing hotspots in the absence of other factors.

scholarly journals Comparative Sequence of Human and Mouse BAC Clones from the mnd2 Region of Chromosome 2p13

1999 ◽  
Vol 9 (1) ◽  
pp. 53-61 ◽  
Author(s):  
Wonhee Jang ◽  
Axin Hua ◽  
Sandra V. Spilson ◽  
Webb Miller ◽  
Bruce A. Roe ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Lysyl Oxidase ◽  
Neuromuscular Disorder ◽  
Bac Clone ◽  
Link Type ◽  
Sequence Elements ◽  
Human And Mouse ◽  
Mouse Genomic

The mnd2 mutation on mouse chromosome 6 produces a progressive neuromuscular disorder. To determine the gene content of the 400-kb mnd2 nonrecombinant region, we sequenced 108 kb of mouse genomic DNA and 92 kb of human genomic sequence from the corresponding region of chromosome 2p13.3. Three genes with the indicated sizes and intergenic distances were identified:D6Mm5e (⩾81 kb)–787 bp–DOK (2 kb)–845 bp–LOR2 (⩾6 kb). D6Mm5e is expressed in many tissues at very low abundance and the predicted 526-residue protein contains no known functional domains. DOK encodes the p62dok rasGAP binding protein involved in signal transduction. LOR2 encodes a novel lysyl oxidase-related protein of 757 amino acid residues. We describe a simple search protocol for identification of conserved internal exons in genomic sequence. Evolutionary conservation proved to be a useful criterion for distinguishing between authentic exons and artifactual products obtained by exon amplification, RT–PCR, and 5′ RACE. Conserved noncoding sequence elements longer than 80 bp with ⩾75% nucleotide sequence identity comprise ∼1% of the genomic sequence in this region. Comparative analysis of this human and mouse genomic DNA sequence was an efficient method for gene identification and is independent of developmental stage or quantitative level of gene expression.[The sequence data described in this paper have been submitted to the GenBank data library under the following accession numbers: AC003061, mouse BAC clone 245c12; AC003065, human BAC clone h173(E10); AF053368, mouse Lor2 cDNA; AF084363, 108-kb contig from mouse BAC 245c12; AF084364, mouse D6Mm5ecDNA.]

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