A genome-wide and nonredundant mouse transcription factor database

Kanamori, Mutsumi; Konno, Hiroyuki; Osato, Naoki; Kawai, Jun; Hayashizaki, Yoshihide; Suzuki, Harukazu

doi:10.1016/j.bbrc.2004.07.179

Cited by 123 publications

(104 citation statements)

References 14 publications

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“…We integrated the 1675 non-redundant mouse transcription factors in the TFdb (Riken Transcription Factor Database) with the 1727 mouse transcription factors collected by Ravasi et al [46,47], and identified 125 significantly up-regulated and 420 significantly down-regulated transcription factors in PN2 compared to PN1, and 10 significantly up-regulated and 17 significantly down-regulated transcription factors in PN3 compared to PN2.…”

Section: Differentially Expressed Transcription Factorsmentioning

confidence: 99%

Transcriptome profiling of the developing postnatal mouse testis using next-generation sequencing

Gong

Pan

Lin

et al. 2012

Sci. China Life Sci.

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Mammalian testis development is a complex and highly sophisticated process. To study the dynamic change of normal testis development at the transcriptional level, we investigated mouse testes at three postnatal ages: 6 days postnatal, 4 weeks old, and 10 weeks old, representing infant (PN1), juvenile (PN2), and adult (PN3) stages, respectively. Using ultra high-throughput RNA sequencing (RNA-seq) technology, we obtained 211 million reads with a length of 35 bp. We identified 18837 genes that were expressed in mouse testes, and found that genes expressed at the highest level were involved in spermatogenesis. The gene expression pattern in PN1 was distinct from that in PN2 and PN3, which indicates that spermatogenesis has commenced in PN2. We analyzed a large number of genes related to spermatogenesis and somatic development of the testis, which play important roles at different developmental stages. We also found that the MAPK, Hedgehog, and Wnt signaling pathways were significantly involved at different developmental stages. These findings further our understanding of the molecular mechanisms that regulate testis development. Our study also demonstrates significant advantages of RNA-seq technology for studying transcriptome during development. next-generation sequencing, transcriptome, mouse testis, development Citation:Gong W, Pan L L, Lin Q, et al. Transcriptome profiling of the developing postnatal mouse testis using next-generation sequencing.

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Section: Differentially Expressed Transcription Factorsmentioning

confidence: 99%

Transcriptome profiling of the developing postnatal mouse testis using next-generation sequencing

Gong

Pan

Lin

et al. 2012

Sci. China Life Sci.

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“…We extracted the expression profiles of 1675 mouse transcription factors from the Riken genome-wide and nonredundant mouse-transcription-factor database [17]. This process identified 375 down-regulated and 36 up-regulated DEGs between pregnancy and lactation, whereas 363 DEGs were up-regulated, but only nine were down-regulated between lactation and involution.…”

Section: Expression Of Transcription Factors Relevant To the Pl Cyclementioning

confidence: 99%

“…The provision of high-quality transcriptome data has allowed us to apply the concept of housekeeping (HK) and tissue-specific (TS or mammogenesis-specific, MS) genes [15], to define the differentially expressed genes (DEGs) during the three stages of mammogenesis. In addition, we investigated protein-coding and non-coding RNAs (ncRNAs), and focused our analyses on transcription factors [17] and lysosomal enzymes that may play key roles in the lactating mammary gland as well as in involution [1820].…”

mentioning

confidence: 99%

Transcriptomic analysis reveals key regulators of mammogenesis and the pregnancy-lactation cycle

Zhou

Gong

Xiao

et al. 2014

Sci. China Life Sci.

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An organ unique to mammals, the mammary gland develops 90% of its mass after birth and experiences the pregnancy-lactation-involution cycle (PL cycle) during reproduction. To understand mammogenesis at the transcriptomic level and using a ribo-minus RNA-seq protocol, we acquired greater than 50 million reads each for the mouse mammary gland during pregnancy (day 12 of pregnancy), lactation (day 14 of lactation), and involution (day 7 of involution). The pregnancy-, lactation-and involution-related sequencing reads were assembled into 17344, 10160, and 13739 protein-coding transcripts and 1803, 828, and 1288 non-coding RNAs (ncRNAs), respectively. Differentially expressed genes (DEGs) were defined in the three samples, which comprised 4843 DEGs (749 up-regulated and 4094 down-regulated) from pregnancy to lactation and 4926 DEGs (4706 up-regulated and 220 down-regulated) from lactation to involution. Besides the obvious and substantive upand down-regulation of the DEGs, we observe that lysosomal enzymes were highly expressed and that their expression coincided with milk secretion. Further analysis of transcription factors such as Trps1, Gtf2i, Tcf7l2, Nupr1, Vdr, Rb1, and Aebp1, Let7,, and mir-15 has enabled us to identify key regulators in mammary gland development and the PL cycle. mouse mammary gland, mammogenesis, transcriptome, rmRNA-seq, miRNAs, transcription factors Citation:

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“…The TRANSFAC (Braunschweig) tree was used to guide a computer-assisted manual annotation effort that identified 3,108 probe sets for 1,567 genes encoding known DNAbinding domains. The RIKEN Genome Science Center recently has reported the nonredundant number of mouse transcription factors at 1,585 (33). However, this group includes general transcription factors and chromatin remodeling factors in their collection.…”

Section: Synchronous Lbx1mentioning

confidence: 99%

Prediction of active nodes in the transcriptional network of neural tube patterning

Kioussi¹,

Shih²,

Loflin

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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A transcriptional network governs patterning in the developing spinal cord. As the developmental program runs, the levels of sequence-specific DNA-binding transcription factors (SSTFs) in each progenitor cell type change to ultimately define a set of postmitotic populations with combinatorial codes of expressed SSTFs. A network description of the neural tube (NT) transcriptional patterning process will require definition of nodes (SSTFs and target enhancers) and edges (interactions between nodes). There are 1,600 SSTF nodes in a given mammalian genome. To limit the complexity of a network description, it will be useful to discriminate between active and passive SSTF nodes. We define active SSTF nodes as those that are differentially expressed within the system. Our system, the developing NT, was partitioned into two pools of genetically defined populations by using flow sorting. Microarray comparisons across the partition led to an estimate of 500 -700 active SSTF nodes in the transcriptional network of the developing NT. These included most of the 66 known SSTFs assembled from review articles and recent reports on NT patterning. Empirical cutoffs based on the performance of knowns were used to identify 188 further active SSTFs nodes that performed similarly. The general utility and limitations of the population-partitioning paradigm are discussed.Lbx1 ͉ microarray ͉ mouse ͉ spinal cord S pinal cord development begins when the neural tube (NT) forms from a sheet of proliferative neuroepithelium. The proliferative ventricular zone around the lumen sheds postmitotic cells into a mantle layer from embryonic day (E)9.5 to E13.0 of mouse development. Many sequence-specific DNA-binding transcription factors (SSTFs) that mark discrete neuronal subpopulations during ontogeny have been identified (1-10). SSTFs also mark subdivisions in the motor neuron (MN) pool (11-15) and mark different types of ventral interneurons (16). Gene knockout experiments show that SSTFs specify neuronal types (17-21). Mutating them often leads to respecification of populations. The Lbx1 homeobox gene contributes to the specification of at least four spinal cell types. Loss of Lbx1 function leads to an organized respecification of transcription factor codes and projection patterns in Lbx1-marked populations (22, 23). It therefore is thought that a network of SSTFs can be used to describe patterning and specification in the NT.The neuronal diversity generated by patterning mechanisms in the mouse NT between E9.0 to E13.0 is not greatly influenced by classic synaptic function. Voltage-dependent Na ϩ conductance first appears at E12 (24), periodic MN bursting begins at E12.5, and a full locomotor pattern generator is not observed until E16.5 (25). Electrical connectivity during the patterning phase of development appears to be limited to gap junctions (26). In addition, the primary afferent neurons begin to enter the dorsal horn only at the end of this phase, suggesting that there is little sensory contact with the external environment. The absen...

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A genome-wide and nonredundant mouse transcription factor database

Cited by 123 publications

References 14 publications

Transcriptome profiling of the developing postnatal mouse testis using next-generation sequencing

Transcriptome profiling of the developing postnatal mouse testis using next-generation sequencing

Transcriptomic analysis reveals key regulators of mammogenesis and the pregnancy-lactation cycle

Prediction of active nodes in the transcriptional network of neural tube patterning

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