MicroRNA roles in signalling during lactation: an insight from differential expression, time course and pathway analyses of deep sequence data

Abstract

The study examined microRNA (miRNA) expression and regulatory patterns during an entire bovine lactation cycle. Total RNA from milk fat samples collected at the lactogenesis (LAC, day1 [D1] and D7), galactopoiesis (GAL, D30, D70, D130, D170 and D230) and involution (INV, D290 and when milk production dropped to 5 kg/day) stages from 9 cows was used for miRNA sequencing. A total of 475 known and 238 novel miRNAs were identified. Fifteen abundantly expressed miRNAs across lactation stages play regulatory roles in basic metabolic, cellular and immunological functions. About 344, 366 and 209 miRNAs were significantly differentially expressed (DE) between GAL and LAC, INV and GAL, and INV and LAC stages, respectively. MiR-29b/miR-363 and miR-874/miR-6254 are important mediators for transition signals from LAC to GAL and from GAL to INV, respectively. Moreover, 58 miRNAs were dynamically DE in all lactation stages and 19 miRNAs were significantly time-dependently DE throughout lactation. Relevant signalling pathways for transition between lactation stages are involved in apoptosis (PTEN and SAPK/JNK), intracellular signalling (protein kinase A, TGF-β and ERK5), cell cycle regulation (STAT3), cytokines, hormones and growth factors (prolactin, growth hormone and glucocorticoid receptor). Overall, our data suggest diverse, temporal and physiological signal-dependent regulatory and mediator functions for miRNAs during lactation.

Non-Coding RNA Roles in Ruminant Mammary Gland Development and Lactation

“…Le Guillou et al [61] identify 167 novel miRNAs in the bovine MG, many of which were also detected in mouse MG. Analysing three milk fractions (fat, whey and cells) and mammary gland tissues, we reported 210, 200 and 249 known and 33, 31 and 36 novel miRNAs in milk fat, whey and cells, respectively, and 321 known and 176 novel miRNAs in mammary gland tissues [62]. Deep sequencing the milk fat across the lactation curve, we also identified a total of 475 known and 238 novel miRNAs [63].…”

“…Li et al [50] in the dry period (30 days prepartum) compared to early lactation period (7 days postpartum) and one upregulated miRNA (miR-31) in early lactation compared to the dry period. Previously, we examined miRNA expression pattern during a lactation cycle to explore it regulatory mechanisms during lactation using milk fat as input tissue for sampling [63]. In a previous investigation, we have shown that milk fat miRNA transcriptome closely resemble the miRNome of MG tissue [62].…”

“…In a previous investigation, we have shown that milk fat miRNA transcriptome closely resemble the miRNome of MG tissue [62]. We collected samples at the lactogenesis (LAC) (day 1 and 7), galactopoiesis (GAL) (day 30, 70, 130, 170 and 230) and involution (INV) (day 290 and when milk production dropped to 5 kg/day) stages from nine cows for deep sequencing [63]. We observed that 15 miRNAs (miR-30a-5p, miR-30d, miR-21-5p, miR-26a, miR-148a, let-7a-5p, let-7b, let-7f, let-7g, miR-99a-5p, miR-191, miR-200a, miR-200c, miR-186, miR-92a) were highly expressed across lactation stages [63].…”

“…We collected samples at the lactogenesis (LAC) (day 1 and 7), galactopoiesis (GAL) (day 30, 70, 130, 170 and 230) and involution (INV) (day 290 and when milk production dropped to 5 kg/day) stages from nine cows for deep sequencing [63]. We observed that 15 miRNAs (miR-30a-5p, miR-30d, miR-21-5p, miR-26a, miR-148a, let-7a-5p, let-7b, let-7f, let-7g, miR-99a-5p, miR-191, miR-200a, miR-200c, miR-186, miR-92a) were highly expressed across lactation stages [63]. MiR-148a and miR-26a were the most abundantly expressed accounting for more than 10% of the read counts in each stage of lactation.…”

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

“…For example, De Vliegher et al [85] used miRbase [86] and UNAFold [87] for miRNA annotation and discovery in bovine mammary gland tissues while Peng et al [88] used miRbase [86] and RNAfold [89] for these purposes in porcine mammary glands. In our own studies, miRbase [86] and mirDeep2 [74] were used to identify miRNAs in various tissues including bovine mammary gland tissues [90], milk fat [90][91][92], milk whey and cells [90].…”