Aiolos controls gene conversion and cell death in DT40 B cells

Transcription factor binding at Ig enhancers is linked to somatic hypermutation targeting

Secondary diversification of the Ig repertoire occurs through somatic hypermutation (SHM), gene conversion (GCV), and class switch recombination (CSR)-three processes that are initiated by activation-induced cytidine deaminase (AID). AID targets Ig genes at orders of magnitude higher than the rest of the genome, but the basis for this specificity is poorly understood. We have previously demonstrated that enhancers and enhancer-like sequences from Ig genes are capable of stimulating SHM of neighboring genes in a capacity distinct from their roles in increasing transcription. Here, we use an in vitro proteomics approach to identify E-box, MEF2, Ets, and Ikaros transcription factor family members as potential binders of these enhancers. ChIP assays in the hypermutating Ramos B cell line confirmed that many of these factors bound the endogenous Igλ enhancer and/or the IgH intronic enhancer (Eμ) in vivo. Further investigation using SHM reporter assays identified binding sites for E2A and MEF2B in Eμ and demonstrated an association between loss of factor binding and decreases in the SHM stimulating activity of Eμ mutants. Our results provide novel insights into trans-acting factors that dictate SHM targeting and link their activity to specific DNA binding sites within Ig enhancers.

Changes in bursal B cells in chicken during embryonic development and early life after hatching

The bursa of Fabricius, the primary lymphoid organ for B cell development found only in birds, offers novel approaches to study B cell differentiation at various developmental stages. Here, we explored the changes and mechanism involved in the developmental stages of bursal B cells. The bursal B cells rapidly increased in the late embryonic stage and around hatching, which coincided with changes in specific cell surface markers. Moreover, the cells in the bursa were divided by size into small (low forward- and side-scatter) or large (high forward- and side-scatter) via flow cytometry. It is intriguing that the proportion of small and large B cells was reversed during this period. Because little is known about this phenomenon, we hypothesized that size-based B cell population could be used as an indicator to distinguish their status and stage during B cell development in chicken. The results demonstrated that large B cells are actively proliferating cells than small B cells. Additionally, large B cells showed higher mRNA expression of both proliferation- and differentiation-associated genes compared to small B cells. Taken together, these data show that large bursal B cells are the main source of proliferation and differentiation during B cell development in chickens.

The Ikaros family of zinc-finger proteins

Ikaros represents a zinc-finger protein family important for lymphocyte development and certain other physiological processes. The number of family members is large, with alternative splicing producing various additional isoforms from each of the five homologous genes in the family. The functional forms of Ikaros proteins could be even more diverse due to protein–protein interactions readily established between family members. Emerging evidence suggests that targeting Ikaros proteins is feasible and effective in therapeutic applications, although the exact roles of Ikaros proteins remain elusive within the intricate regulatory networks in which they are involved. In this review we collect existing knowledge as to the functions, regulatory pathways, and molecular mechanisms of this family of proteins in an attempt to gain a better understanding through the comparison of activities and interactions among family members.

Allelic imbalance of multiple sclerosis susceptibility genes IKZF3 and IQGAP1 in human peripheral blood

Background

Multiple sclerosis is a chronic inflammatory, demyelinating disease of the central nervous system. Recent genome-wide studies have revealed more than 110 single nucleotide polymorphisms as associated with susceptibility to multiple sclerosis, but their functional contribution to disease development is mostly unknown.

Results

Consistent allelic imbalance was observed for rs907091 in IKZF3 and rs11609 in IQGAP1, which are in strong linkage disequilibrium with the multiple sclerosis associated single nucleotide polymorphisms rs12946510 and rs8042861, respectively. Using multiple sclerosis patients and healthy controls heterozygous for rs907091 and rs11609, we showed that the multiple sclerosis risk alleles at IKZF3 and IQGAP1 are expressed at higher levels as compared to the protective allele. Furthermore, individuals homozygous for the multiple sclerosis risk allele at IQGAP1 had a significantly higher total expression of IQGAP1 compared to individuals homozygous for the protective allele.

Conclusions

Our data indicate a possible regulatory role for the multiple sclerosis-associated IKZF3 and IQGAP1 variants. We suggest that such cis-acting mechanisms may contribute to the multiple sclerosis association of single nucleotide polymorphisms at IKZF3 and IQGAP1.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0367-4) contains supplementary material, which is available to authorized users.

IRF4 Deficiency Leads to Altered BCR Signalling Revealed by Enhanced PI3K Pathway, Decreased SHIP Expression and Defected Cytoskeletal Responses

The graded expression of transcription factor interferon regulatory factor 4 (IRF4) regulates B cell development and is critical for plasma cell differentiation. However, the mechanisms, by which IRF4 elicits its crucial tasks, are largely unknown. To characterize the molecular targets of IRF4 in B cells, we established an IRF4-deficient DT40 B cell line. We found that in the absence of IRF4, the expression of several molecules involved in BCR signalling was altered. For example, the expression of B cell adaptor for PI3K (BCAP) was upregulated, whereas the SHIP (SH2-containing Inositol 5?-Phosphatase) expression was downregulated. These molecular unbalances were accompanied by increased BCR-induced calcium signalling, attenuated B cell linker protein (BLNK) and ERK activity and enhanced activity of PI3K/protein kinase B (Akt) pathway. Further, the IRF4-deficient cells showed dramatically diminished cytoskeletal responses to anti-IgM cross-linking. Our results show that IRF4 has an important role in the regulation of BCR signalling and help to shed light on the molecular mechanisms of B cell development and germinal centre response.

Overexpression of Aiolos in Peripheral Blood Mononuclear Cell Subsets from Patients with Systemic Lupus Erythematosus and Rheumatoid Arthritis

Genetic studies demonstrate that the Aiolos polymorphisms contribute to the susceptibility to autoimmune diseases. The purpose of the study was to investigate the Aiolos expression in lymphocytes and monocytes in the peripheral blood from patients with SLE and RA, and to explore the correlation between Aiolos expression in cell subsets and laboratory measurements. Peripheral blood mononuclear cells (PBMC) from 32 patients with SLE, 35 patients with RA, and 37 healthy controls were purified. Aiolos expression in PBMC subsets was examined by flow cytometry. In SLE patients, a much higher percentage of Aiolos + CD8+ T cells and Aiolos + CD14+ monocytes was found, when compared with healthy controls (p = 8.29 × 10(-5) and p = 1.01 × 10(-5), respectively). Furthermore, the percentage of CD4+ and CD8+ T cells, CD19+ B cells, and CD14+ monocytes expressing Aiolos in RA patients was also determined and each found higher than that in healthy controls (p = 0.009, p = 4.11 × 10(-5), p = 0.001, and p = 1.11 × 10(-5), respectively). The percentage of Aiolos + CD8+ T cells was weakly correlated with ESR in SLE patients and RF in RA patients (r s = 0.37, p = 0.038; r s = 0.34, p = 0.044, respectively). On the other hand, the percentage of Aiolos + CD14+ monocytes was significantly correlated with multiple laboratory measurements, including ESR, creatinine, CRP, LDH, proteinuria, albumin, and ACCPA in patients (r s = 0.62, p < 0.001; r s = 0.65, p < 0.001; r s = 0.44, p = 0.010; r s = 0.42, p = 0.022; r s = 0.52, p = 0.013; r s = 0.34, p = 0.048, respectively). To our knowledge, it is the first study to demonstrate overexpression of Aiolos in PBMC subsets in SLE and RA patients. The results indicate that overexpression of Aiolos may contribute to pathogenesis of SLE and RA.

Overexpression of Aiolos in Nalm-6 acute lymphoblastic leukaemia cells reduces apoptosis by suppressing phosphatase and tensin homologue deleted on chromosome 10 and activating the phosphatidylinositol-3-kinase/Akt signalling pathway

The aim of the present study was to elucidate the molecular mechanism of Aiolos in the regulation of B‑cell leukaemia. A lentiviral system was used for overexpression of the Aiolos gene in Nalm‑6 cells to determine the effects of Aiolos on proliferation, apoptosis and the cell cycle. The expression and activation of phosphatase and tensin homolog deleted on chromosome ten (PTEN) and Akt were also investigated. Upregulation of Aiolos inhibited cell growth and arrested an increased number of Nalm‑6 cells at the G0/G1 phase. The apoptotic cell quantities were also significantly lower in the Aiolos‑transfected Nalm‑6 cells. In addition, Aiolos overexpression downregulated PTEN, but increased the expression and phosphorylation of Akt in the Nalm‑6 cells. The Akt inhibitor, Akti‑1/2, reduced the percentage of viable Aiolos‑overexpressed Nalm‑6 cells, however, it had no effect on cell cycle arrest or proliferation. Aiolos upregulation in the Nalm‑6 cells inhibited cell proliferation, suppressed apoptosis and arrested the cell cycle at the G0/G1 phase. Aiolos improved the survival of Nalm‑6 cells via PTEN‑ and Akt‑dependent processes.

Upregulation of AIOLOS induces apoptosis and enhances etoposide chemosensitivity in Jurkat leukemia cells

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive neoplastic disorder of immature hematopoietic precursors committed to T-cell lineage. T-ALL accounts for ~15% of pediatric ALL cases and is prone to early relapse. With new and improved treatment protocols, the prognosis of T-ALL has improved particularly in children; however, the outcome of relapsed T-ALL cases remains poor. The AIOLOS gene is necessary to control lymphocyte differentiation and may be a potential target of T-ALL therapy. In the present study, Jurkat cells were divided into three groups: untransfected (UT) control, lentiviral vector control (Lenti-Mock) and AIOLOS-overexpressing (Lenti-AIOLOS) groups. Lenti-AIOLOS Jurkat cells were constructed by lentiviral transduction; cell cycle analysis, apoptosis and cytotoxicity assays were then performed to evaluate the effects of AIOLOS on cell cycle distribution, apoptosis and cell chemosensitivity to etoposide of Jurkat cells in vitro. Moreover, the expression levels of genes associated with apoptosis and cell cycle were investigated by quantitative reverse transcription-polymerase chain reaction. Results showed that the percentage of Jurkat cells in the G0/G1 phase increased from 71.5 (UT) to 85.4% (Lenti-AIOLOS; P<0.05), yet the percentage of cells in the S-phase decreased from 15.1 (UT) to 11.6% (Lenti‑AIOLOS; P<0.05). The percentage of total apoptotic cells was significantly increased in the AIOLOS-transfected Jurkat cells (21.93%) compared with this percentage in the Lenti-Mock (13.35%) or the UT group (13.30%; P<0.05). Consistent with these results, AIOLOS overexpression induced P21 and P27 upregulation and CCND3 and SKP2 downregulation. Furthermore, AIOLOS overexpression synergistically increased the cytotoxic effects of etoposide and downregulated NF-κB expression. Our findings revealed that lentivirus-mediated AIOLOS overexpression in Jurkat cells induced cell apoptosis, arrested the cell cycle at the G0/G1 phase, and synergistically increased the sensitivity of Jurkat cells to etoposide by inhibiting NF-κB activity.

Association between polymorphisms of the IKZF3 gene and systemic lupus erythematosus in a Chinese Han population

Objective

It has been reported that IKAROS family of zinc finger 3 (IKZF3)-deficient mice spontaneously develop human systemic lupus erythematosus (SLE)-like phenotypes and produce anti-dsDNA Ab leading to immune complex-mediated glomerulonephritis. Polymorphism of the IKZF3 gene corresponds with the susceptibility to several immune-related diseases. Our intention was to establish an association between polymorphisms in the IKZF3 gene and SLE in the Chinese Han population.

Methods

The study involved obtaining blood samples for DNA extraction and genotyping the 4 selected single-nucleotide polymorphisms (SNPs) in IKZF3, including rs12150079, rs9909593, rs907091, and rs2872507, by performing PCR restriction fragment length polymorphism analysis (PCR-RFLP). A group of 366 SLE patients were compared to 455 healthy controls.

Results

A significant decrease in frequencies of the rs907091 CC genotype and C allele appeared in the SLE patients unlike that observed in the controls (p = 0.001 and 0.015, respectively). The frequencies of the rs12150079 genotype and allele were different between the SLE patients and the control individuals, although the significance was only marginal (p = 0.046 and 0.049, respectively). In addition, a significantly low frequency of the GGCG haplotype was observed in the SLE patients, suggesting that it may provide protection against SLE (p = 0.011).

Conclusion

To the best of our knowledge, this is the first study to demonstrate an important association between polymorphisms in IKZF3 and SLE in the Chinese Han population. A strong association between rs907091 in the IKZF3 gene and SLE was identified.

Overexpression of AIOLOS inhibits cell proliferation and suppresses apoptosis in Nalm-6 cells

The AIOLOS gene is important in the control of mature B-lymphocyte differentiation and proliferation. Previous research has shown that deregulated AIOLOS expression is associated with adult B-cell acute lymphoblastic leukemia (ALL) and chronic lymphocytic leukemia in human patients. However, the function of AIOLOS in childhood B-cell precursor (BCP)-ALL is not fully understood. In the present study, Nalm-6 cells were divided into three groups: the untransfected control (UT), the lentiviral vector control (Lenti-Mock) and the AIOLOS-overexpressing (Lenti-AIOLOS) group. Lenti-AIOLOS Nalm-6 cells were constructed by lentiviral transduction, followed by cell proliferation assay, cell-cycle analysis and apoptosis assay, to evaluate the effects of AIOLOS on proliferation, cell cycle distribution and apoptosis of Nalm-6 cells in vitro. Moreover, the expression levels of genes associated with apoptosis and the cell cycle, as well as the transcription factors IKZF1 and NF-κB, were investigated by quantitative reverse transcription-polymerase chain reaction and western blot analysis. The results showed that the proliferation of Nalm-6 cells in the Lenti-AIOLOS group was reduced by 16% on day 8 compared with cells in the UT group (P>0.05). The reduction peaked at 29% on day 10 (P<0.05). The percentage of Nalm-6 cells in the G0/G1 phase increased from 70.4 (UT) to 84.1% (Lenti-AIOLOS) (P<0.01), and the S-phase cells decreased from 20.3 (UT) to 11.7% (Lenti-AIOLOS) (P<0.01). Total apoptotic cells significantly decreased in AIOLOS-transfected Nalm-6 cells (10.75%) compared with those in the Lenti-Mock (17.00%) or UT group (19.05%) (P<0.01). In particular, the difference between the groups in the percentage of late apoptotic cells was significant (2.85 vs. 7.95%; P<0.01). In addition, overexpression of AIOLOS resulted in upregulation of BCL-2 and downregulation of CCND3, BAX, IKZF1 and NF-κB. No changes were detected on C-MYC and P27. Our findings indicate that lentivirus-mediated overexpression of AIOLOS in Nalm-6 cells could inhibit cell proliferation, suppress cell apoptosis and arrest the cell cycle at the G0/G1 phase in vitro.

Possible involvement of Helios in controlling the immature B cell functions via transcriptional regulation of protein kinase Cs

The transcription factor Ikaros family consists of five zinc-finger proteins: Ikaros, Aiolos, Helios, Eos and Pegasus; these proteins except Pegasus are essential for development and differentiation of lymphocytes. However, in B lymphocytes, the physiological role of Helios remains to be elucidated yet, because its expression level is very low. Here, we generated the Helios-deficient DT40 cells, Helios (-/-), and showed that the Helios-deficiency caused significant increases in transcriptions of four protein kinase Cs (PKCs); PKC-δ, PKC-ε, PKC-η and PKC-ζ, whereas their expressions were drastically down-regulated in the Aiolos-deficient DT40 cells, Aiolos (-/-). In addition, Helios (-/-) was remarkably resistant against phorbol 12-myristate 13-acetate (PMA)/ionomycin treatment, which mimics the B cell receptor (BCR)-mediated stimulation. In the presence of PMA/ionomycin, their viability was remarkably higher than that of DT40, and their DNA fragmentation was less severe than that of DT40 in the opposite manner for the Aiolos-deficiency. The resistance against the PMA/ionomycin-induced apoptosis of Helios (-/-) was sensitive to Rottlerin but not to Go6976. In addition, the Helios-deficiency caused remarkable up-regulation of the Rottlerin-sensitive superoxide (O2 (-))-generating activity. These data suggest that Helios may contribute to the regulation of the BCR-mediated apoptosis and O2 (-)-generating activity, via transcriptional regulation of these four PKCs (especially PKC-δ) in immature B lymphocytes. Together with previous data, our findings may significantly help in the understanding of the B lymphocyte-specific expressions of PKC genes and molecular mechanisms of both the BCR-mediated apoptosis involved in negative selection and the O2 (-)-generating system in immature B lymphocytes.

Gene interaction network regulates plasma cell differentiation

Effective humoral immunity depends on B cells, plasma cells and follicular helper T cells (TFH) and secreted high-affinity antibodies. The differentiation of mature B cell into plasma cells is ultimately hardwired in a regulatory network of transcription factors. This circuitry is responding to extracellular stimuli, which leads to production of higher-affinity antibodies after germinal centre (GC) reaction. The understanding of the transcriptional regulation of GCs and the initiation of plasma cell differentiation is becoming increasingly clear. It is evident that transcriptional repressor Blimp-1 can drive the plasma cell differentiation, but the initiation of plasma cell differentiation in GCs is likely coupled to the loss of B cell characteristics maintained by transcription factors Pax5 and Bcl6.

Alternate pathways for Bcl6-mediated regulation of B cell to plasma cell differentiation

The transcription factor Bcl6 regulates germinal center formation and differentiation of B cells into high-affinity antibody-producing plasma cells. The direct double-negative regulatory circuit between Bcl6 and Blimp-1 is well established. We now reveal alternative mechanisms for Bcl6-mediated regulation of B-cell differentiation to plasma cells and show with DT40 cells that Bcl6 directly promotes the expression of Bach2, a known suppressor of Blimp-1. Moreover, Bcl6 suppresses Blimp-1 expression through direct binding to the IRF4 gene, as well as by promoting the expression of MITF, a known suppressor of IRF4. We also provide evidence that Bcl6 is needed for the expression of AID and UNG, the indispensable proteins for somatic hypermutation and class-switch recombination, and UNG appears to be a direct Bcl6 target. Our findings reveal a complex regulatory network in which Bcl6 acts as a key element dictating the transition of DT40 B cells to plasma cells.

The Ikaros gene family: transcriptional regulators of hematopoiesis and immunity

The Ikaros family of proteins - comprising Ikaros, Aiolos, Helios, Eos and Pegasus - are zinc finger transcription factors. These proteins participate in a complex network of interactions with gene regulatory elements, other family members and a raft of other transcriptional regulators to control gene expression including via chromatin remodelling. In this way, Ikaros family members regulate important cell-fate decisions during hematopoiesis, particularly in the development of the adaptive immune system. Mutation of several family members results in hematological malignancies,especially those of a lymphoid nature. This review describes the key roles of Ikaros proteins in development and disease, their mechanisms of action and gene targets, as well as explaining their evolutionary origins and role in the emergence of adaptive immunity.

Deregulation of Aiolos expression in chronic lymphocytic leukemia is associated with epigenetic modifications

Chronic lymphocytic leukemia (CLL) is characterized by a clonal accumulation of mature neoplastic B cells that are resistant to apoptosis. Aiolos, a member of the Ikaros family of zinc-finger transcription factors, plays an important role in the control of mature B lymphocyte differentiation and maturation. In this study, we showed that Aiolos expression is up-regulated in B-CLL cells. This overexpression does not implicate isoform imbalance or disturb Aiolos subcellular localization. The chromatin status at the Aiolos promoter in CLL is defined by the demethylation of DNA and an enrichment of euchromatin associated histone markers, such as the dimethylation of the lysine 4 on histone H3. These epigenetic modifications should allow its upstream effectors, such as nuclear factor-κB, constitutively activated in CLL, to gain access to promoter, resulting up-regulation of Aiolos. To determine the consequences of Aiolos deregulation in CLL, we analyzed the effects of Aiolos overexpression or down-regulation on apoptosis. Aiolos is involved in cell survival by regulating the expression of some Bcl-2 family members. Our results strongly suggest that Aiolos deregulation by epigenetic modifications may be a hallmark of CLL.

Concerted action of Helios and Ikaros controls the expression of the inositol 5-phosphatase SHIP

Ikaros family transcription factors have a key role in lymphoid development, and their aberrant function contributes to a multitude of lymphoid malignancies. Ikaros and Helios bind to similar DNA sequences, and Helios associates with Ikaros-containing chromatin remodeling complexes. Previously, we have shown that loss of Ikaros leads to diminished BCR-signaling strength. In this study, we describe a Helios-deficient chicken DT40 B-cell line with a BCR signaling phenotype that is the opposite to that of Ikaros-deficient cells. In contrast to Ikaros-deficient cells, Helios(-/-) B cells exhibit increased calcium release to the cytoplasm after BCR crosslinking, but diminished BCR-induced phosphorylation of signaling molecules. The inositol 5-phosphatase SHIP, an important regulator in several signaling pathways, is differentially expressed in Ikaros- and Helios-deficient cells. In the absence of Ikaros, SHIP is upregulated, whereas Helios deficiency leads to the downregulation of SHIP expression. We also show with ChIP that Ikaros binds to the promoter of the INPP5D gene-encoding SHIP. Considering the critical role of SHIP in the BCR signaling pathway, our findings provide insight into the mechanism of how both Helios and Ikaros are involved in the regulation of BCR signaling.

Differential aiolos expression in human hematopoietic subpopulations

The Aiolos transcription factor plays a crucial role in the control of lymphocyte differentiation and proliferation. The expression of Aiolos isoform has been studied in lymphoid pathologies but nothing is known about its expression in unaffected human hematopoietic subpopulations. In this manuscript we show for the first time the differential Aiolos expression at the RNA and protein level in hematopoietic cell subpopulations. B cells express higher levels of Aiolos than NK and T cells while monocytes express almost undetectable levels of Aiolos. Moreover, human CD34 (+) progenitors do not express Aiolos. We did not observe significant difference when comparing naive to memory T and B cells, but we observed an important difference between Bright and Dim NK cells. Furthermore, we show that, in addition to hematopoietic cells, non hematopoietic cell lines such as MCF-7, SW480, HEK, PC3 and HeLa also express Aiolos.

Evolution of the Ikaros gene family: implications for the origins of adaptive immunity

Members of the Ikaros family of transcription factors are important for immune system development. Analysis of Ikaros-related genes from a range of species suggests the Ikaros family derived from a primordial gene, possibly related to the present-day protostome Hunchback genes. This duplicated before the divergence of urochordates to produce two distinct lineages: one that generated the Ikaros factor-like (IFL) 2 genes of urochordates/lower vertebrates and the Pegasus genes of higher vertebrates, and one that generated the IFL1 genes of urochordates/lower vertebrates, the IKFL1 and IKFL2 genes of agnathans and the remaining four Ikaros members of higher vertebrates. Expansion of the IFL1 lineage most likely occurred via the two intervening rounds of whole genome duplication. A proposed third whole genome duplication in teleost fish produced a further increase in complexity of the gene family with additional Pegasus and Eos members. These findings question the use of IFL sequences as evidence for the existence of adaptive immunity in early chordates and vertebrates. Instead, this study is consistent with a later emergence of adaptive immunity coincident with the appearance of the definitive lymphoid markers Ikaros, Aiolos, and Helios.

The Aiolos transcription factor is up-regulated in chronic lymphocytic leukemia

The Aiolos transcription factor, member of the Ikaros family of zinc finger proteins, plays an important role in the control of mature B lymphocyte differentiation and proliferation, and its function appears to be modulated through alternative splicing. To assess Aiolos isoform role in humans' pathologies, we studied Aiolos variant distribution and expression in mature B lymphoproliferative disorders (chronic lymphocytic leukemia [CLL] and other B-cell lymphomas). We demonstrated that more than 80% of expressed Aiolos in normal as well as in malignant B cells is of the hAio1 type, and we showed for the first time a homogeneous overexpression of the total amounts of Aiolos transcripts in the B cells of CLL patients, independently of ZAP-70 and IgVH mutational status prognosis factors. This up-regulation of Aiolos, confirmed at protein level, seems independent of Aiolos promoter H3K9 acetylation and H3K4 trimethylation.

Avian model for B-cell immunology--new genomes and phylotranscriptomics

The purpose of this review is to discuss the use of chicken and other model organisms in the study of B-cell development and function as well as to highlight the opportunities afforded by the expanded genome-sequencing efforts. A brief introduction on chicken B-cell biology is followed by discussion of somatic cell reverse genetic approaches using the DT40 cell line. The unique advantages of the DT40 system are emphasized with discussion on B-cell receptor signalling research as well as on DNA repair and mechanisms of immunoglobulin diversification. An attempt is made to compare and contrast the results from chicken with mouse knockouts on the one hand and RNAi with human cell lines on the other. Chicken is also emerging strongly as a platform for gene expression analysis, and avian studies are compared with mammalian studies. Multi-species gene co-expression analysis, which could also be termed phylotranscriptomics, aims to use the evolutionary distance between organisms to its advantage. This approach, still in its infancy, is also reviewed and its applicability to the chicken is discussed.